Bio-Rad Electrophoresis Polyacrylamide Gel Guide

Electrophoresis
A Guide to Polyacrylamide Gel
Electrophoresis and Detection
BEGIN
Electrophoresis Guide
Table of Contents
Part I: Theory and Product Selection
5
Chapter 1 Overview
5
How Protein Electrophoresis Works
General Considerations and Workflow
Polyacrylamide Gels
27
Polymerization
27
Percentage
28
6
Precast vs. Handcast
29
6
Format (Size and Comb Type)
29
Chapter 2 Protein Electrophoresis Methods
and Instrumentation
9
Protein Electrophoresis Methods
10
29
31
Laemmli (Tris-HCl) Protocols
Sample Preparation
General Tips for Sample Preparation
51
52
52
52
Lysis (Cell Disruption)
52
Protein Solubilization
52
Preparation for PAGE
52
Human Cells
53
Suspension Cultured Cells
53
Bis-Tris 31
Tris-Acetate 31
Tris-Tricine 31
10
IEF
31
10
Zymogram
31
SDS-PAGE 11
Products for Handcasting Gels
32
12
32
12
AnyGel™ Stands
32
Zymogram PAGE 12
Multi-Casting Chambers
32
Isoelectric Focusing (IEF)
13
Standard Assay Protocol (5 ml)
56
Gradient Formers
32
2-D Electrophoresis
13
Microcentrifuge Tube Assay Protocol (1.5 ml)
56
Polyacrylamide Gel Electrophoresis (PAGE)
Discontinuous Native PAGE
Other Types of PAGE
Blue Native PAGE (BN-PAGE)
TABLE OF CONTENTS
Electrophoresis Cells and Power Supplies
13
Electrophoresis Cells 13
Power Supplies for PAGE Applications 15
Chapter 3 Sample Preparation for
Electrophoresis17
Premade Buffers and Reagents
Chapter 5 Performing Electrophoresis 36
58
Useful Equations
36
Joule Heating
36
Other Factors Affecting Electrophoresis
36
Selecting Power Supply Settings
37
20
Chaotropic Agents
21
Buffers and Salts
21
Common Solutions for Protein Solubilization 21
Removal of Interfering Substances Chapter 6 Protein Detection and Analysis
21
Products for Sample Preparation
Protein Stains
21
Sample Quantitation (Protein Assays)
22
22
Dodeca™ High-Throughput Stainers
42
Recombinant Standards
26
Natural Standards 27
57
Running Conditions
Reducing Agents
26
Handcasting Polyacrylamide Gels
58
Protein Standards
56
Pour the Stacking Gel
20
26
55
Sample Quantitation (RC DC™ Protein Assay)
Pour the Resolving Gel
Detergents
General Considerations
55
Protein Fractions from Chromatography
36
20
25
54
Microbial Cultures
System Setup
Protein Solubilization
Chapter 4 Reagent Selection and
Preparation
Plant Leaves
57
19
23
54
35
Cell Disruption Plus Spectrophotometer
53
Mammalian Tissue
Single-Percentage Gels
19
Protein Assays Monolayer Cultured Cells
General Considerations
SmartSpec™
2
Buffer Systems and Gel Chemistries
Part II: Methods
Separations Under Constant Voltage
37
Separations Under Constant Current
37
Separations Under Constant Power
37
General Guidelines for Running Conditions
37
Gel Disassembly and Storage
37
39
Gradient Gels
59
60
Performing Electrophoresis
General Protocols: SDS-PAGE
Total Protein Staining
60
62
Bio-Safe™ Coomassie Stain
62
Oriole™ Fluorescent Gel Stain
62
Flamingo™ Fluorescent Gel Stain
62
63
Silver Staining (Bio-Rad Silver Stain)
Molecular Weight Estimation
63
Buffer Formulations
64
Sample Preparation Buffers
64
65
Gel Casting Reagents
40
Sample Buffers 65
Total Protein Stains
40
Running Buffers 66
Specific Protein Stains
40
Buffer Components 66
Imaging 42
Part III: Troubleshooting
Imaging Systems
42
Imaging Software
44
Sample Preparation
70
Gel Casting and Sample Loading
70
Electrophoresis
71
Total Protein Staining
72
Evaluation of Separation
73
77
Analysis
44
Molecular Weight (Size) Estimation
44
Quantitation 45
Chapter 7 Downstream Applications
47
69
Western Blotting (Immunoblotting)
48
Part IV: Appendices
Gel Drying
48
Glossary
78
Electroelution
48
References and Related Reading
83
Spot Excision (Cutting)
49
Ordering Information
86
3
Electrophoresis Guide
Chapter 1: Overview
Theory and Product Selection
PART I
TABLE OF CONTENTS
Theory and
Product
Selection
CHAPTER 1
Overview
Protein electrophoresis is the
movement of proteins within an
electric field. Popular and widely
used in research, it is most commonly
used to separate proteins for the
purposes of analysis and purification.
This chapter provides a brief overview
of the theory and workflow behind
protein electrophoresis.
4
5
Electrophoresis Guide
Chapter 1: Overview
How Protein Electrophoresis Works
The term electrophoresis refers to the movement
of charged molecules in response to an electric
field, resulting in their separation.
TABLE OF CONTENTS
In an electric field, proteins move toward the
electrode of opposite charge. The rate at which
they move (migration rate, in units of cm2/Vsec) is
governed by a complex relationship between the
physical characteristics of both the electrophoresis
system and the proteins. Factors affecting protein
electrophoresis include the strength of the electric
field, the temperature of the system, the pH, ion type,
and concentration of the buffer as well as the size,
shape, and charge of the proteins (Garfin 1990)
(Figure 1.1). Proteins come in a wide range of sizes
and shapes and have charges imparted to them
by the dissociation constants of their constituent
amino acids. As a result, proteins have characteristic
migration rates that can be exploited for the purpose
of separation. Protein electrophoresis can be
performed in either liquid or gel-based media and
can also be used to move proteins from one medium
to another (for example, in blotting applications).
Over the last 50 years, electrophoresis techniques
have evolved as refinements have been made to the
buffer systems, instrumentation, and visualization
techniques used. Protein electrophoresis can be used
for a variety of applications such as purifying proteins,
assessing protein purity (for example, at various stages
during a chromatographic separation), gathering data
on the regulation of protein expression, or determining
protein size, isoelectric point (pI), and enzymatic
activity. In fact, a significant number of techniques
including gel electrophoresis, isoelectric focusing (IEF),
electrophoretic transfer (blotting), and two-dimensional
(2-D) electrophoresis can be grouped under the term
“protein electrophoresis” (Rabilloud 2010). Though
some information is provided about these methods in
the following chapters, this guide focuses on the onedimensional separation of proteins in polyacrylamide
gels, or polyacrylamide gel electrophoresis (PAGE).
Power supply
Theory and Product Selection
Protein Electrophoresis Workflow
Method Selection
Electrodes
Anode +
–
Cathode –
–
+
+
Consider the experimental goals in selecting
the appropriate electrophoresis method.
Instrumentation selection depends on the desired
resolution and throughput.
Sample Preparation
–
+
Fig. 1.1. Movement of proteins during electrophoresis.
The protein sample may be prepared from
a biological sample, or it may come from a step in
a purification workflow. In either case, prepare the
protein at a concentration and in a buffer suitable
for electrophoresis.
General Considerations and Workflow
The electrophoresis workflow (Figure 1.2) involves the
selection of the appropriate method, instrumentation,
and reagents for the intended experimental goal.
Once proteins are separated, they are available for
a number of downstream applications, including
enzymatic assays, further purification, transfer
to a membrane for immunological detection
(immunoblotting or western blotting), and elution and
digestion for mass spectrometric analysis.
Gel and Buffer Preparation
Whether handcast or precast, the gel
type used should suit the properties of the protein
under investigation, the desired analysis technique,
and overall goals of the experiment. Buffer selection
depends on the gel type and type of
electrophoresis performed.
Performing Electrophoresis
Gels are placed in the electrophoresis cell,
buffer is added, and samples are loaded. Select
running conditions that provide optimum resolution
while maintaining the temperature of the system
during separation.
Related Literature
Protein Blotting Guide,
A Guide to Transfer
and Detection,
bulletin 2895
2-D Electrophoresis for
Proteomics: A Methods
and Product Manual,
bulletin 2651
Protein Detection and Analysis
Select a visualization technique that
matches sensitivity requirements and available
imaging equipment.
Fig. 1.2. Protein electrophoresis workflow.
6
7
Electrophoresis Guide
Chapter 2: Protein Electrophoresis Methods and Instrumentation
Theory and Product Selection
TABLE OF CONTENTS
CHAPTER 2
Protein
Electrophoresis
Methods and
Instrumentation
Consider the experimental goals in
selecting the appropriate electrophoresis
method; selection of instrumentation
depends on the number and volume
of samples, desired resolution, and
throughput. This chapter describes the
most common techniques and systems
in use today.
8
9
Electrophoresis Guide
Chapter 2: Protein Electrophoresis Methods and Instrumentation
Protein Electrophoresis Methods
Two types of buffer systems can be used:
By choosing suitable separation matrices and
corresponding buffer systems, a range of experimental
objectives can be met using protein electrophoresis
(Zewart and Harrington 1993).
■■
Polyacrylamide Gel Electrophoresis (PAGE)
When electrophoresis is performed in acrylamide or
agarose gels, the gel serves as a size-selective sieve
during separation. As proteins move through a gel in
response to an electric field, the gel’s pore structure
allows smaller proteins to travel more rapidly than larger
proteins (Figure 2.1). For protein separation, virtually
all methods use polyacrylamide as an anticonvective,
sieving matrix covering a protein size range of
5–250 kD. Some less common applications such as
immunoelectrophoresis and the separation of large
proteins or protein complexes >300 kD rely on the larger
pore sizes of agarose gels.
■■
ontinuous buffer systems use the same buffer
C
(at constant pH) in the gel, sample, and electrode
reservoirs (McLellan 1982). Continuous systems are
not common in protein separations; they are used
mostly for nucleic acid analysis
iscontinuous buffer systems use a gel separated
D
into two sections (a large-pore stacking gel on top of
a small-pore resolving gel, Figure 2.2) and different
buffers in the gels and electrode solutions (Wheeler
et al. 2004)
Direction of protein migration
TABLE OF CONTENTS
In gel electrophoresis, proteins do not all enter the
gel matrix at the same time. Samples are loaded
into wells, and the proteins that are closer to the gel
enter the gel first. In continuous systems, the uniform
separation matrix yields protein bands that are diffuse
and poorly resolved. In discontinuous systems, on the
other hand, proteins first migrate quickly through the
In most PAGE applications, the gel is mounted between large-pore stacking gel and then are slowed as they
two buffer chambers, and the only electrical path
enter the small-pore resolving gel. As they slow down,
between the two buffers is through the gel. Usually, the they stack on top of one another to form a tight band,
gel has a vertical orientation, and the gel is cast with
which improves resolution. Discontinuous systems also
a comb that generates wells in which the samples are
use ions in the electrophoresis buffer that sandwich
applied (Figure 2.1). Applying an electrical field across
the proteins as they migrate through the gel, and this
the buffer chambers forces the migration of protein into tightens the protein bands even more (Figure 2.2).
and through the gel (Hames 1998).
Discontinuous buffer systems provide higher resolution
than continuous systems, and varying the buffers used
in the sample, gel, and electrode chambers creates
Cathode
a variety of discontinuous buffer systems that can be
used for a variety of applications.
Discontinuous Native PAGE
Well
Buffer
Larger
(high MW)
protein
Protein band
Smaller
(low MW)
protein
Theory and Product Selection
Anode
Gel
Fig. 2.1. Schematic of electrophoretic protein separation in a
polyacrylamide gel. MW, molecular weight.
The original discontinuous gel system was developed
by Ornstein and Davis (Ornstein 1964, Davis 1964)
for the separation of serum proteins in a manner
that preserved native protein conformation, subunit
interactions, and biological activity (Vavricka 2009).
In such systems, proteins are prepared in nonreducing,
nondenaturing sample buffer, and electrophoresis
is also performed in the absence of denaturing and
reducing agents.
Data from native PAGE are difficult to interpret. Since
the native charge-to-mass ratio of proteins is preserved,
protein mobility is determined by a complex combination
of factors. Since protein-protein interactions are retained
during separation, some proteins may also separate
as multisubunit complexes and move in unpredictable
ways. Moreover, because native charge is preserved,
proteins can migrate towards either electrode,
depending on their charge. The result is that native
PAGE yields unpredictable separation patterns that
are not suitable for molecular weight determination.
Related Literature
Gel Electrophoresis:
Separation of Native Basic
Proteins by Cathodic,
Discontinuous Polyacrylamide
Gel Electrophoresis,
bulletin 2376
Stacking gel
4%T*, pH 6.8
Resolving gel
7.5%T to 15%T,
pH 8.8
Fig. 2.2. Migration of proteins and buffer ions in a denaturing discontinuous PAGE system. A, Denatured sample proteins are loaded
into the wells; B, Voltage is applied and the samples move into the gel. The chloride ions already present in the gel (leading ions) run faster
than the SDS-bound proteins and form an ion front. The glycinate ions (trailing ions) flow in from the running buffer and form a front behind
the proteins; C, A voltage gradient is created between the chloride and glycinate ions, which sandwich the proteins in between them; D, The
proteins are stacked between the chloride and glycinate ion fronts. At the interface between the stacking and resolving gels, the percentage
of acrylamide increases and the pore size decreases. Movement of the proteins into the resolving gel is met with increased resistance; E, The
smaller pore size resolving gel begins to separate the proteins based on molecular weight only, since the charge-to-mass ratio is equal in all
the proteins of the sample; F, The individual proteins are separated into band patterns ordered according to their molecular weights.
* %T refers to the total monomer concentration of the gel (see Chapter 4 for more information).
Nevertheless, native PAGE does allow separation of
proteins in their active state and can resolve proteins of
the same molecular weight.
As a result, the rate at which SDS-bound protein
migrates in a gel depends primarily on its size, enabling
molecular weight estimation.
SDS-PAGE
The original Laemmli system incorporated SDS in
the gels and buffers, but SDS is not required in the
gel. SDS in the sample buffer is sufficient to saturate
proteins, and the SDS in the cathode buffer maintains
the SDS saturation during electrophoresis. Precast gels
(manufactured gels such as Bio-Rad’s Mini-PROTEAN®
and Criterion™ gels) do not include SDS and so can
be used for either native or SDS-PAGE applications.
A range of gel and buffer combinations can be used for
native and SDS-PAGE, each with its own advantages
(see Chapter 4 for more details).
To overcome the limitations of native PAGE systems,
Laemmli (1970) incorporated the detergent sodium
dodecyl sulfate (SDS) into a discontinuous denaturing
buffer system, creating what has become the most
popular form of protein electrophoresis, SDS-PAGE.
When proteins are separated in the presence of SDS
and denaturing agents, they become fully denatured
and dissociate from each other. In addition, SDS binds
noncovalently to proteins in a manner that imparts:
■■
■■
■■
An overall negative charge on the proteins.
Since SDS is negatively charged, it masks the
intrinsic charge of the protein it binds
A similar charge-to-mass ratio for all proteins in a
mixture, since SDS binds at a consistent rate of
1.4 g of SDS per 1 g protein (a stoichiometry of
about one SDS molecule per two amino acids)
O–
S
O
O–
S
O
O
O
O O
SDS
O–Na+
O
O
S
O
O–
S
O–
S
O
O
O
O
O O
long, rod-like shape on the proteins instead of a
A
complex tertiary conformation (Figure 2.3)
Fig. 2.3. Effect of SDS on the conformation and charge of a protein.
10
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Electrophoresis Guide
Chapter 2: Protein Electrophoresis Methods and Instrumentation
Isoelectric Focusing (IEF)
Automated Electrophoresis
Automated electrophoresis systems use microfluidic
technology to integrate electrophoretic separation,
fluorescence detection, and data analysis within a
single platform. Using much smaller sample and
reagent quantities and far less time than standard
analysis methods, automated electrophoresis
systems like Bio-Rad’s Experion™ system can
be used in applications such as purity and yield
assessment in protein purification and protocol
optimization workflows. However, samples cannot
be recovered from automated separations, and
downstream applications are thus not possible.
Related Literature
2-D Electrophoresis for
Proteomics: A Methods and
Product Manual,
bulletin 2651
The Experion system employs LabChip microfluidic
technology to automate complete protein and
nucleic acid electrophoresis and analyze up to
12 samples in a single 30–40 min automated step
(analysis of a single sample is accomplished in as
little as 90 sec).
TABLE OF CONTENTS
Protein analysis with the Experion system is
achieved with the Experion Pro260 analysis kit,
which supplies the microfluidic chips, reagents,
and instructions required to separate and analyze
10–260 kD proteins under denaturing conditions.
The sensitivity of the Experion Pro260 analysis kit is
comparable to that of colloidal Coomassie (Brilliant)
Blue staining of SDS-PAGE gels.
Experion software converts a fluorescent signal
into an electropherogram (a plot of fluorescence
vs. time) and a densitometric gel-like image, or
virtual gel. Each lane in the virtual gel corresponds
to a different sample, and the peaks in the
electropherogram correspond to bands in the virtual
gel. The results of data analysis are also presented
in a table at the end of analysis.
Links
Experion Automated
Electrophoresis System
Experion Protein
Analysis Kits
Coomassie Stains
Coomassie Brilliant
Blue G-250 Stain
Coomassie Brilliant
Blue R-250 Stain
12
Other Types of PAGE
Blue Native PAGE (BN-PAGE)
BN-PAGE is used to separate and characterize large
protein complexes in their native and active forms.
Originally described by Schägger and von Jagow
(1987), this technique relies on the solubilization of
protein complexes with mild, neutral detergents and
the binding of negatively charged Coomassie (Brilliant)
Blue G-250 stain to their surfaces. This imparts a high
charge-to-mass ratio that allows the protein complexes
to migrate to the anode as they do in SDS-PAGE.
Coomassie Blue does not, however, denature and
dissociate protein complexes the way SDS does. Highresolution separation is achieved by electrophoresis
into an acrylamide gradient with decreasing pore
The types of data available include the following:
n
Protein size (or mass, in kD)
Protein concentration (in ng/μl): relative and
absolute concentration
n Consider protein purity (% of the total sample) as
an alternative
n The Experion system provides single-step
quantitation and size determination (sizing) of protein
samples useful for quality control, protein purity
and stability analysis, protocol optimization, and
evaluation of recombinant protein expression.
IEF combines the use of an electric field with a pH
gradient to separate proteins according to their pI.
It offers the highest resolution of all electrophoresis
techniques (Westermeier 2004).
When a protein moves through a pH gradient, its net
charge changes in response to the pH it encounters.
Under the influence of an electric field, a protein in a
pH gradient migrates to a pH where its net charge is
zero (the protein’s pI). If the protein moves out of that
position, it acquires a charge and is forced back to
the zero-charge position (Figure 2.4). This focusing is
responsible for the high resolution of IEF. pI values of
proteins usually fall in the range of pH 3–11.
4
3
NH+3
4
NH+3
COOH
COOH
5
6
7
NH2
NH2
COOH
COOH
COOH
8
9
10
NH2
NH2
COOH
COOH
COO-
COO-
Net Charge
2
3
5
a
b
The Experion system. The system includes: 1, automated
electrophoresis station; 2, priming station; 3, vortex station
used only for nucleic acid analysis; 4, system operation and
data analysis tools (software); and 5, analysis kits, which
include the chips (a) and reagents (b) for protein (Pro260 kit),
standard-sensitivity RNA (StdSens kit), high-sensitivity RNA
(HighSens kit), and DNA (DNA 1K and 12K kits) analyses.
sizes; the protein complexes become focused at the
corresponding pore size limit (Nijtmans et al. 2002,
Reisinger and Eichacker 2008).
Zymogram PAGE
Zymogram PAGE is used to detect and characterize
collagenases and other proteases within the gel.
Gels are cast with gelatin or casein, which acts as a
substrate for the enzymes that are separated in the
gel under nonreducing conditions. The proteins are
run with denaturing SDS in order to separate them
by molecular weight. After renaturing the enzymes
and then allowing them to break down the substrate,
zymogram gels are stained with Coomassie (Brilliant)
Blue R-250 stain, which stains the substrate while
leaving clear areas around active proteases.
Bio-Rad’s PROTEAN® i12™ IEF system provides
individual lane control for up to 12 IPG strips, making
it possible to run different sample types, different pH
gradients, and multiple protocols at the same time. IEF
can be run under either native or denaturing conditions.
Native IEF retains protein structure and enzymatic
activity. However, denaturing IEF is performed in
the presence of high concentrations of urea, which
dissociates proteins into individual subunits and
abolishes secondary and tertiary structures. Whereas
native IEF may be a more convenient option because
it can be performed with a variety of precast gels,
denaturing IEF often offers higher resolution and is more
suitable for the analysis of complex protein mixtures.
2-D Electrophoresis
pH
1
Theory and Product Selection
Fig. 2.4. Isoelectric focusing. A protein is depicted in a pH
gradient in an electric field. A pH gradient formed by ampholyte
molecules under the influence of an electric field is indicated.
The gradient increases from acidic (pH 3) at the anode to basic
(pH 10) at the cathode. The hypothetical protein in the drawing bears
a net charge of +2, 0, or –2, at the three positions in the pH gradient
shown. The electric field drives the protein toward the cathode when
it is positively charged and toward the anode when it is negatively
charged, as shown by the arrows. At the pI, the net charge on the
protein is zero, so it does not move in the field. The protein loses
protons as it moves toward the cathode and becomes progressively
less positively charged. Conversely, the protein gains protons as
it moves toward the anode and becomes less negatively charged.
When the protein becomes uncharged (pI), it ceases to move in the
field and becomes focused.
The sequential application of different electrophoresis
techniques produces a multi-dimensional separation.
The most common 2-D technique (O’Farrell 1975)
subjects protein samples first to denaturing IEF on
a tube gel or IPG gel strip (for separation by pI), then
to SDS-PAGE for further separation by molecular
weight. High-resolution 2-D methods enable separation
of thousands of polypeptides in a single slab gel.
The resulting spots can be visualized by gel staining,
or they can be transferred to a membrane support
for total protein staining or analysis with specific
antibody detection. For more details, refer to 2-D
Electrophoresis for Proteomics (bulletin 2651).
Electrophoresis Cells and Power Supplies
Electrophoresis Cells
Vertical electrophoresis cells are plastic boxes with
anode and cathode buffer compartments that contain
Two methods are used to generate a stable, continuous electrodes (Figure 2.5). The electrodes (typically
platinum wire) connect to a jack attached to a
pH gradient between the anode and cathode:
power supply. The gels are held vertically between
■■ Carrier ampholytes — heterogeneous mixtures
the electrode chambers during electrophoresis
of small (300–1,000 Da) conductive polyamino(Andrews 1986).
polycarboxylate compounds that carry multiple
charges with closely spaced pI values. When voltage
Electrodes
is applied across an ampholyte-containing solution
or gel, the ampholytes align themselves according
to their pIs and buffer the pH in their proximity,
establishing a pH gradient. Ampholytes can be used
in gels (for example, tube gels or vertical gels) or in
Lid
solution (for example, liquid-phase IEF)
■■
Immobilized pH gradients (IPG) strips — formed
by covalently grafting buffering groups to a
polyacrylamide gel backbone. A gradient of different
buffering groups generates a stable pH gradient that
can be tailored for different pH ranges and gradients
(Bjellquist et al. 1982)
Links
Mini Format 1-D
Electrophoresis Systems
Mini-PROTEAN Precast Gels
Mini-PROTEAN Tetra Cell
Mini-PROTEAN 3 Dodeca Cell
idi Format 1-D
M
Electrophoresis Systems
Criterion Precast Gels
Criterion Cell
Criterion Dodeca Cell
L arge-Format 1-D
Electrophoresis Systems
PROTEAN II xi Cell
PROTEAN II XL Cell
PROTEAN II xi and XL Multi-Cells
Gel box
Running
module
Fig. 2.5. Components of a vertical electrophoresis cell.
PROTEAN Plus Dodeca Cell
PROTEAN i12 IEF System
13
Electrophoresis Guide
Related Literature
Mini-PROTEAN Tetra Cell
Brochure, bulletin 5535
Criterion Precast Gel System
Brochure, bulletin 2710
Chapter 2: Protein Electrophoresis Methods and Instrumentation
Vertical electrophoresis cells are made in different size
formats to accommodate different gels sizes. Deciding
which cell to use depends on the requirements for speed,
resolution, and throughput (both the number of samples
and gels) as well as the volume of sample available
(Table 2.1).
■■
PROTEAN II xi/XL Cells Product
Information Sheet, bulletin 1760
ini-format systems — accommodate small gels
M
(up to 8.6 x 6.7 cm). The short separation distance
maximizes the electrical field strength (V/cm) to yield
rapid separations with moderate resolution. Use these
systems for rapid analysis, method development, or
when sample volumes are limited. The Mini-PROTEAN®
system includes the Mini-PROTEAN Tetra cell (with a
capacity of up to four gels) and the high-throughput
Mini-PROTEAN® 3 Dodeca™ cell (for running
up to 12 gels); both cells are compatible with
Mini-PROTEAN precast gels
■■
■■
idi-format systems — accommodate 13.3 x 8.7 cm
M
gels and offer rapid runs with more samples per
gel and enhanced separation over mini-format gels.
The Criterion™ system includes the Criterion cell
(for 1–2 gels) and the high-throughput Criterion™
Dodeca™ cell (for 1–12 gels); both cells are
compatible with Criterion precast gels
arge-format systems — accommodate large gels
L
(up to 20 x 18.3 cm for the PROTEAN® II system
Table 2.1. Vertical electrophoresis system selection guide.
TABLE OF CONTENTS
Advantages
Mini-PROTEAN System Run 1–4 precast or handcast gels
in the Mini-PROTEAN Tetra cell and
up to 12 gels in the Mini-PROTEAN
Dodeca cell in mini format
Wing clamp assembly allows faster
setup and leak-free operation
Criterion System
Fast setup with drop-in gel and
cell design (precast or handcast)
Run 1–2 precast Criterion or
handcast gels in the Criterion cell
and up to 12 gels in the Criterion
Dodeca cell
Integrated upper buffer chamber
allows leak-free operation
Compatible Gel Formats
Mini-PROTEAN precast gels
Precast
PROTEAN II System
Large-format gel system
offers greater resolution over
smaller formats
Can accommodate up to 4 gels
and is available in xi or XL formats
for running a variety of gel sizes
PROTEAN Plus System
Offers maximum resolution in a
single gel and the longest range
of separation (with the ability to
run up to 12 gels)
Specifically for the second
dimension of 2-D electrophoresis
Multi-cell is available for running
up to 6 gels
Criterion precast gels
Ready Gel empty cassettes
Criterion empty cassettes
PROTEAN II casting plates
PROTEAN Plus casting equipment
Mini-PROTEAN casting plates
Electrophoresis Cells
Mini-PROTEAN Tetra
Criterion
PROTEAN II xi/XL
Mini-PROTEAN 3 Dodeca
Criterion Dodeca
PROTEAN II xi/XL multi-cells
Precast Gel Dimensions
W x L x thickness
Mini-PROTEAN precast gels:
8.6 x 6.7 x 0.1 cm
PROTEAN Plus Dodeca
Criterion precast gels:
13.3 x 8.7 x 0.1 cm
Compatible Transfer Systems
Mini Trans-Blot® cell
Wet/tank transfer
15.0 x 10.6 cm
20.0 x 18.3 cm
Criterion wire blotter
Trans-Blot cell
Criterion blotter
Criterion plate blotter
Trans-Blot Plus cell
Trans-Blot® cell
Trans-Blot cell
Trans-Blot Plus cell
Semi-dry transfer
14
Trans-Blot® Turbo™ system
Trans-Blot Turbo system
Trans-Blot SD cell
Trans-Blot SD cell
Power supplies are available to meet the power
requirements of numerous applications. The choice
Table 2.2. PowerPac™ power supplies selection guide.
Technique and Recommended
Apparatus
PowerPac
Power Supply
Laemmli (SDS),
O’Farrell Second Dimension (SDS)
Mini-PROTEAN Tetra cell
Criterion cell
PROTEAN II xi cell
PROTEAN II XL cell
Basic or HC
Basic or HC
HV or Universal
HV or Universal
High-Throughput Electrophoresis
Mini-PROTEAN 3 Dodeca cell
Criterion Dodeca cell
PROTEAN II xi/XL multi-cell
PROTEAN Plus Dodeca cell
HC or Universal
HC or Universal
Universal
HC or Universal
Western Blotting
Mini Trans-Blot cell
Criterion blotter
Wire electrodes
Plate electrodes
Trans-Blot cell
Wire electrodes
Plate electrodes
High-intensity transfer
Trans-Blot Plus cell
Trans-Blot SD cell
Protein
DNA/RNA
■■
■■
■■
Trans-Blot SD cell
18.5 x 20.5 cm
20.0 x 20.5 cm
20.0 x 20.5 cm
Trans-Blot Plus cell
Related Literature
PowerPac Basic 300 V Power
Supply Flier, bulletin 2881
se the PowerPac Basic or PowerPac HC highU
current power supply for mini-format vertical
PAGE applications
PowerPac HC High-Current
Power Supply Flier,
bulletin 2882
se the PowerPac HV high-voltage or PowerPac
U
Universal power supply for large-format vertical
PAGE applications
PowerPac Universal Power
Supply Brochure,
bulletin 2885
se the PowerPac HC power supply for applications
U
that require high currents, such as PAGE with the
high-throughput Dodeca cells
PowerPac HV Power Supply
Brochure, bulletin 3189
PowerPac HC High-Current Power Supply
PowerPac Basic Power Supply
HC
HC
HC
HC
HC
HC
HC
HC
HC
Preparative electrophoresis techniques separate
large amounts of protein (nanogram to gram
quantities) for the purposes of purification or
fractionation (to reduce sample complexity).
The same principles that are applied for analytical
work can be applied for preparative work.
PAGE
Ready Gel precast gels:
8.3 x 6.4 x 0.1 cm
Cassette Dimensions (for Handcasting Gels)
10.0 x 8.0 cm
Power Supplies for PAGE Applications
of power supply for PAGE applications usually depends
on the size and number of gels being run. Table 2.2
compares the Bio-Rad PowerPac power supplies
recommended for vertical electrophoresis applications.
PowerPac Universal Power Supply
PowerPac HV High-Voltage Power Supply
Fig. 2.6. PowerPac power supplies.
Links
Preparative Electrophoresis
Ready Gel® precast gels
Handcast
and 20 x 20.5 cm for the PROTEAN Plus System)
and offer maximum resolution. The PROTEAN II
system provides a choice of glass plates, spacer,
and sandwich clamps to cast two gel lengths:
16 or 20 cm. The PROTEAN® Plus Dodeca™ cell
allows maximum throughput with the capability to
run up to 12 gels at a time
Theory and Product Selection
Preparative PAGE can be accomplished using a
standard slab gel or special instrumentation. With the
slab gel, a single preparative or “prep” well is cast,
which allows a large volume of a single sample to
be applied within one well. With this approach, the
separated protein is retained within the gel for further
analysis or purification (for example, by electroelution).
Alternatively, continuous-elution gel electrophoresis
using the Model 491 prep cell or mini prep cell yields
high-resolution separations and proteins in liquid
fractions, ready for downstream use.
Liquid-Phase IEF
Liquid-phase IEF devices, such as the Rotofor®
cell, mini Rotofor cell, and MicroRotofor™ cell,
fractionate proteins in free solution according to
their pI. This nondenaturing technique produces
fractions that can be collected, pooled, and even
refractionated for further purification. Fractionation
by liquid-phase IEF is particularly useful for proteins
that do not separate well in gel-based IEF media.
The pH gradient used for separation is generated
by ampholytes, allowing a continuous and
customizable pH gradient to be formed.
Combination Approaches (2-D Separations)
Preparative IEF and PAGE can be combined
(for separation on multiple dimensions) for even
greater separation.
Preparative Electrophoresis
Power Supplies
PowerPac Universal
Power Supply
PowerPac HC High-Current
Power Supply
PowerPac HV High-Voltage
Power Supply
PowerPac Basic
Power Supply
Model 491 Prep Cell and
Mini Prep Cell
Rotofor and Mini Rotofor Cells
MicroRotofor Cell
15
Electrophoresis Guide
Chapter 3: Sample Preparation for Electrophoresis
Theory and Product Selection
TABLE OF CONTENTS
CHAPTER 3
Sample Preparation
for Electrophoresis
Sample preparation involves the
extraction and solubilization of
a protein sample that is free of
contaminants and that has a total
protein concentration suitable for
electrophoresis. The quality of sample
preparation can greatly affect the
quality of the data that are generated.
General guidelines and some of the
most common methods for protein
sample preparation are provided in
this chapter.
16
17
Electrophoresis Guide
Chapter 3: Sample Preparation for Electrophoresis
Sample Preparation Workflow
Cell Disruption
Different biological materials require different cell disruption
strategies. Use chemical inhibitors and controlled temperature
to minimize the activity of proteases and other enzymes that
may modify the protein composition of the sample.
General Considerations
Cell Disruption
Due to the great diversity of protein sample types
and sources, no single sample preparation method
works with all proteins; for any sample, the optimum
procedure must be determined empirically. However,
the following general sample preparation guidelines
should be kept in mind to avoid a number of common
pitfalls during sample preparation for protein
electrophoresis (Posch et al. 2006):
The effectiveness of a cell disruption method
determines the accessibility of intracellular proteins
for extraction and solubilization (Huber et al. 2003).
Different biological materials require different cell
disruption strategies, which can be divided into
two main categories: gentle and harsher methods
(Table 3.1).
■■
■■
Protein Solubilization
For successful PAGE, proteins must be well solubilized.
Use solubilization solutions that contain chaotropic agents,
detergents, reducing agents, buffers, and salts as needed and
that are compatible with the electrophoretic technique used.
■■
■■
TABLE OF CONTENTS
■■
Contaminant Removal, Desalting,
Concentration (as needed)
Remove interfering substances that can negatively impact
SDS-PAGE (salts, detergents, denaturants, or organic solvents).
Use either buffer exchange (desalting) or protein precipitation
(which can also help concentrate the sample if needed).
Quantitation
Determine the concentration of protein in a
sample by protein assay. Adjust the concentration
as necessary for analysis by PAGE.
Preparation for PAGE
Sample
Buffer
Dilute the sample in the appropriate sample buffer
to a final sample buffer concentration of 1x.
Fig. 3.1. Protein sample preparation workflow.
18
eep the sample preparation workflow as simple as
K
possible (increasing the number of sample handling
steps may increase variability)
ith cell or tissue lysates, include protease inhibitors
W
to minimize artifacts generated by proteolysis;
protease inhibitors are generally not required for
samples like serum or plasma
■■
■■
■■
etermine the amount of total protein in each
D
sample using a protein assay that is compatible with
chemicals in your samples
olubilize proteins in a buffer that is compatible with
S
the corresponding electrophoresis technique
se protein extracts immediately or aliquot them into
U
appropriately sized batches and store them at –80°C
to avoid freeze-thaw cycles
■■
■■
Theory and Product Selection
se gentle cell disruption protocols when the sample
U
consists of cells that lyse easily, such as red blood
cells or tissue culture cells
se harsher methods, which are based mainly on
U
mechanical rupture (Goldberg 2008), with biological
materials that have tough cell walls (for example,
plant cells, tissues, and some microbes)
hen working with a new sample, use at least two
W
different cell disruption protocols and compare their
efficiency in terms of yield (by protein assay) and
qualitative protein content (by SDS-PAGE)
ptimize the power settings of mechanical rupture
O
systems and incubation times for all lysis approaches
echanical cell lysis usually generates heat; use
M
cooling where required to avoid overheating
the sample
Table 3.1. Suitability of cell disruption methods to various sample types.
Yeast, Green
Mammalian
Algae, Plant
SoftCell
Technique
Description
Bacteria
Fungi
Seeds
Material Tissues Culture
Gentle Methods
Osmotic lysis
Suspension of cells in hypotonic solution;
cells swell and burst, releasing cellular contents
—
—
—
—
—
•
Freeze-thaw lysis
Freezing in liquid nitrogen and subsequent
thawing of cells
—
—
—
—
—
•
Detergent lysis
Suspension of cells in detergent-containing
solution to solubilize the cell membrane; this
method is usually followed by another
disruption method, such as sonication
—
—
—
—
—
•
Enzymatic lysis
Suspension of cells in iso-osmotic solutions containing enzymes that digest the cell wall
(for example, cellulase and pectinase for plant
cells, lyticase for yeast cells, and lysozyme for
bacterial cells); this method is usually followed by
another disruption method, such as sonication
•
•
—
•
—
—
•
•
—
—
—
•
Harsher Methods
Sonication
Disruption of a cell suspension, cooled on ice
to avoid heating and subjected to short bursts
of ultrasonic waves
French press
Application of shear forces by forcing a cell
suspension through a small orifice at high pressure
•
•
—
—
—
•
Grinding
Breaking cells of solid tissues and microorganisms with a mortar and pestle;
usually, the mortar is filled with liquid nitrogen and
the tissue or cells are ground to a fine powder
•
•
•
•
•
—
Mechanical
homogenization
Homogenization with either a handheld device (for
—
example, Dounce and Potter-Elvehjem homogenizers),
blenders, or other motorized devices; this approach
is best suited for soft, solid tissues
—
—
•
•
—
Glass-bead
homogenization
Application of gentle abrasion by vortexing
cells with glass beads
•
—
—
—
•
•
19
Electrophoresis Guide
Chapter 3: Sample Preparation for Electrophoresis
All cell disruption methods cause the release of
compartmentalized hydrolases (phosphatases,
glycosidases, and proteases) that can alter the protein
composition of the lysates. In experiments where
relative amounts of protein are to be analyzed, or in
experiments involving downstream immunodetection,
the data are only meaningful when the protein
composition is preserved. Avoid enzymatic degradation
by using one or a combination of the following
techniques:
■■
■■
■■
■■
TABLE OF CONTENTS
■■
isrupt the sample or place freshly disrupted samples
D
in solutions containing strong denaturing agents
such as 7–9 M urea, 2 M thiourea, or 2% SDS. In this
environment, enzymatic activity is often negligible
erform cell disruption at low temperatures to
P
diminish enzymatic activity
yse samples at pH >9 using either sodium
L
carbonate or Tris as a buffering agent in the lysis
solution (proteases are often least active at basic pH)
dd a chemical protease inhibitor to the lysis
A
buffer. Examples include phenylmethylsulfonyl
fluoride (PMSF), aminoethyl-benzene sulfonyl
fluoride (AEBSF), tosyl lysine chloromethyl ketone
(TLCK), tosyl phenyl chloromethyl etone (TPCK),
ethylenediaminetetraacetic acid (EDTA), benzamidine,
and peptide protease inhibitors (for example,
leupeptin, pepstatin, aprotinin, and bestatin). For
best results, use a combination of inhibitors in a
protease inhibitor cocktail
If protein phosphorylation is to be studied, include
phosphatase inhibitors such as fluoride and vanadate
Following cell disruption:
■■
■■
heck the efficacy of cell wall disruption by
C
light microscopy
If this is not possible or desirable, proteins must be
prepared in sample solubilization solutions that typically
contain a number of compounds, including chaotropic
agents, detergents, reducing agents, buffers, salts,
and ampholytes. These are chosen from a small list of
compounds that meet the requirements, both electrically
and chemically, for compatibility with the electrophoretic
technique being used. In these cases, the sample will
have to be diluted with concentrated electrophoresis
sample buffer to yield a 1x final buffer concentration.
Detergents
Detergents are classified as nonionic, zwitterionic,
anionic, and cationic, and they disrupt hydrophobic
interactions between and within proteins (Luche et al.
2003). Some proteins, especially membrane proteins,
require detergents for solubilization during isolation
and to maintain solubility. Nonionic detergents
such as NP-40 and Triton X-100 are not very effective
at solubilizing hydrophobic proteins; zwitterionic
detergents such as CHAPS and sulfobetaines
(for example, SB 3-10 or ASB-14) provide higher
solubilization efficiency, especially for integral membrane
proteins. Sample preparation for PAGE commonly uses
the anionic detergent SDS, which is unparalleled in its
ability to efficiently and rapidly solubilize proteins.
Reducing Agents
Thiol reducing agents such as 2-mercaptoethanol
(bME) and dithiothreitol (DTT) disrupt intramolecular and
intermolecular disulfide bonds and are used to achieve
complete protein unfolding and to maintain proteins in
their fully reduced states (Figure 3.2).
bME is volatile, evaporates from solution, and reduces
protein disulfide bonds by disulfide exchange. There
is an equilibrium between free thiols and disulfides,
so bME is used in large excess in sample buffers to
entrifuge all extracts extensively (20,000 x g for
C
15 min at 15°C) to remove any insoluble material;
solid particles may block the pores of the gel
S S
Protein Solubilization
Protein solubilization is the process of breaking
interactions involved in protein aggregation, for example,
disulfide bonds, hydrogen bonds, van der Waals
forces, ionic interactions, and hydrophobic interactions
(Rabilloud 1996). If these interactions are not prevented,
proteins can aggregate or precipitate, resulting in
artifacts or sample loss. For successful PAGE, proteins
must be well solubilized.
Ideally, cell lysis and protein solubilization are carried
out in the sample buffer that is recommended for
the particular electrophoresis technique, especially
when native electrophoresis is the method of choice.
20
S S
Reduction
Reduction
SH
SH
SH
SH
Fig. 3.2. Reduction of proteins with DTT.
drive the equilibrium reaction toward completion. If the
concentration of bME drops and proteins reoxidize,
fuzzy or spurious artifactual bands may result.
DTT is less volatile and is altered during the disulfide
reduction reaction to form a ring structure from its
original straight chain. The equilibrium favors protein
reduction, so lower concentrations of DTT are needed
(higher concentrations are recommended for proteins
with large numbers of disulfide bonds).
Phosphines such as tributylphosphine (TBP) and Triscarboxyethylphosphine (TCEP)* offer an alternative to
thiols as reducing agents because they can be used at
lower concentrations and over a wider pH range than
the sulfhydryl reductants.
Chaotropic Agents
Chaotropic compounds such as urea disrupt hydrogen
bonds and hydrophobic interactions both between and
within proteins. When used at high concentrations, they
destroy secondary protein structure and bring proteins
into solution that are not otherwise soluble.
Urea and substituted ureas like thiourea improve
solubilization of hydrophobic proteins. Currently,
the best solution for denaturing electrophoresis
is a combination of 7 M urea and 2 M thiourea in
combination with appropriate detergents like CHAPS.
Samples containing urea and thiourea can be used
in SDS-PAGE when diluted with SDS-PAGE sample
buffer. The protein solution should not be heated above
37ºC because urea and thiourea get hydrolyzed (to
cyanate and thiocyanate, respectively) and modify
amino acids on proteins (carbamylation), giving rise to
artifactual charge heterogeneity.
fuzzy bands and narrowing of gel lanes toward the
bottom of the gel. If the ionic strength is very high, no
bands will appear in the lower part of the gel (a vertical
streak will appear instead) and the dye front will be wavy
instead of straight. Deionize any sample with a total ionic
strength over 50 mM using columns such as
Micro Bio-Spin™ columns, which contain 10 mM Tris at a
pH suitable for SDS-PAGE.
Common Solutions for Protein Solubilization
Ideally, cell lysis and protein solubilization are carried
out in the sample buffer that is recommended for
the particular electrophoresis technique, especially
for native electrophoresis. If this is not possible or
desirable, dilute the protein solution with concentrated
electrophoresis sample buffer to yield a 1x final
buffer concentration.
Formulas for various sample buffers are provided in
Part II of this guide.
Removal of Interfering Substances
Success or failure of any protein analysis depends
on sample purity. Interfering substances that can
negatively impact SDS-PAGE include salts, detergents,
denaturants, or organic solvents (Evans et al. 2009).
Highly viscous samples indicate high DNA and/or
carbohydrate content, which may also interfere with
PAGE separations. In addition, solutions at extreme
pH values (for example, fractions from ion exchange
chromatography) diminish the separation power of most
electrophoresis techniques. Use one of the following
methods as needed to remove these contaminants:
■■
Buffers and Salts
Both pH and ionic strength influence protein solubility,
making buffer choice important, especially when native
electrophoresis conditions are required. Many proteins
are more soluble at higher pH; therefore, Tris base is
often included to elevate the pH. However, proteins
differ in their solubility at different pH values, so
different buffers can extract different sets of proteins.
The choice of buffer and pH of the sample preparation
solution can strongly influence which proteins show up
in a separation.
Even in the presence of detergents, some proteins have
stringent salt requirements to maintain their solubility,
but salt should be present only if it is an absolute
requirement. Excess salt in SDS-PAGE samples causes
*TCEP is included in Bio-Rad’s XT sample buffers. Although TCEP can
be added to SDS-PAGE sample buffer, it must first be neutralized with
NaOH; otherwise, it will hydrolyze proteins.
Theory and Product Selection
■■
rotein precipitation — the most versatile method to
P
selectively separate proteins from other contaminants
consists of protein precipitation by trichloroacetic
acid (TCA)/acetone followed by resolubilization
in electrophoresis sample buffer. A variety of
commercial kits can simplify and standardize
laboratory procedures for protein isolation from
biological samples
uffer exchange — size exclusion chromatography
B
is another effective method for removing salts,
detergents, and other contaminants
Products for Sample Preparation
Bio-Rad’s solution to successful and reproducible
sample preparation is the MicroRotofor™ lysis kits
(Figure 3.3), which provide cell lysis and protein
extraction protocols tailored to the specific needs of
different sample sources. All four kits are based on
the same chaotropic protein solubilization buffer (PSB),
which contains nondetergent sulfobetaine 201
(NDSB 201) and urea, thiourea, and CHAPS for
particularly effective solubilization (Vuillard et al. 1995).
Links
Micro Bio-Spin 6 and
Micro Bio-Spin 6 Columns
MicroRotofor Lysis Kits
21
Electrophoresis Guide
Chapter 3: Sample Preparation for Electrophoresis
The kits generate total protein samples that are
ready to be applied to SDS-PAGE, IEF, and 2-D
gel electrophoresis. Different sample types have
different requirements for effective cell disruption,
and all four kits combine PSB with other elements to
accommodate these specific needs.
■■
■■
Related Literature
■■
MicroRotofor Lysis Kits Flier,
bulletin 5517
■■
MicroRotofor™ cell lysis kit (mammal) — for use
with samples from mammalian sources, but it may
also be applied to other animal tissues
icroRotofor cell lysis kit (bacteria) — for use
M
with both gram-negative and gram-positive
bacterial cultures
icroRotofor cell lysis kit (plant) — for use with
M
soft plant tissues and cultured cells
icroRotofor cell lysis kit (yeast) — for use with
M
yeast cultures (~60 µl wet cell pellet)
Sample Quantitation (Protein Assays)
Table 3.2. Bio-Rad protein assay selection guide.
Determine the concentration of protein in a sample
(Berkelman 2008) by using protein assays to:
Quick Start™
BradfordBio-Rad DC™
RC DC™
Method
Bradford
Lowry
•
—
—
•
■■
■■
nsure that the amount of protein to be separated
E
is appropriate for the lane dimensions and
visualization method
acilitate comparison among similar samples;
F
image-based analysis is simplified when equivalent
quantities of proteins have been loaded in the lanes
of the gel
The most commonly used protein assays are
colorimetric assays in which the presence of protein
causes a color change that can be measured with
a spectrophotometer (Sapan et al. 1999, Noble and
Bailey 2009). All protein assays utilize a dilution series
of a known protein (usually bovine serum albumin or
bovine g-globulin) to create a standard curve from
which the concentration of the sample is derived (for a
protocol describing protein quantitation, refer to Part II
of this guide).
TABLE OF CONTENTS
■■
Fig. 3.3. MicroRotofor cell lysis kit.
For contaminant removal Bio-Rad offers the following
(Figure 3.4):
■■
Standard Bradford Detergent compatible
assay, not to be
(DC); Lowry assay
used with elevated
modified to save time
levels of detergents
(>0.1% SDS)
Reducing agent
detergent
compatible (RC DC)
Standard-Concentration Assay
Sample volume
Linear range
100 µl
0.125–1.5 mg/ml
100 µl
0.125–1.5 mg/ml
100 µl
0.125–1.5 mg/ml
100 µl
0.2–1.5 mg/ml
Low-Concentration Assay
Sample volume
Linear range
Microplate assay volume
Minimum incubation
Assay wavelength
1 ml
1.25–25 µg/ml
5 µl
5 min
595 nm
800 µl
1.25–25 µg/ml
10 µl
5 min
595 nm
200 µl
5–250 µg/ml
5 µl
15 min
650–750 nm 200 µl
5–250 µg/ml
**
15 min
650–750 nm
proportional to the amount of bound dye, and thus
to the amount (concentration) of protein in the
sample. Compared with other protein assays,
the Bradford protein assay is less susceptible to
interference by various chemicals that may be
present in protein samples*
Links
■■
Rotofor and Mini
Rotofor Cells
MicroRotofor Cell
MicroRotofor Lysis Kits
MicroRotofor Cell Lysis Kit
(Mammal)
MicroRotofor Cell Lysis Kit
(Bacteria)
Bio-Spin® and Micro Bio-Spin 6 columns — provide
rapid salt removal in an easy-to-use spin-column
format. Accommodating up to 100 µl of sample,
these columns remove compounds <6 kD; proteins
can be eluted in electrophoresis sample buffer
End cap
End cap
Reservoir
Reservoir
3 cm
2 cm working bed height
5 cm
0.8 ml bed volume
3.7 cm working bed height
1.2 ml bed volume
Porous 30 µm
polyethylene bed
support retains
fine particles
Luer end fitting
with snap-off tip
Micro Bio-Spin
Column
Luer end fitting
with snap-off tip
Bio-Spin Column
ReadyPrep 2-D
Cleanup Kit
Bio-Spin 6 and Micro
Bio-Spin 6 Columns
■■
owry (Lowry et al. 1951) — combines the reactions
L
of cupric ions with peptide bonds under alkaline
conditions and the oxidation of aromatic protein
residues. The Lowry method is based on the reaction
of Cu+, produced by the peptide-mediated reduction
of Cu2+, with Folin-Ciocalteu reagent (a mixture of
phosphotungstic acid and phosphomolybdic acid in
the Folin-Ciocalteu reaction)
Fig. 3.4. Bio-Rad products that can be used for contaminant
removal. Top, Micro Bio-Spin and Bio-Spin columns; Bottom,
ReadyPrep 2-D cleanup kit.
SmartSpec™ Plus Spectrophotometer
The color change observed in protein assays is
monitored and quantitated by a spectrophotometer.
Bio-Rad’s SmartSpec Plus spectrophotometer
(Figure 3.5) has preprogrammed methods for protein
quantitation and a working wavelength range of
200–800 nm. It can be used for routine applications
such as:
■■
■■
■■
■■
■■
uantitation of proteins via the Bradford, Lowry,
Q
and BCA assay methods
Quantitation of DNA, RNA, and oligonucleotides
Monitoring bacterial culture growth
Simple kinetic assays
Wavelength scans with peak detection
CA (bicinchoninic acid, Smith et al. 1985) — reacts
B
directly with Cu+ (generated by peptide-mediated
reduction of Cu2+) to produce a purple end product.
The reagent is fairly stable under alkaline conditions
and can be included in the copper solution to make
the assay a one-step procedure
To measure protein concentration in Laemmli buffers,
use the reducing agent detergent compatible (RC DC™)
protein assay, which is compatible with reducing
agents and detergents. For more information on protein
quantitation using colorimetric assays, refer to Bio-Rad
bulletin 1069.
*The Bradford assay is, however, highly sensitive to ionic detergents
like SDS.
MicroRotofor Cell Lysis Kit
(Plant)
MicroRotofor Cell Lysis Kit
(Yeast)
■■
radford assays (Bradford 1976) — are based on
B
an absorbance shift of Coomassie (Brilliant) Blue
G-250 dye under acid conditions. A redder form of
the dye is converted into a bluer form upon binding
to protein. The increase of absorbance at 595 nm is
ReadyPrep™ 2-D cleanup kit — uses a modification
of the traditional TCA protein precipitation protocol.
The kit offers quantitative protein recovery but
also ensures easy and reproducible removal of
interfering substances
—
•
Description
One-step determination;
not to be used with high
levels of detergents
(>0.025% SDS)
Protein Assays
The chemical components of the sample buffer and the
amount of protein available for assay dictate the type of
assay that may be used (Table 3.2).
•
—
Theory and Product Selection
Related Literature
Modification of Bio-Rad DC
Protein Assay for Use with
Thiols, bulletin 1909
Colorimetric Proteins Assays,
bulletin 1069
SmartSpec Plus
Spectrophotometer
Brochure, bulletin 2826
Links
Sample Buffers
and Reagents
Protein Assay Kits
and Cuvettes
Disposable Cuvettes
for Protein Assays
Fig. 3.5. SmartSpec Plus spectrophotometer.
Features built into the SmartSpec assay methods
facilitate data collection and present a complete
analysis of assay results. Bio-Rad also offers
compatible quartz and UV-transparent plastic cuvettes.
Quick Start Bradford
Protein Assay
Bio-Rad Protein Assay
DC Protein Assay
RC DC Protein Assay
SmartSpec Plus
Spectrophotometer
ReadyPrep 2-D Cleanup Kit
22
23
Electrophoresis Guide
Chapter 4: Reagent Selection and Preparation
Theory and Product Selection
TABLE OF CONTENTS
CHAPTER 4
Reagent Selection
and Preparation
This chapter details how to select
and prepare the reagents (protein
standards, gels, and buffers) required
for various PAGE applications.
The types of gels and buffers selected
should suit the size of the protein
under investigation, the desired
analysis technique, and the overall
goals of the experiment.
24
25
Electrophoresis Guide
Chapter 4: Reagent Selection and Preparation
General Considerations
Links
Recombinant Protein
Standards (Markers)
Precision Plus Protein
Unstained Standards
■■
Precision Plus Protein
Prestained Standards
Precision Plus Protein
All Blue Standards
■■
Precision Plus Protein
Dual Color Standards
■■
Precision Plus Protein
Dual Xtra Standards
Precision Plus Protein
Kaleidoscope Standards
■■
Precision Plus Protein
WesternC Standards
■■
rotein standards — select protein standards that
P
provide maximum resolution in the size range of
interest and that offer compatibility and utility for
downstream applications such as western blotting
el percentage — choose the percentage that offers
G
the best resolution in the range of interest
andcast vs. precast gels — precast gels offer
H
greater convenience and superior quality control and
reproducibility than handcast gels; handcast gels
provide customized percentages and gradients
el format — select mini- or midi-format gels when
G
throughput is important or sample size is limited;
select large-format gels for higher resolution. Select
a comb type and gel thickness to accommodate the
sample number and volume you are working with
uffer system — choose the system that offers the
B
best resolution and compatibility with the protein and
application of interest
Protein Standards
Protein standards are mixtures of well-characterized or
recombinant proteins that are loaded alongside protein
samples in a gel. They are used to monitor separation
as well as estimate the size and concentration of the
proteins separated in a gel.
Table 4.1. Applications of Bio-Rad’s protein standards.
Electrophoresis
Accurate MW estimation
Visualize electrophoresis
Orientation
Extended MW range
Coomassie staining
Fluorescent staining
Blotting
Monitoring transfer efficiency
Coomassie staining
Immunodetection
Fluorescent blots*
•
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•
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•
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•
•
•
•
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•
—
•
•
—
•
•
•
•
•
•
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•
•
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•
•
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•
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•
•
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•
•
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—
•
—
—
•
—
•
•
—
—
•
•
—
—
■■
ood resolution of the proteins in the size range
G
of interest
ompatibility with downstream analysis (for
C
example, blotting)
Protein standards are available as prestained or
unstained sets of purified or recombinant proteins. In
general, prestained standards allow easy and direct
visualization of their separation during electrophoresis
and their subsequent transfer to membranes. Although
prestained standards can be used for size estimation,
unstained protein standards will provide the most
accurate size determinations.
Applications and details of Bio-Rad’s protein standards
are provided in Table 4.1.
Recombinant Standards
Recombinant standards are engineered to display
specific attributes such as evenly spaced molecular
weights or affinity tags for easy detection. Bio-Rad’s
recombinant standards are the Precision Plus Protein
standards family and are available as stained or
unstained standards (Figure 4.1). These standards
contain highly purified recombinant proteins with
molecular masses of 10–250 kD (or 2–250 kD for the
Dual Xtra standards).
■■
recision Plus Protein unstained standards —
P
include three high-intensity reference bands
(25, 50, and 75 kD) and contain a unique affinity
Strep-tag, which allows detection and molecular
weight determination on western blots. These
standards offer absolute molecular weight accuracy
confirmed by mass spectrometry. Because
—
•
—
—
•
—
•
•
—
—
■■
recision Plus Protein prestained standards
P
(All Blue, Dual Color, and Kaleidoscope) — include
a proprietary staining technology that provides
batch-to-batch molecular mass consistency and
reproducible migration. The ability to visualize these
standards makes them ideal for monitoring protein
separation during gel electrophoresis
—250
—150
—100
— 75
—
•
—
—
•
—
— 50
— 37
— 25
— 20
— 15
•
•
—
—
— 10
— 5
—
Dual ColorKaleidoscope Dual Xtra
All Blue
WesternC Unstained
Fig. 4.1. Precision Plus Protein family of protein standards.
Bio-Rad offers the following prestained and unstained
natural standards (Figure 4.2):
■■
■■
■■
■■
recision Plus Protein Dual Xtra standards —
P
prestained standards with additional 2 and 5 kD bands
to enable molecular mass estimation below 10 kD
Acrylamide Polymerization —
A Practical Approach, bulletin 1156
restained SDS-PAGE standards — blue colored
P
standards available in low, high, and broad ranges
The Little Book of Standards,
bulletin 2414
nstained SDS-PAGE standards — available in low,
U
high, and broad ranges. These standards are blended
to give uniform band intensities when stained with
Coomassie (Brilliant) Blue R-250 or zinc stains
olypeptide SDS-PAGE standards — for molecular
P
weight determination of peptides and small proteins
resolved on Tricine gels
Polyacrylamide Gels
MW, kD
Myosin
b-Galactosidase
Bovine serum
albumin
Carbonic
anhydrase
Soybean trypsin
inhibitor
Lysozyme
Aprotinin
MW, kD
216
132
78
45.7
MW, kD
210
Myosin
b-Galactosidase
Bovine serum
albumin
125
101
Ovalbumin
56.2
Carbonic
anhydrase
32.5 Soybean trypsin
inhibitor
18.4
7.6
Kaleidoscope
prestained
standard
35.8
29
Lysozyme
21
Aprotinin
6.9
Broad range
prestained
SDS-PAGE
standard
2
Myosin
200
b-Galactosidase
116.3
Phosphorylase b
97.4
Bovine serum
albumin
66.2
MW, kD
Phosphorylase b
Bovine serum
albumin
Ovalbumin
Carbonic
anhydrase
Soybean trypsin
inhibitor
Ovalbumin
Related Literature
aleidoscope standards — individually colored
K
proteins to allow instant orientation on gels and blots
Polyacrylamide is stable, chemically inert, electrically
neutral, hydrophilic, and transparent for optical
detection at wavelengths greater than 250 nm.
■■ Precision Plus Protein™ WesternC™ standards — dual These characteristics make polyacrylamide ideal
color, prestained, and broad range protein standards for protein separations because the matrix does not
that enable chemiluminescence detection when probed interact with the solutes and has a low affinity for
with StrepTactin-HRP conjugates; the protein standard common protein stains (Garfin 2009).
appears directly on a film or CCD image. Additionally
Polymerization
this protein standard has fluorescent properties that
Polyacrylamide gels are prepared by free radical
enable detection for fluorescent blots*
polymerization of acylamide and a comonomer
Natural Standards
cross-linker such as bis-acrylamide. Polymerization
Natural standards are blended from naturally occurring is initiated by ammonium persulfate (APS) with
proteins. Although prestained natural standards are
tetramethylethylenediamine (TEMED) acting as a
effective for monitoring gel separation and efficiency,
catalyst (Figure 4.3). Riboflavin (or riboflavin-5'they covalently bind the dye in different amounts and
phosphate) may also be used as a source of free
at different locations. This may produce broader bands radicals, often in combination with TEMED and APS.
than are seen with recombinant standards, making
Polymerization speed depends on various factors
them less desirable for molecular weight estimations.
(monomer and catalyst concentration, temperature,
■■
MW, kD
Natural
Kaleidoscope
Broad Range
Low Range
—
•
—
—
•
—
MW = molecular weight.
*F
or use with fluorescent blots, not to be confused with fluorescent total blot stains. Precision Plus Protein
prestained standards contain dyes with fluorescent properties. See bulletin 5723 for details on using
precision Plus Protein WesternC standards for fluorescent multiplexing.
26
■■
Prestained Natural Standards
High Range
Unstained
WesternC™
All Blue
Dual Xtra
Kaleidoscope™
Precision Plus Protein™ Standards Dual Color
TABLE OF CONTENTS
Precision Protein
StrepTactin-HRP
Conjugate
they contain a known amount of protein in each
band, they also allow approximation of protein
concentration. These standards are compatible with
Laemmli and neutral pH buffer systems and are an
excellent choice for use with Stain-Free™ technology
(since they do not contain dye that can interfere with
stain-free detection). See Stain-Free Technology box
in Chapter 6 for more details
Select protein standards that offer:
No particular gel type or buffer is useful for all proteins,
and choosing the buffer systems and gel types that
offer the highest resolution in the size range of interest
may require some experimentation. In selecting
reagents for PAGE, consider the following:
Theory and Product Selection
45
High range
SDS-PAGE
standard stained
with Coomassie
R-250 stain
Lysozyme
MW, kD
97.4
66.2
Triosephosphate
isomerase
45
Myoglobin
b-Lactalbumin
31
26.6
17.0
14.4
Aprotinin
6.5
Insulin chain B,
oxidized
Bacitracin
21.5
3.5
1.4
Increase Western Blot Throughput
with Multiplex Fluorescent Detection,
bulletin 5723
Precision Plus Protein
Dual Xtra Standards—New Protein
Standards with an Extended Range
from 2 to 250 kD, bulletin 5956
Links
Natural Standards
Prestained
SDS-PAGE Standards
Kaleidoscope
Prestained Standards
High Range Prestained
SDS-PAGE Standards
Low Range Prestained
SDS-PAGE Standards
Broad Range Prestained
SDS-PAGE Standards
Unstained SDS-PAGE
Standards
High Range Unstained
SDS-PAGE Standards
Low Range Unstained
SDS-PAGE Standards
Broad Range Unstained
SDS-PAGE Standards
Polypeptide SDS-PAGE
Standards
Coomassie Stains
Coomassie Brilliant Blue
R-250 Stain
Coomassie Brilliant Blue
G-250 Stain
14.4
Low range
SDS-PAGE
standard stained
with Coomassie
R-250 stain
Protein Standards Application
Guide, bulletin 2998
Polypeptide
SDS-PAGE
standard stained
with Coomassie
G-250 stain
Fig. 4.2. Bio-Rad’s natural protein standards.
*Prestained standards are not recommended for use on gels that will be stained with fluorescent dyes.
27
Electrophoresis Guide
Chapter 4: Reagent Selection and Preparation
CH
NH
O
C
NH
CH
C
CH
HN
C
O
CH
HN
O
CH
C
O
CH
N,N’-Methylenebisacrylamide
cross-linking monomer
CH
CH
Acrylamide monomer
Gels can be made with a single, continuous percentage
throughout the gel (single-percentage gels), or they can
be cast with a gradient of %T through the gel (gradient
gels). Typical gel compositions are between 7.5% and
20% for single-percentage gels, and typical gradients
are 4–15% and 10–20%. Use protein migration charts
and tables to select the gel type that offers optimum
resolution of your sample (Figure 4.4):
■■
■■
Mini-PROTEAN TGX
TGX
Mini-PROTEAN
Precision Plus Protein Unstained
Precision Plus Protein Unstained
CH
C
CH
O
CH
C
CH
O
C
NH
NH
CH
CH
O
CH
C
NH
CH
7.5%
7.5%
10%
10%
12%
12%
4–15%
4–15%
4–20%
4–20%
Any kD
Any kD
O
NH
■■
NH
C
CH
O
CH
Cross-link
NH
NH
C
CH
CH
O
C
CH
250
250
NH
O
CH
C
CH
CH
150
150
O
250
250
150
150
100
100
CH
100
100
75
75
TABLE OF CONTENTS
and purity of reagents) and must be carefully
controlled because it generates heat and may lead to
nonuniform pore structures if it is too rapid.
250
250
100
100
150
150
75
75
50
50
Polyacrylamide
Fig. 4.3. Polymerization of acrylamide monomers and
bisacrylamide.
250
250
150
150
75
75
50
50
37
37
50
50
37
37
25
25
20
20
37
37
25
25
20
20
15
15
Percentage
Polyacrylamide gels are characterized by two
parameters: total monomer concentration (%T, in
g/100 ml) and weight percentage of cross-linker (%C).
By varying these two parameters, the pore size of the
gel can be optimized to yield the best separation and
resolution for the proteins of interest. %T indicates the
relative pore size of the resulting polyacrylamide gel; a
higher %T refers to a larger polymer-to-water ratio and
smaller average pore sizes.
%T = g acrylamide + g cross-linker x 100
Total volume, ml
g cross-linker
%C =
x 100
g acrylamide + g cross-linker
7.5%
7.5%
200
200
116
116
Broad Range Unstained
SDS-PAGE Standards
28
200
200
116
116
97.4
97.4
97.4
97.4
66
66
66
66
Links
Precision Plus Protein
Unstained Standards
10%
10%
45
45
100
100
75
75
50
50
45
45
31
31
31
31
21.5
21.5
250
250
150
150
150
150
100
100
100
100
75
75
50
50
37
37
37
37
25
25
20
20
15
15
10
10
25
25
20
20
15
15
10
10
Broad Range Unstained
Broad Range Unstained
12%
4–15%
4–20%
12%
4–15%
4–20%
200
200
200
200
116
116
97.4
97.4
116
116
66
66
97.4
97.4
45
45
66
66
31
31
200
200
116
116
97.4
97.4
66
66
45
45
75
75
50
50
37
37
25
25
20
20
15
15
10
10
Any kD
Any kD
200
200
116
116
97.4
97.4
66
66
45
45
31
31
45
45
31
31
31
31
The practical ranges for monomer concentration are
stock solutions of 30–40%, with different ratios of
acrylamide monomer to cross-linker. The designations
19:1, 29:1, or 37.5:1 on acrylamide/bis solutions
represent cross-linker ratios of 5%, 3.3%, and 2.7%
(the most common cross-linker concentrations for
protein separations).
250
250
21.5
21.5
21.5
21.5
14.4
14.4
14.4
14.4
6.5
6.5
Fig. 4.4. Examples of migration charts.
21.5
21.5
21.5
21.5
14.4
14.4
6.5
6.5
14.4
14.4
6.5
6.5
se single-percentage gels to separate bands
U
that are close in molecular weight. Since optimum
separation occurs in the lower half of the gel, choose
a percentage in which your protein of interest
migrates to the lower half of the gel
se gradient gels to separate samples containing
U
a broad range of molecular weights. Gradient gels
allow resolution of both high- and low-molecular
weight bands on the same gel. The larger pore size
toward the top of the gel permits resolution of larger
molecules, while pore sizes that decrease toward
the bottom of the gel restrict excessive separation of
small molecules
or new or unknown samples, use a broad gradient,
F
such as 4–20% or 8–16%, for a global evaluation
of the sample. Then move to using an appropriate
single-percentage gel once a particular size range of
proteins has been identified
Precast vs. Handcast
Precast gels are ready to use and offer greater
convenience, more stringent quality control, and higher
reproducibility than handcast gels. Many precast gels
also provide a shelf life of up to 12 months, allowing gels
to be stored and used as needed (this is not possible
with handcast gels, as they degrade within a few days).
Handcast gels, on the other hand, must be prepared
from acrylamide and bisacrylamide monomer solutions;
the component solutions are prepared, mixed
together, and then poured between two glass plates
to polymerize (see Part II of this guide for a detailed
protocol). Because acrylamide and bisacrylamide are
neurotoxins when in solution, care must be taken to
avoid direct contact with the solutions and to clean
up any spills. In addition, the casting process requires
hours to complete, is not as controlled as it is by gel
manufacturers, and contributes to more irregularities
and less reproducibility with handcast gels.
Although handcasting offers the benefit of customized
percentages, chemistries, and gradients, precast
gels are sized to fit specific electrophoresis cells and
are available in a range of chemistries, formulations,
comb types, and thicknesses. Precast gels differ from
their handcast counterparts in that they are cast with
a single buffer throughout. Bio-Rad’s precast gels
(Table 4.3) also do not contain SDS and can be used
for native or denaturing PAGE. For a complete and
current list of available precast gels, visit the Bio-Rad
website at www.bio-rad.com.
Theory and Product Selection
Format (Size and Comb Type)
The size format of the gel used depends on the
electrophoresis cell selected (see Chapter 2). Precast
gels are available for Bio-Rad’s mini- and midi-format
electrophoresis systems, and handcasting accessories
are available to fit all Bio-Rad electrophoresis cells.
Additional parameters to consider include the number
of wells and gel thickness, which depend on the
number and volume of samples to analyze. To create
sample wells in a gel, a comb is placed into the top
of the gel prior to polymerization. When the comb is
removed, a series of sample wells is left behind. The
number and size of these wells dictate how many
samples and what volume may be loaded (Table 4.2).
The thickness of the gel also plays a role in determining
the sample volume that can be loaded. A variety of
comb types are available for handcasting; refer to
www.bio-rad.com for more information.
Table 4.2. Comb types available for Bio-Rad precast
polyacrylamide gels.
Comb Thickness, 1.0 mm
Number of Wells
Well Volume
Mini-Format Gels (Ready Gel® and
Mini-PROTEAN ®) 8+1
10
12
15
IPG
30 µl
30 µl and 50 µl
20 µl
15 µl
7 cm IPG strip
Midi-Format Gels
(Criterion™)
12+2
18
26
Prep+2
IPG+1
45 µl
30 µl
15 µl
800 µl
11 cm IPG strip
Buffer Systems and Gel Chemistries
The pH and ionic composition of the buffer system
determine the power requirements and heavily influence
the separation characteristics of a polyacrylamide gel.
Buffer systems include the buffers used to:
■■
■■
■■
Cast the gel
Prepare the sample (sample buffer)
Fill the electrode reservoirs (running buffer)
Most common PAGE applications utilize discontinuous
buffer systems (Niepmann 2007), where two ions
differing in electrophoretic mobility form a moving
boundary when a voltage is applied (see Chapter 2).
Proteins have an intermediate mobility, making them
stack, or concentrate, into a narrow zone at the
beginning of electrophoresis. As that zone moves
through the gel, the sieving effect of the gel matrix
causes proteins of different molecular weights to move
at different rates (see Figure 2.2). Varying the types
of ions used in the buffers changes the separation
characteristics and stability of the gel. Table 4.3
summarizes the various types of gel and buffer
systems available.
Links
Mini Format 1-D
Electrophoresis Systems
Ready Gel Precast Gels
Mini-PROTEAN Precast Gels
Midi Format 1-D
Electrophoresis Systems
Criterion Precast Gels
29
Electrophoresis Guide
Chapter 4: Reagent Selection and Preparation
Laemmli (Tris-HCl)
Table 4.3. Gel and buffer chemistries for PAGE. For a current list of precast gels available from Bio-Rad, visit www.bio-rad.com.
Gel Type
Selection Criteria
Buffers
Sample
Running
Precast (Format) Gels
Mini-PROTEAN* Criterion
Handcast
SDS-PAGE
Tris-HCI, pH 8.6
TGX ™
Easy to prepare, reagents inexpensive
Laemmli
Tris/glycine/SDS
and readily available; best choice when
switching between precast and handcast
gels and need to compare results
Laemmli-like extended shelf life gels;
Laemmli
Tris/glycine/SDS
best choice when long shelf life is needed
and traditional Laemmli separation
patterns are desired
Laemmli-like gels with trihalo compounds
Stain-Free™
for rapid fluorescence detection without
staining
TGX Stain-Free™
Bis-Tris, pH 6.4
•
•­•
(Mini-PROTEAN)
—
—
Laemmli-like extended shelf life gels with
Laemmli
Tris/glycine/SDS
•
trihalo compounds for rapid fluorescence
(Mini-PROTEAN)
detection without staining
•
—
Offer longest shelf life, but reagents XT may be costly Offer best resolution of high molecular
weight proteins; useful in peptide
sequencing or mass spectrometry
applications
XT or Tricine
Tris/glycine/SDS­—
•
•
Tris-acetate,
pH 7.0
Laemmli
•
(Ready Gel)
XT MOPS or XT MES
—
•
—
XT Tricine or
Tris/Tricine/SDS
—
•
•
Native PAGE
Tris-HCI, pH 8.6
TABLE OF CONTENTS
Retention of native protein structure,
Native
Tris/glycine
•
•
resolution of proteins with similar (Ready Gel)
molecular weight
•
TGX
Laemmli-like extended shelf life gels; best
Native
Tris/glycine choice when long shelf life is needed and
traditional Laemmli separation patterns
are desired
Stain-Free
Laemmli-like gels with trihalo compounds
for rapid fluorescence detection without
staining
Native
Tris/glycine
TGX Stain-Free
Laemmli-like extended shelf life gels with
Native
Tris/glycine
trihalo compounds for rapid fluorescence
detection without staining
Tris-acetate, pH 7.0
Offer best separation of high molecular
weight proteins and protein complexes
Native
Tris/glycine
•
(Mini-PROTEAN)
•
—
—
•
—
•
(Mini-PROTEAN)
•
—
—
•
•
•
•
(Mini-PROTEAN)
•
Peptide Analysis
Tris-Tricine
Optimized for separating peptide and
Tricine
Tris/Tricine/SDS
proteins with molecular weight <1,000
IEF
IEF
50% glycerol IEF cathode and
Cast with Bio-Lyte® ampholytes, allow
separation by protein pl; contain no
IEF anode buffers
denaturing agents, so IEF is performed
under native conditions
•
(Ready Gel)
•
—
Protease Detection
Zymogram
Cast with gelatin or casein, which acts
Zymogram Tris/glycine/SDS
as a substrate for proteases that are
separated in the gel under nondenaturing
conditions
•
(Ready Gel)
•
* The Mini-PROTEAN gel running systems are compatible with both Ready Gels and Mini-PROTEAN gels. For gel types available in a
Mini-PROTEAN compatible format, the table indicates whether they are available as Ready Gels or Mini-PROTEAN gels.
•
The Laemmli system has been the standard system
for SDS- and native PAGE applications for many
years. Many researchers use Tris-HCl gels because
the reagents are inexpensive and readily available;
precast gels are also readily available in a wide variety
of gel percentages.
This discontinuous buffer system relies on the stacking
effect of a moving boundary formed between the
leading ion (chloride) and the trailing ion (glycinate). Tris
buffer is the common cation. Tris-HCl gels can be used
in either denaturing SDS-PAGE mode (using Laemmli
sample buffer and Tris/glycine/SDS running buffer) or
in native PAGE mode (using native sample and running
buffers without denaturants or SDS).
Tris-HCl resolving gels are prepared at pH 8.6–8.8.
At this basic pH, polyacrylamide slowly hydrolyzes to
polyacrylic acid, which can compromise separation.
For this reason, Tris-HCl gels have a relatively short
shelf life. In addition, the gel pH can rise to pH 9.5 during
a run, causing proteins to undergo deamination and
alkylation. This may diminish resolution and complicate
postelectrophoresis analysis.
Bio-Rad has developed TGX™ (Tris-Glycine eXtended
shelf life) precast gels, modified Laemmli gels with a
proprietary modification that extends shelf life to 12
months and allows gels to be run at higher voltages
without producing excess heat. The TGX formulation
yields run times as short as 15 min and Laemmli-like
separation patterns with exceptionally straight lanes and
sharp bands. TGX gels offer excellent staining quality and
transfer efficiency (with transfer times as short as
15 min for tank blotting and as short as 3 min with the
Trans-Blot® Turbo™ system), and they do not require
special, expensive buffers. Like Tris-HCl gels, TGX
gels use a discontinuous buffer system, with glycinate
as the trailing ion, and are, therefore, compatible with
conventional Laemmli and Tris/glycine/SDS buffers.
These are the best choice when long shelf life is needed
and traditional Laemmli separation patterns are desired.
Bio-RAD’S TGX Stain-Free™ gels are Laemmli-like,
extended shelf life gels that allow rapid fluorescent
detection of proteins with the Gel Doc™ EZ or
ChemiDoc™ MP imaging systems, eliminating staining/
destaining steps for completion of protein separation,
visualization, and analysis in 25 min (see Stain-Free™
Technology box in Chapter 6 for more details).
Bis-Tris
These systems employ chloride as the leading ion and
MES or MOPS as the trailing ion. The common cation
is formed from Bis-Tris buffer. The gels are prepared
at pH 6.4 to enhance gel stability. Running the same
Bis-Tris gels with either MES or MOPS denaturing
30
running buffer produces different migration patterns:
MES buffer is used for small proteins, and MOPS
buffer is used for mid-sized proteins.
Precast Bis-Tris gels (for example, Criterion™ XT
Bis-Tris gels) offer extended shelf life (compared to
Tris-HCl gels) and room temperature storage. These
gels are popular because of their stability but they
require special buffers, and the gel patterns cannot
be compared to those of Tris-HCl gels.
Common reducing agents such as bME and DTT
are not ionized at the relatively low pH of Bis-Tris
gels and so do not enter the gel and migrate with
the proteins. Alternative reducing agents are,
therefore, used with Bis-Tris gels to maintain a
reducing environment and prevent protein reoxidation
during electrophoresis.
Tris-Acetate
This discontinuous buffer system uses acetate as the
leading ion and Tricine as the trailing ion and is ideally
suited for SDS-PAGE of large proteins. Tris-acetate
gels can be used for both SDS- and native PAGE.
Like Bis-Tris gels, they offer extended shelf life and
room temperature storage. Because of their lower
pH, these gels offer better stability than Tris-HCl gels
and are best suited for peptide sequencing and mass
spectrometry applications.
Tris-Tricine
One of the drawbacks to using SDS in a separation
system is that excess SDS runs as a large front at the
low molecular weight end of the separation. Smaller
polypeptides do not separate from this front and,
therefore, do not resolve into discrete bands. Replacing
the glycine in the Laemmli running buffer with Tricine
yields a system that separates the small SDSpolypeptides from the broad band of SDS micelles
that forms behind the leading-ion front. Proteins as
small as 1–5 kD can be separated in these gels.
IEF
Isoelectric focusing (IEF) separates proteins by their
net charge rather than molecular weight. IEF gels
are cast with ampholytes, amphoteric molecules
that generate a pH gradient across the gels. Proteins
migrate to their pI, the pH at which the protein has
no net charge. Since IEF gels contain no denaturing
agents, IEF is performed under native conditions.
Zymogram
Zymogram gels contain either gelatin or casein, which
are substrates for various proteases. Samples are run
under denaturing but nonreducing conditions and are
then allowed to renature and consume the substrate.
Samples with proteolytic activity can be visualized as
clear bands against a blue background after using
Coomassie (Brilliant) Blue R-250 stain.
Theory and Product Selection
Related Literature
Mini-PROTEAN TGX Precast
Gels Product Information Sheet,
bulletin 5871
Mini-PROTEAN TGX Precast
Gel: A Gel for SDS-PAGE with
Improved Stability — Comparison
with Standard Laemmli Gels,
bulletin 5910
Mini-PROTEAN TGX Precast
Gel: A Versatile and Robust
Laemmli-Like Precast Gel for
SDS-PAGE, bulletin 5911
Ready Gel to Mini-PROTEAN TGX
Precast Gels Catalog Number
Conversion Chart, bulletin 5932
NuPAGE Bis-Tris Precast
Gels (MOPS Buffer) to
Mini-PROTEAN TGX
Precast Gels Catalog Number
Conversion Chart, bulletin 5934
Criterion XT Precast Gels Product
Information Sheet, bulletin 2911
Criterion TGX Stain-Free
Precast Gels Product Information
Sheet, bulletin 5974
Links
Mini Format 1-D
Electrophoresis Systems
Mini-PROTEAN TGX
Precast Gels
Midi Format 1-D
Electrophoresis Systems
Criterion TGX Stain-Free
Precast Gels
Criterion XT Bis-Tris
Precast Gels
Trans-Blot Turbo
Transfer System
Imaging Systems
ChemiDoc MP System
Gel Doc EZ Imaging System
Coomassie Stains
Coomassie Brilliant
Blue R-250 Stain
Coomassie Brilliant
Blue G-250 Stain
Sample Buffers and Reagents
Running Buffers and Reagents
31
Electrophoresis Guide
Chapter 4: Reagent Selection and Preparation
Products for Handcasting Gels
The following products are available to facilitate
handcasting gels. For detailed handcasting protocols,
refer to Part II of this guide.
Related Literature
Ready-to-Run Buffers and
Solutions Brochure,
bulletin 2317
Premade Buffers and Reagents
Electrophoresis buffers and reagents are available
as individual reagents or as premixed gel-casting,
sample, and running buffers. Use of commercially
prepared, premixed buffers, which are made with
electrophoresis-purity reagents and are quality
controlled for reproducible results, saves time but
also maximizes reproducibility, prevents potential
mistakes in buffer concentration, and standardizes
electrophoresis runs. There are no reagents to weigh
or filter; just dilute with distilled or deionized water.
mixed in a gradient former before being introduced into
the gel cassette. Typically, two solutions are prepared:
the light solution (equivalent to the lowest %T in the
range to be poured) and a heavy solution (equivalent
to the maximum %T to be poured). The most common
gradient gel contains 4–20% acrylamide; however, the
range of acrylamide concentrations should be chosen
on the basis of the size of the proteins being separated.
Two gradient formers are available for PAGE systems.
Depending on the gel format, prepare either a single
gel using the gradient former or couple the gradient
former with a multi-casting chamber to prepare up
to 12 gels simultaneously (Figure 4.6).
■■
AnyGel™ Stands
AnyGel stands (Figure 4.5) provide stabilization and
access to gels for casting and sample loading. The
clamping mechanism secures gel cassettes vertically
without excess pressure. They are available in two
sizes, single- and six-row.
Theory and Product Selection
■■
se the Model 485 gradient former to cast a
U
minimum of 4 mini-format gels at a time using the
Mini-PROTEAN 3 multi-casting chamber, or to cast
a single, large-format (PROTEAN II or PROTEAN
Plus) gel
se the Model 495 gradient former to prepare 4–12
U
large-format gels (PROTEAN II and PROTEAN Plus)
using the multi-gel casting chambers
TABLE OF CONTENTS
Fig. 4.5. AnyGel stands.
Multi-Casting Chambers
Links
AnyGel Stand
Polyacrylamide Gel
Reagents
Premixed Casting Buffers
Mini-PROTEAN Tetra
Handcast Systems
PROTEAN Plus
Multi-Casting Chamber
Multi-casting chambers are used to cast multiple gels
of various thicknesses simultaneously. Acrylic blocks
act as space fillers when fewer than the maximum
number of gels are cast. These chambers work in
concert with the gradient formers through a bottom
filling port to ensure reproducibility. Multi-casting
chambers are available for casting gels for the
Mini-PROTEAN, PROTEAN® II, and PROTEAN
Plus systems.
Fig. 4.6. Multi-casting chambers and gradient formers.
Gradient Formers
Gradient gels have a gradient of acrylamide
concentration that increases from top to bottom. To
create this gradient, the acrylamide solutions must be
PROTEAN Plus Hinged
Spacer Plates and Combs
Model 485 Gradient Former
Model 495 Gradient Former
32
33
Electrophoresis Guide
Chapter 5: Performing Electrophoresis
Theory and Product Selection
TABLE OF CONTENTS
CHAPTER 5
Performing
Electrophoresis
In this phase of the workflow,
the electrophoresis system is
assembled, samples are loaded,
and electrophoresis is initiated by
programming the power supply.
Select running conditions that
provide optimum resolution while
maintaining the temperature of the
system during separation.
34
35
Electrophoresis Guide
Chapter 5: Performing Electrophoresis
System Setup
System setup involves placing the gels in the tank,
filling the tank with running buffer, loading the samples
and protein standards, and programming the power
supply. Follow the instructions for system setup in
the instruction manuals for the system you are using.
General procedures and tips are provided in Part II
of this guide.
Running Conditions
Regulated direct current (DC) power supplies allow
control over every electrophoresis mode (constant
voltage, current, or power). The choice of which
electrical parameter to control is usually a matter
of preference.
Useful Equations
TABLE OF CONTENTS
In PAGE separations, the gel containing the protein
sample is placed in the electrophoresis chamber
between two electrodes. The driving force behind the
separation is the voltage (V, in volts) applied across the
electrodes. This leads to a current flow (I, in amperes)
through the gel, which has an intrinsic resistance (R, in
ohms). Ohm’s law describes the mutual dependence of
these three parameters:
I = V/R or V = IR or R = V/I
The applied voltage and current are determined by the
user and the power supply settings; the resistance is
inherent in the system and is determined by the ionic
strength of the buffer, the conductivity of the gel, and
other factors.
The power (P, in watts) consumed by an electrical
current element is equal to the product of the voltage
and current:
that occurs depends on the conductivity of the buffer
used, the magnitude of the applied field, and the total
resistance within the system.
The heat generated is proportional to the power
consumed (P):
Heat = P/4.18 cal/sec
Understanding the relationships between power,
voltage, current, resistance, and heat is central to
understanding the factors that influence the efficiency
and efficacy of electrophoresis. The optimum condition
is to run at the highest electric field strength possible
within the heat dissipation capabilities of the system.
During an electrophoretic separation using the OrnsteinDavis and Laemmli systems, the running buffer warms
as a result of Joule heating. The increase in temperature
may lead to inconsistent field strength and separation
and may cause the buffer to lose its buffering capacity
or the gel to melt or become distorted. Under normal
running conditions, the running buffer absorbs most of
the heat that is generated. However, during extended
runs or high-power conditions, active buffer cooling is
required to prevent uncontrolled temperature increases.
Other Factors Affecting Electrophoresis
The following variables also change the resistance
of the system and, therefore, affect separation efficiency
and current and voltage readings:
■■
■■
■■
P = VI = I2R = V2 /R
The strength of the electric field E (V/cm) applied
between the two electrodes is an important
parameter in electrophoresis, because it exerts a
force on electrically charged objects like proteins
and determines their migration rate (where d is the
distance in cm):
E = V/d
Most vertical electrophoresis chambers are operated
at a field strength of 10–20 V/cm for 1 mm thick
polyacrylamide gels.
Joule Heating
The electric field strength (E, in V/cm) that can be
generated between the electrodes is limited by the heat
that is inevitably produced during electrophoresis. This
Joule heating can lead to band distortion, increased
diffusion, and protein denaturation when not efficiently
removed from the system. The amount of Joule heating
36
■■
■■
■■
■■
lterations to buffer composition; that is, the
A
addition of SDS or changes in ion concentration
due to the addition of acid or base to adjust the
pH of a buffer
Gel pH, ionic strength, and percentage of acrylamide
umber of gels (current increases as the number
N
of gels increases)
olume of buffer (current increases when
V
volume increases)
ransfer temperature (current increases when
T
temperature increases)
el length (increasing gel length demands higher
G
voltage settings to increase field strength accordingly)
el thickness (increasing gel width or thickness at
G
identical gel length leads to higher current; voltage
must be kept unchanged)
Selecting Power Supply Settings
Power supplies that are used for electrophoresis hold
one parameter constant (either voltage, current, or
power). The PowerPac™ HC and PowerPac Universal
power supplies also have an automatic crossover
capability that allows the power supply to switch over
to a variable parameter if a set output limit is reached.
This prevents damage to the electrophoresis cell.
The resistance, however, does not remain constant
during a run:
■■
■■
In continuous buffer systems (for example, those
used for blotting or DNA separation), resistance
declines with increasing temperature caused by
Joule heating
In discontinuous systems, such as the Ornstein-Davis
(native) and Laemmli (SDS-PAGE) systems, resistance
also changes as discontinuous buffer ion fronts move
through the gel; in SDS-PAGE, resistance increases
as the run progresses. Depending on the buffer and
which electrical parameter is held constant, Joule
heating of the gel may increase or decrease over the
period of the run
Separations Under Constant Voltage
If the voltage is held constant throughout a separation,
the current and power (heat) decrease as the
resistance increases. This leads to increased run times,
which allow the proteins more time to diffuse. But this
appears to be offset by the temperature-dependent
increase in diffusion rate of the constant current mode.
Separations using constant voltage are often preferred
because a single voltage that is independent of the
number of gels being run is specified for each gel type.
Separations Under Constant Current
If the current is held constant during a run, the voltage,
power, and consequently the heat of the gel chamber
increase during the run. As a rule, constant current
conditions result in shorter but hotter runs than
constant voltage runs.
Separations Under Constant Power
Holding the power constant minimizes the risk
of overheating.
Theory and Product Selection
General Guidelines for Running Conditions
Electrophoresis cells require different power settings
with different buffer systems. The values presented are
guidelines — conditions should be optimized for each
application. In every case, run the gel until the dye front
reaches the bottom of the gel.
Use external cooling during long, unsupervised runs.
Temperature-controlled runs often yield more uniform and
reproducible results.
For best results:
■■
■■
■■
Increase run times for gradient gels and decrease
them as needed for low molecular weight proteins
or the first ~10 min of a run, allow the sample to stack
F
using a field strength of 5–10 V/cm gel length. Then
continue with the maximum voltage recommended in
the instruction manual of the electrophoresis system
If using multiple cells and constant voltage, use the
same voltage for multiple cells as you would for
one cell. The current drawn by the power supply
doubles with two — compared to one — cells. Set
the current limit high enough to permit this additive
function. Also be sure to use a power supply that can
accommodate this additive current
Gel Disassembly and Storage
Remove the gel cassette and open it according to
the manufacturer’s instructions. Before handling the
gel, wet your gloves with water or buffer to keep the
gel from sticking and to minimize the risk of tearing.
Sometimes it is also helpful to lift one edge of the gel
with a spatula.
Stain, blot, or process the gel as soon as possible
to maintain the resolution achieved during
electrophoresis and to keep the gel from drying out
(see Chapters 6 and 7). For long-term storage, either
dry stained gels in a 10% glycerol solution (storage at
4°C) or with the GelAir™ drying system, which allows
gels to dry between two sheets of cellophane within
60 min. This yields clear, publication-quality gels ideal
for densitometry.
Links
Power Supplies
PowerPac HC High-Current
Power Supply
PowerPac Universal
Power Supply
GelAir Drying System
37
Electrophoresis Guide
Chapter 6: Protein Detection and Analysis
Theory and Product Selection
TABLE OF CONTENTS
CHAPTER 6
Protein Detection
and Analysis
Following electrophoresis, protein
band patterns can be visualized
and subjected to qualitative and
quantitative analysis. Since most
proteins cannot be seen in a gel with
the naked eye, protein visualization
is usually achieved through use of
protein stains. Once the gel is stained,
it can be imaged and analyzed
using imaging instruments and
accompanying software.
38
39
Electrophoresis Guide
Related Literature
Rapid Validation of Purified
Proteins Using Criterion Stain
Free Gels, bulletin 6001
Sensitivity and Proteinto-Protein Consistency of
Flamingo Fluorescent Gel Stain
Compared to Other Fluorescent
Stains, bulletin 5705
Comparison of SYPRO Ruby
and Flamingo Fluorescent
Gel Stains With Respect
to Compatibility With Mass
Spectrometry, bulletin 5754
Oriole Fluorescent Gel
Stain: Characterization and
Comparison with SYPRO Ruby
Gel Stain, bulletin 5921
Bio-Safe Coomassie Stain
Brochure, bulletin 2423
Flamingo Fluorescent Gel Stain
Product Information Sheet,
bulletin 5346
TABLE OF CONTENTS
Links
Chapter 6: Protein Detection and Analysis
Protein Stains
■■
High sensitivity and reproducibility
■■
Wide linear dynamic range
■■
■■
■■
■■
Washing to remove excess dye (destaining)
Total Protein Stains
■■
Total protein stains allow visualization of the protein
separation pattern in the gel. Table 6.1 compares the
advantages and disadvantages of several total
protein staining techniques.
■■
Coomassie Stains
Bio-Safe Coomassie Stain
Coomassie Brilliant
Blue R-250 Stain
Coomassie Brilliant
Blue G-250 Stain
Fluorescent Protein Stains
Negative Stains
■■
rotein fixation, usually in acidic methanol or ethanol
P
(a few staining protocols already contain acid or
alcohols for protein fixation and so do not require
this separate step)
Exposure to dye solution
Mini-PROTEAN TGX
Stain-Free Gels
Silver Stains
Robust, fast, and uncomplicated protocol
■■
Criterion TGX Stain-Free
Precast Gels
Oriole Fluorescent Gel Stain
ompatibility with downstream technologies
C
such as protein extraction and assay, blotting,
or mass spectrometry
Staining protocols usually involve the following three
steps (protocols are available in Part II of this guide):
Criterion Precast Gels
Flamingo Fluorescent
Gel Stain
In comparison to Coomassie or silver staining
techniques, however, fluorescent dyes are more
expensive and require either a CCD (charge-coupled
device) camera or fluorescence scanner for gel
imaging. For these reasons, fluorescent stains are
often used in proteomics applications and on 2-D
gels, where the relative quantitation of proteins in
complex mixtures is performed over several orders of
abundance and protein identity is determined using
in-gel proteolytic digestion and mass spectrometry.
Examples include Flamingo™ and Oriole™ fluorescent
gel stains
In many cases, the choice of staining technique
depends on the availability of imaging equipment.
However, a protein staining technique should offer the
following features (Miller et al. 2006):
■■
oomassie stains — the most popular anionic
C
protein dye, Coomassie (Brilliant) Blue stains
almost all proteins with good quantitative linearity
at medium sensitivity. There are two variants of
Coomassie (Brilliant) Blue: R-250 (R for reddish),
which offers shorter staining times, and G-250 (G
for greenish), which is available in more sensitive
and environmentally friendly formulations (Simpson
2010, Neuhoff et al. 1988). Coomassie dyes are
also the favorite stains for mass spectrometry and
protein identification. Bio-Safe™ Coomassie stain is a
nonhazardous formulation of Coomassie Blue G-250
that requires only water for rinsing and destaining.
It offers a sensitivity that is better than conventional
Coomassie R-250 formulations and equivalent to
Coomassie Blue G-250, but with a simpler and
quicker staining protocol
luorescent stains — fulfill almost all of the
F
requirements for an ideal protein stain by offering
high sensitivity, a wide linear dynamic range over
four orders of magnitude, a simple and robust
protocol, and compatibility with mass spectrometry.
■■
ilver stains — offer the highest sensitivity, but
S
with a low linear dynamic range (Merril et al. 1981,
Rabilloud et al. 1994). Often, these protocols
are time-consuming, complex, and do not offer
sufficient reproducibility for quantitative analysis.
In addition, their compatibility with mass
spectrometry for protein identification purposes is
lower than that of Coomassie stains and fluorescent
dyes (Yan et al. 2000)
egative stains — rapid negative stains require only
N
~15 min for high-sensitivity staining, where protein
bands appear as clear areas in a white background.
Zinc and copper stains do not require gel fixation,
ensuring that proteins are not altered or denatured.
Negative stains can be used as a quality check
before transfer to a western blot or analysis by mass
spectrometry, although they are not the best choice
when quantitative information is desired
tain-free technology — a haloalkane compound
S
in Bio-Rad’s Criterion™, Criterion™ TGX, and MiniPROTEAN® TGX Stain-Free™ gels covalently binds to
tryptophan residues of proteins when activated with
UV light. This allows protein detection (with a stainfree compatible imager) in a gel both before and
after transfer, as well as total protein detection on a
blot when using PVDF membranes (see Stain-Free™
Technology box)
Specific Protein Stains
Specific protein stains are used to visualize specific
protein classes such as glycoproteins (Hart et al. 2003)
and phosphoproteins (Steinberg et al. 2003, Agrawal
and Thelen 2009), which are of special interest to
researchers working in the life sciences (examples
include Pro-Q Diamond and Pro-Q Emerald).
Theory and Product Selection
Table 6.1. Bio-Rad Gel stain selection guide.
Total Protein Stain
Sensitivity
(Lower Limit) Time
Comments
Detection
Method
Coomassie Stains
Colorimetric
Bio-Safe Coomassie G-250
8–28 ng 1–2.5 hr
Nonhazardous staining in aqueous solution; premixed, mass spectrometry compatible
Coomassie Brilliant Blue R-250
36–47 ng
2.5 hr
Simple and consistent; mass spectrometry
compatible; requires destaining with methanol
Silver Stains
Colorimetric
0.25–0.5 ng
3 hr
Dodeca™ silver stain kit
Simple, robust; mass spectrometry compatible;
ideal for use with Dodeca stainers (Sinha et al. 2001)
Silver Stain Plus™ kit
0.6–1.2 ng
1.5 hr
Simple, robust; mass spectrometry compatible
(Gottlieb and Chavko 1987)
Silver stain (Merril et al. 1981)
0.6–1.2 ng
2 hr
Stains glycoproteins, lipoproteins, lipopolysaccharides,
nucleic acids
Fluorescent Stains
Fluorescent
Oriole fluorescent gel stain*
0.5–1 ng
1.5 hr
Rapid protocol, requires no destaining, mass spectrometry
compatible; compatible only with UV excitation
Flamingo fluorescent gel stain
0.25–0.5 ng
5 hr
High sensitivity; broad dynamic range; simple protocol requires no destaining;
mass spectrometry compatible; excellent for laser-based scanners
SYPRO Ruby protein gel stain
1–10 ng
3 hr
Fluorescent protein stain; simple, robust protocol;
broad dynamic range; mass spectrometry compatible
Negative Stains
Colorimetric
Zinc stain
6–12 ng
15 min
High-contrast results; simple, fast, and reversible; compatible
with elution or blotting as well as mass spectrometry
(Fernandez-Patron et al. 1992)
Copper stain
6–12 ng
10 min
Single reagent; simple, fast, and reversible; compatible with
elution or blotting as well as mass spectrometry (Lee et al. 1987)
* Do not use Oriole gel stain with native gels.
Stain-Free™ Technology
Bio-Rad’s stain-free technology allows direct
visualization, analysis, and documentation
of protein samples in PAGE gels without staining,
destaining, or gel drying.
The system comprises the Gel Doc™ EZ and
ChemiDoc™ MP imagers, Image Lab™ software,
and precast gels that include unique trihalo
compounds that allow rapid fluorescent detection of
proteins — without staining. The trihalo compounds
react with tryptophan residues in a UV-induced
reaction to produce fluorescence, which can be
detected by the imager either within gels or on lowfluorescence PVDF membranes. Activation of the
trihalo compounds in the gels adds 58 Da moieties
to available tryptophan residues and is required for
protein visualization. Proteins that do not contain
tryptophan residues are not detected.
Benefits of stain-free technology include:
■■
■■
■■
■■
■■
limination of staining and destaining steps for
E
faster results
Automated gel imaging and analysis
o background variability within a gel or
N
between gels (as is often seen with standard
Coomassie staining)
isualization of transferred (blotted) proteins
V
on low-fluorescence PVDF membranes
Links
educed organic waste by eliminating the
R
use of acetic acid and methanol in staining
and destaining
SYPRO Ruby Protein
Gel Stain
Dodeca Silver Stain Kit
Silver Stain Plus Kit
Zinc Stain
Copper Stain
The sensitivity of the Stain-Free system is
comparable to staining with Coomassie (Brilliant)
Blue for proteins with a tryptophan content >1.5%;
sensitivity superior to Coomassie staining is possible
for proteins with a tryptophan content >3%.
Imaging Systems
ChemiDoc MP System
Gel Doc EZ System
Image Lab Software
Gel (top) and blot imaged using stain-free technology.
40
41
Electrophoresis Guide
Related Literature
Bio-Rad Imaging Systems
Family Brochure, bulletin 5888
Imaging Fluorescently
Stained Gels with Image Lab
Software Quick Start Guide,
bulletin 5989
Links
High-Throughput Dodeca
Gel Stainers
Criterion Precast Gels
TABLE OF CONTENTS
Coomassie Stains
Bio-Safe Coomassie Stain
Coomassie Brilliant
Blue G-250 Stain
Coomassie Brilliant
Blue R-250 Stain
Fluorescent Protein Stains
Flamingo Fluorescent
Gel Stain
Oriole Fluorescent Gel Stain
SYPRO Ruby Protein
Gel Stain
Silver Stains
Dodeca Silver Stain Kit
Chapter 6: Protein Detection and Analysis
Dodeca™ High-Throughput Stainers
■■
Dodeca stainers are high-throughput gel staining
devices available in two sizes (Figure 6.1): the small size
accommodates up to 24 Criterion gels while the large
size can accommodate up to 12 large-format gels. The
stainers ensure high-quality, consistent results and
eliminate gel breakage from excess handling.
The stainers feature a shaking rack that holds staining
trays at an angle to allow air bubbles to escape and
ensure uniform gel staining by protecting gels from
breaking. They are compatible with the following stains:
■■
Bio-Safe Coomassie (Brilliant) Blue G-250 stain
■■
Coomassie (Brilliant) Blue R-250 stain
■■
Flamingo Fluorescent gel stain
■■
SYPRO Ruby protein gel stain
■■
Oriole fluorescent gel stain
■■
Dodeca silver stain kits
Imaging
Though total protein stains yield visible band
patterns, in modern laboratory environments,
electrophoresis patterns (called electropherograms)
are digitized by dedicated image acquisition devices
and data are analyzed with sophisticated software.
Once the gels are digitized, the raw data can be
stored for further reference.
Imaging Systems
Selecting image acquisition devices for the digitization
of electrophoresis gels depends on the staining
technique used (see also Table 6.2):
■■
ensitometers — based on high-performance
D
document scanners with minor modifications
(water-proof, built-in calibration tool), they utilize
visible light for analysis of electrophoresis gels
(transmission mode) and blots (reflective mode)
stained with visible dyes. Bio-Rad’s GS-800™
calibrated densitometer has a linear response up
to 3.0 optical units in gray levels
Imaging Systems
GS-800 Calibrated
Densitometer
■■
CD (charge-coupled device) cameras — operate
C
with either trans-illumination provided by light boxes
(visible or UV) positioned underneath the gel or blot
for imaging a variety of stains (Coomassie, silver,
fluorescence) or epi-illumination detected using
colorimetric or fluorescent techniques. Supercooled
CCD cameras reduce image noise, allowing
detection of faint luminescent signals. Bio-Rad’s
Gel Doc™ EZ system provides four applicationspecific trays: a UV tray (for ethidium bromide
staining of DNA gels and fluorescence imaging), a
white tray (for Coomassie, copper, silver, and zinc
stains), a blue tray (for nondestructive nucleic acid
imaging), and a stain-free tray for direct visualization,
analysis, and documentation of protein samples in
polyacrylamide gels without staining, destaining, or
gel drying (see Stain-Free Technology box)
aser-based scanners — offer the highest sensitivity,
L
resolution, and linear dynamic range. They are
powerful image acquisition tools for electrophoresis
gels and blots stained with fluorescent dyes like
Flamingo fluorescent gel stain. Lasers can be
matched to the excitation wavelengths of a multitude
of fluorophores. Bio-Rad’s PharosFX™ systems use
multiple lasers, which enhance application flexibility
and allow optimal excitation of single- or multicolor
fluorescent samples to enable detection of almost
any fluorescent dye or label
Theory and Product Selection
Table 6.2. Bio-Rad imaging system selection guide.
Application
Personal
Gel Doc GS-800
Gel Doc ChemiDoc
PharosFX Molecular
ChemiDoc™
MP
EZ
Densitometer XR+ XRS+
PharosFX
Plus
Imager™
Nucleic Acid Detection
Ethidium bromide stain
SYBR® Green I stain
SYBR® Safe stain
Fast Blast™ DNA stain
5
5
5
4
4—
4
—
4
—
4
5
4
4
4
4
4
4
4
4
5
5
5
—
5
5
5
—
—
—
—
—
Protein Detection, 1-D Gels
Stain-free gels
Coomassie Blue stain
Silver stain
SYPRO Ruby protein gel stain
Flamingo fluorescent gel stain
Oriole fluorescent gel stain
5
4
4
4
4
5
5
4
4
4
3
4
—
4
4
4
4
5
—
4
4
4
4
5
—
2
2
5
5
—
—
2
2
5
5
—
—
—
—
—
—
—
Protein Detection, 2-D Gels
Coomassie blue stain
Silver stain
SYPRO Ruby protein gel stain
Flamingo fluorescent gel stain Oriole fluorescent gel stain
Pro-Q stain
Cy2, Cy3, Cy5 label
4
3
43
4
3
4
2
5
3
4
2
4
—
Blot Detection
Stain-free blots
Coomassie Blue stain
Silver stain
SYPRO Ruby protein blot stain*
Immun-Star™ chemiluminescence Chemifluorescence*
Quantum dot* Multiplex fluorescence
55 —— ——
—
—
4
—
5
4
4
2
2
—
5
— 54 42 2—
5
—
—
—
—
5
5
—
5
—
—
—
4
—
—
—
5
— —1144
—
5
2
—
2
2
5
5
—
5
—
—
—
—
5
5
—
—
5
5
—
—
—
5
3
3
2
2—
53 32 2—
—
3
3
5
5
—
—
3
3
5
5
—
—
3
3
—
—
—
—2355
—
—
—
—
5
5
—
Micro- and Macroarray** Detection
Radiolabel
—— —— —— 5 5
Fluorescence
5
— —2255
—
Immun-Star chemiluminescence
5
—
—
—
4
—
—
—
Colony Counting
Colorimetric detection
Fluorescence detection
5
— —4433
—
5
— —4455
—
Isotopic Detection
Radiolabel
X-ray film
—— —— —— 5 5
44 54 43 3—
—Not recommended; 1– 5, recommendation level (5 = highest).
*Optimal with low fluorescence PVDF membrane.
** With spot diameters ≥400 µm.
Links
ChemiDoc MP System
ChemiDoc XRS+ System
Gel Doc EZ System
Personal Molecular
Imager System
PharosFX and PharosFX
Plus Systems
Gel Doc XR+ System
Fig. 6.1. High-throughput Dodeca gel stainers.
42
43
Electrophoresis Guide
Related Literature
Molecular Weight
Determination by SDS-PAGE,
bulletin 3133
Using Precision Plus Protein
Standards to Determine
Molecular Weight,
bulletin 3144
Molecular Weight Estimation
Using Precision Plus Protein
WesternC Standards on
Criterion Tris-HCI and Criterion
XT Bis-Tris Gels, bulletin 5763
Molecular Weight Estimation
and Quantitation of Protein
Samples Using Precision Plus
Protein WesternC Standards,
the Immun-Star WesternC
Chemiluminescent Detection
Kit, and the Molecular Imager
ChemiDoc XRS Imaging
System, bulletin 5576
Chapter 6: Protein Detection and Analysis
Imaging Software
Molecular Weight (Size) Estimation
A robust software package is required for image
acquisition to analyze data and draw conclusions from
PAGE applications. Sophisticated gel analysis software
provides a variety of tools that enhance the user’s
ability to evaluate the acquired data. The software
adjusts contrast and brightness, magnifies, rotates,
resizes, and annotates gel images, which can then be
printed using standard and thermal printers. All data in
the images can be quickly and accurately quantified.
The software can measure total and average quantities
and determine relative and actual amounts of protein.
Gel imaging software is also capable of determining the
presence/absence and up/down regulation of proteins,
their molecular weight, pI, and other values. For more
information on imagers and gel evaluation software,
visit www.bio-rad.com.
SDS-PAGE is a reliable method for estimating the
molecular weight (MW) of an unknown protein, since
the migration rate of a protein coated with SDS is
inversely proportional to the logarithm of its MW.
The key to accurate MW determination is selecting
separation conditions that produce a linear relationship
between log MW and migration within the likely MW
range of the unknown protein. A protocol for MW
estimation is provided in Part II of this guide.
Bio-Rad offers three different software packages for
gel imaging and analysis:
■■
■■
TABLE OF CONTENTS
■■
Links
■■
I mage Lab™ software — image acquisition and
analysis software that runs the ChemiDoc MP,
Gel Doc XR+, Gel Doc EZ, and ChemiDoc XRS+
imaging systems. The software allows automatic
configuration of these imaging systems with
appropriate filters and illumination sources. It also
allows manual or automated analysis of PAGE gels
and western blots
Quantity One® 1-D analysis software — acquires,
quantitates, and analyzes a variety of data, including
radioactive, chemiluminescent, fluorescent, and
color-stained samples acquired from densitometers,
storage phosphor imagers, fluorescence imagers,
and gel documentation systems. The software
allows automatic configuration of these imaging
systems with appropriate filters, lasers, LEDs, and
other illumination sources. It also allows manual or
automated analysis of PAGE gels and western blots
PDQuest™ 2-D analysis software — used for 2-D gel
electrophoretic analysis
Image Lab Software
Analysis
Imaging Systems
Beyond protein band patterns, PAGE can yield
information about a protein’s size (molecular weight)
and yield (quantity). Image analysis software greatly
enhances and facilitates these measurements.
Gel Doc XR+ System
Gel Doc EZ System
ChemiDoc MP System
ChemiDoc XRS+ System
Quantity One 1-D
Analysis Software
PDQuest 2-D
Analysis Software
44
■■
■■
■■
eparate the protein sample on the same gel with a
S
set of MW standards (see Chapter 3 for information
regarding selection of protein standards)
or statistical significance, generate multiple data
F
points (>3 lanes per sample)
se a sample buffer containing reducing agents
U
(DTT or bME) to break disulfide bonds and minimize
the effect of secondary structure on migration
Include SDS in the sample buffer. SDS denatures
secondary, tertiary, and quaternary structures by
binding to hydrophobic protein regions. SDS also
confers a net negative charge on the proteins, which
also results in a constant charge-to-mass ratio
After separation, determine the relative migration
distance (Rf) of the protein standards and of the
unknown protein. Rf is defined as the mobility of a
protein divided by the mobility of the ion front. Because
the ion front can be difficult to locate, mobilities are
normalized to the tracking dye that migrates only
slightly behind the ion front:
Rf = (distance to band)/(distance to dye front)
Using the values obtained for the protein standards, plot
a graph of log MW vs. Rf (Figure 6.3). The plot should
be linear for most proteins, provided that they are fully
denatured and that the gel percentage is appropriate
for the MW range of the sample. The standard curve is
sigmoid at extreme MW values because at high MW,
the sieving affect of the matrix is so large that molecules
are unable to penetrate the gel. At low MW, the sieving
effect is negligible and proteins migrate almost freely.
To determine the MW of the unknown protein band,
interpolate the value from this graph.
The accuracy of MW estimation by SDS-PAGE is in the
range of 5–10%. Glyco- and lipoproteins are usually not
fully coated with SDS and will not behave as expected
in SDS-PAGE, leading to false estimations. For more
details about molecular weight estimation using
SDS-PAGE, refer to bulletin 3133.
For protein quantitation using PAGE to be of value:
log
MW
■■
L in
ear
ra n
ge
■■
■■
To ensure accurate MW determination:
Theory and Product Selection
Rf
■■
Fig. 6.3. Typical characteristics of a log MW vs. Rf
curve for protein standards.
Quantitation
Of all the methods available for protein quantitation
(including UV spectroscopy at 280 nm, colorimetric
dye-based assays, and electrophoresis in combination
with image acquisition analysis), only protein quantitation
by electrophoresis enables evaluation of purity, yield,
or percent recovery of individual proteins in complex
sample mixtures.
■■
■■
mploy sample preparation procedures that
E
avoid nonspecific protein loss due to insolubility,
precipitation, and absorption to surfaces
nsure all proteins enter the electrophoretic
E
separation medium
ptimize the quality of the electrophoretic
O
separation. For example, wavy, distorted
protein bands and comigration of bands lead
to questionable results
hen possible, separate a dilution series of pure
W
proteins in parallel. This enables the creation
of a calibration curve (as for molecular weight
determination with SDS-PAGE, above)
nalyze all samples (including samples for
A
calibration) at least in duplicate
se a stain that offers sufficient sensitivity and
U
a high dynamic range. Fluorescent stains like
Flamingo and Oriole fluorescent gel stains are
recommended over Coomassie and silver
staining techniques
Two types of quantitation are possible: relative quantitation
(quantitation of one protein species relative to the quantity
of another) and absolute quantitation (quantitation of a
protein by using a calibration curve generated by a range
of known concentrations of that protein). Because proteins
interact differently with protein stains, the staining
intensity of different proteins at identical protein loads
can be very different. Thus, only relative quantitative
values can be determined in most cases. Absolute protein
measurements can only be made if the protein under
investigation is available in pure form and is used as
the calibrant.
Links
Fluorescent Protein Stains
Flamingo Fluorescent Gel Stain
Oriole Fluorescent Gel Stain
Coomassie Stains
Silver Stains
45
Electrophoresis Guide
Chapter 7: Downstream Applications
Theory and Product Selection
TABLE OF CONTENTS
CHAPTER 7
Downstream
Applications
Following electrophoresis, the
entire gel might be blotted (proteins
transferred to a membrane) or dried,
or individual proteins might be excised
or eluted from the gel for analysis.
46
47
Electrophoresis Guide
Chapter 7: Downstream Applications
Western Blotting (Immunoblotting)
When specific antibodies are available, transferring
the proteins to a membrane (blotting) followed by
immunological staining is an attractive complement
to general protein stains and provides additional
information. A typical immunoblotting experiment
consists of five steps (Figure 7.1). Following PAGE:
Related Literature
Protein Blotting Guide, A Guide
to Transfer and Detection,
bulletin 2895
Western Blotting Detection
Reagents Brochure,
bulletin 2032
1.Proteins are transferred from the gel to a membrane
where they become immobilized as a replica of the
gel’s band pattern (blotting).
2.Unoccupied protein-binding sites on the membrane
are saturated to prevent nonspecific binding of
antibodies (blocking).
3.The blot is probed for the proteins of interest with
specific primary antibodies.
4.Secondary antibodies, specific for the primary
antibody type and conjugated to detectable reporter
groups such as enzymes or radioactive isotopes, are
used to label the primary antibodies.
TABLE OF CONTENTS
5.Labeled protein bands are visualized by the bound
reporter groups acting on an added substrate or by
radioactive decay.
Transfer
Block unbound
membrane sites
Incubate with
primary antibody
Incubate with conjugated
secondary antibody or ligand
Wash
Bio-Rad offers a complete range of products for
blotting, including blotting cells for protein transfers,
blotting membranes, filter paper, premixed blotting
buffers, reagents, protein standards, and detection
kits. Please refer to the Protein Blotting Guide (Bio-Rad
bulletin 5294) for more information.
Gel Drying
Before the advent of modern gel imaging equipment,
gels were dried in a format that not only preserved
them, but made them more amenable to densitometry
or autoradiography. The Model 583 and GelAir™ gel
dryer systems dry gels between two sheets of
cellophane.
Electroelution, as its name implies, is a technique that
applies the principles of electrophoresis to enable
recovery (elution) of molecules such as proteins from
gels and gel slices. It can be used with either slices
from a gel containing the protein of interest or with
entire preparative gels. Electroelution uses an electrical
field and the charged nature of proteins to move
them from the gel and into a buffer solution. Once
eluted, proteins can be assayed for activity, applied to
subsequent purification steps, or subjected to mass
spectrometry or a variety of other applications.
The Model 422 electro-eluter (Figure 7.2) combines with
the tank and lid of the Mini Trans-Blot® cell (or older
Mini-PROTEAN® II or Mini-PROTEAN 3 cells) to elute
macromolecules from single or multiple gel slices. The
electro-eluter has six vertical glass tubes connecting
the upper and lower buffer chambers. A frit at the
bottom of each tube retains the gel slice but permits
macromolecules to migrate through when current
is applied. When the macromolecules have passed
through the frit, they are collected in the membrane cap
for further analysis or testing. Depending on the buffer
system, the Model 422 electro-eluter can be used for
elution or dialysis of up to six samples.
Develop signal based on
color chemiluminescence
Fig. 7.1. Western blotting workflow.
Fig. 7.3. Whole gel eluter and mini whole gel eluter.
■■
Table 7.1. Whole gel eluter specifications.
Whole Gel Eluter
Mini Whole Gel Eluter
Gel area
14 x 16 cm
6.5 x 5.5 cm
Fraction volume
30 x 3 ml
14 x 0.5 ml
Sample load
mg
µg
■■
■■
reestanding, plastic- or glass-backed 2-D and 1-D
F
SDS-PAGE gels
PVDF and nitrocellulose membrane blots
Links
els or membranes stained for proteins with visible
G
stains (such as silver and Coomassie blue stains) or
fluorescent stains (such as Flamingo™, Oriole™, and
SYPRO Ruby protein stain)
Whole Gel Eluter and
Mini Whole Gel Eluter
Safety lid with
top electrode
Fig. 7.2. Model 422 electro-eluter
EXQuest Spot Cutter
PDQuest 2-D Analysis
Software
Filter papers
Preparation gel
Elution
chamber core
Quantity One 1-D Analysis
Software
Cellophane
Filter papers
Silver Stains
Base with bottom
electrode
Coomassie Stains
Fluorescent Protein Stains
Flamingo Fluorescent
Gel Stain
Fig. 7.5. EXQuest spot cutter.
Model 422 Electro-Eluter
Mini Trans-Blot Cell
The EXQuest spot cutter allows the use of the following
common proteome separation and staining methods:
Fig. 7.4. Whole gel eluter and mini whole gel eluter elute protein
bands into discrete liquid fractions. Proteins are electrophoretically
eluted from the gel into precisely spaced channels of the elution
chamber core. Liquid fractions are then harvested into a harvesting box.
Wash
Model 583 Gel Dryer
GelAir Drying System
Spot Excision (Cutting)
Bands containing proteins of interest can be excised
from gels either by hand (for example, using a razor
blade) or with the help of automated spot cutting
systems, such as those commonly used in 2-D
gel-based proteomics workflows. The proteins in
the bands can then be either eluted from the gel
piece (for example, by electroelution) or subjected to
downstream processing (for example, tryptic digestion)
while still in the gel.
Automated spot cutting instruments (spot cutters)
are used to excise protein spots of interest from gels
and to transfer them to microplates or other vessels
for further analysis. Bio-Rad’s EXQuest™ spot cutter
(Figure 7.5) locates and excises protein bands or spots
from 1-D and 2-D gels or blots and loads them into
96- and 384-well microplates or 96-tube racks for
downstream processing and analysis. The spot cutter
can be fully integrated with the PDQuest™ 2-D analysis
software or Quantity One® 1-D analysis software, and
it works with the imaging system to visualize gels and
blots that are either visibly or fluorescently stained. In
2-D PAGE applications, PDQuest software tracks the
protein bands or spots through spot cutting and mass
spectrometric protein analysis.
Electroelution
Links
Gel Drying Equipment
The whole gel eluter and mini whole gel eluter (Figure
7.3, Table 7.1) simultaneously elute and collect protein
fractions from preparative slab gels into liquid fractions
(Figure 7.4). Applications include screening of crude
mixtures of proteins to identify immunologically relevant
antigens and purification of multiple bands of nucleic
acids or proteins.
Theory and Product Selection
Oriole Fluorescent
Gel Stain
SYPRO Ruby Protein
Gel Stain
Mini-PROTEAN Cell
48
49
Electrophoresis Guide
Methods
TABLE OF CONTENTS
Part II
Methods
50
51
Electrophoresis Guide
Methods
Protocols
Protocols
Sample Preparation
Sample Preparation
General Tips for Sample Preparation
Protein Solubilization
Keep the sample preparation workflow simple (increasing the
number of sample handling steps may increase variability).
■■
Lysis (Cell Disruption)
■■
■■
uspend ~1 mg (wet weight) pelleted cells in ~10 µl
S
SDS-PAGE sample buffer for a protein concentration of
3–5 µg/µl. If disrupted in liquid nitrogen, tissue samples
like liver biopsies and plant leaves contain 10–20% and
1–2% protein, respectively
isrupt the sample or place freshly disrupted samples
D
in solutions containing strong denaturing agents
such as 7–9 M urea, 2 M thiourea, or 2% SDS. In this
environment, enzymatic activity is often negligible
■■
■■
TABLE OF CONTENTS
■■
■■
■■
■■
■■
■■
To diminish endogenous enzymatic activity:
■■
■■
■■
erform cell disruption at low temperatures to
P
diminish enzymatic activity
yse samples at pH >9 using either sodium carbonate
L
or Tris as a buffering agent in the lysis solution
(proteases are often least active at basic pH)
Add a chemical protease inhibitor to the lysis buffer.
Examples include phenylmethylsulfonyl fluoride
(PMSF), aminoethyl-benzene sulfonyl fluoride
(AEBSF), tosyl lysine chloromethyl ketone
(TLCK), tosylphenylchloromethyletone (TPCK),
ethylenediaminetetraacetic acid (EDTA), benzamidine,
and peptide protease inhibitors (for example,
leupeptin, pepstatin, aprotinin, and bestatin). For best
results, use a combination of inhibitors in a protease
inhibitor cocktail
■■
■■
■■
■■
■■
If protein phosphorylation is to be studied, include
phosphatase inhibitors such as fluoride and vanadate
hen working with a new sample, use at least two different
W
cell disruption protocols and compare the protein yield (by
protein assay) and qualitative protein content (by SDS-PAGE)
ptimize the power settings of mechanical rupture systems
O
and incubation times for all lysis approaches. Because
mechanical cell lysis usually generates heat, employ cooling
where required to avoid overheating of the sample
ollowing cell disruption, check the efficacy of cell wall
F
disruption by light microscopy and centrifuge all extracts
extensively (20,000 x g for 15 min at 15°C) to remove any
insoluble material; solid particles may block the pores of the
electrophoresis gel
Dissolve pelleted protein samples in 1x sample buffer
ilute dissolved protein samples with sample buffer stock
D
solutions to a final sample buffer concentration of 1x
erform a protein quantitation assay to determine the amount of
P
total protein in each sample. Use a protein assay that is tolerant
to chemicals in your samples. For samples in Laemmli sample
buffer, for example, use the DC™ or RC DC™ protein assays,
which can tolerate up to 10% detergent. Omit the protein assay if
sample amount is limited.
Human Cells
Use the MicroRotofor™ cell lysis kit (mammalian) or the protocol detailed here, which uses sonication and
radioimmunoprecipitation assay (RIPA) buffer, for cell lysis and protein extraction.
Reagents
Suspension Cultured Cells
■■
1
Pellet the cells by centrifugation
at 2,000 × g for 5 min at 4°C.
2
Discard the supernatant and
wash pelleted cells in cold PBS.
Repeat steps 1 and 2 twice.
3
Add RIPA buffer to the pelleted
cells and suspend the pellet
with a pipet.
or long-term sample storage, store aliquots at –80°C;
F
avoid repeated thawing and freezing of protein samples
ighly viscous samples likely have a very high DNA or
H
carbohydrate content. Fragment DNA with ultrasonic waves
during protein solubilization or by adding endonucleases like
benzonase. Use protein precipitation with TCA/acetone (for
example, with the ReadyPrep™ 2-D cleanup kit) to diminish
carbohydrate content
hen a sample preparation protocol calls for a dilution, the two
W
parts are stated like a ratio, but what is needed is a fraction. For
example, “Dilute 1:2,” means to take 1 part of one reagent and
mix with 1 part of another, essentially diluting the part by half.
“Dilute 1:4,” means to take 1 part and mix with 3 parts, making
a total of 4 parts, diluting the part by a quarter
■■
■■
■■
■■
■■
issolve dry protein samples directly in 1x sample buffer;
D
prepare other protein samples such that the final sample
buffer concentration is 1x
Incubate samples in sample buffer at 95°C for 5 min (or at
70°C for 10 min) after addition of sample buffer for more
complete disruption of molecular interactions
hen preparing SDS-PAGE sample buffer, use either
W
5% (~100 mM) 2-mercaptoethanol (bME) or 5–10 mM
dithiothreitol (DTT)
he final protein concentration in the sample solution for
T
1-D electrophoresis should not be <0.5 mg/ml
Carefully remove (decant)
culture medium from cells.
Wash cells twice in cold PBS.
2
Add RIPA buffer to the cells and
keep on ice for 5 min. Swirl the
plate occasionally to spread the
buffer around the plate.
3
se a cell scraper to collect
U
the lysate and transfer to a
microcentrifuge tube.
■■
4
Place the cell suspension on ice,
incubate 5 min, and sonicate at
appropriate intervals. Check lysis
efficacy by light microscopy.
5
Centrifuge
cell debris at ~14,000 × g for
15 min at 4°C and transfer supernatant
to a new vial.
6
Perform a protein assay of the
supernatant. A protein concentration of
3–5 µg/µl is best for PAGE.
7
Add 2x SDS-PAGE sample buffer to
the protein solution to yield a 1x sample
buffer concentration.
Phosphate buffered
saline (PBS)
RIPA solubilization buffer
(use 1 ml RIPA buffer
with 3 × 107 cells; store
and use RIPA buffer at
4°C
SDS-PAGE sample
buffer (2x)
Equipment
■■
repare SDS-PAGE sample buffer without reducing agent, then
P
aliquot and store at room temperature
repare fresh reducing agent, and add it to SDS-PAGE
P
sample buffer immediately before use
1
■■
ilute or concentrate samples as needed to yield a final protein
D
concentration of >0.5 mg/ml
se protein extracts immediately or aliquot them into
U
appropriately sized batches and store them at –80°C to avoid
freeze-thaw cycles
Monolayer Cultured Cells
Preparation for PAGE
■■
52
olubilize proteins in a buffer that is compatible with the
S
corresponding electrophoresis technique
■■
Centifuge
Sonicator
Links
DC Protein Assay
RC DC Protein Assay
SDS-PAGE Sample Buffer
MicroRotofor Cell Lysis Kit
(Mammal)
ReadyPrep 2-D Cleanup Kit
53
Electrophoresis Guide
Methods
Protocols
Protocols
Sample Preparation
Sample Preparation
Tips
n
n
Use liquid nitrogen and a
mortar and pestle to grind the
samples while they are still
frozen. Mill any larger pieces
beforehand (for example,
wrap the frozen tissue
sample in aluminum foil and
crush with a hammer)
With plant leaves, precipitate
proteins with 20% TCA in
prechilled acetone (–20°C).
To remove the plant phenols,
rinse the pellet at least
twice with cold acetone
(–20°C) and air-dry samples
in a vacuum
TABLE OF CONTENTS
Reagents
Mammalian Tissue
■■ Lysis buffer
■■ S DS-PAGE sample
buffer (2x)
Plant Leaves
■■ Protein precipitation solution
■■ Wash solution
■■ S DS-PAGE sample
buffer (1x)
Equipment
■■
Mammalian Tissue
Plant Leaves
Microbial Cultures
Protein Fractions from Chromatography
Use the MicroRotofor cell lysis kit (mammal).
Alternatively, use the protocol here, which involves
freezing mammalian tissue samples (for example,
biopsy samples) in liquid nitrogen at –196°C.
To minimize the deleterious effects of endogenous
plant compounds, use the MicroRotofor cell lysis kit
(plant) or the protocol here, which involves grinding the
tissue in a mortar and pestle with liquid nitrogen.
Use the MicroRotofor cell lysis kit (bacteria) or the
MicroRotofor cell lysis kit (yeast). Alternatively, use the
protocol detailed here, which relies on cell lysis with
ultrasonic waves in combination with a solubilization
in SDS under elevated temperature. This ensures
deactivation and denaturation of proteases.
When checking fraction purity or the enrichment of a
particular protein after a chromatographic separation,
you can observe the presence of high concentrations
of salt, detergent, denaturants, and organic solvents.
For example, in ion exchange chromatography, proteins
are eluted by a salt gradient. But the salt concentration
of the corresponding fractions can be as high as 0.5 M,
a concentration that interferes with SDS-PAGE.
1
2
3
4
MicroRotofor Cell Lysis Kit
(Mammal)
SDS-PAGE Sample Buffer
Immediately after grinding, transfer
60 mg tissue powder to a
microcentrifuge tube containing
1.0 ml lysis buffer.
Optional: sonicate the sample on
ice 5 times, for 2 sec every time.
Pause between sonication steps to
avoid overheating.
1
2
3
4
Incubate the sample at room
temperature for 30 min. Vortex
from time to time.
5
6
7
entrifuge at 35,000 x g for 30 min
C
at room temperature.
erform a protein assay
P
to determine the protein
concentration of the supernatant,
which should be 5–10 µg/µl.
Dilute supernatant with 2x SDSPAGE sample buffer (to a final 1x
concentration), and incubate for
20 min at room temperature.
Do not heat the sample.
6
7
1
lace 3–4 leaves in the mortar, add
P
liquid nitrogen, and grind the leaves in
the liquid nitrogen to a fine powder.
Transfer leaf powder into 20 ml of protein
precipitation solution and incubate for
1 hr at –20°C. Stir occasionally.
Centrifuge the solution at –20°C for
15 min at 35,000 x g. Discard
supernatant, add wash solution and
suspend the pellet. Incubate for 15 min
at –20°C, stirring occasionally. Repeat
until wash solution turns light green.
Centrifuge the solution at –20°C for
15 min at 35,000 x g and discard
supernatant. Resuspend pellet in 2 ml
wash solution.
Transfer suspension into a shallow
ceramic shell and cover with perforated
parafilm. Put shell into a dessicator and
apply a vacuum until the pellet (acetone
powder) is dry.
Mix 3 mg of sample powder with 1 ml 1x
SDS-PAGE sample buffer and incubate
for 30 min at room temperature. Vortex
from time to time.
8
Centrifuge the solution at –20°C for
15 min at >16,000 x g. Collect and heat
the supernatant for 3 min at 95°C.
9
Cool solution to room temperature and
perform the protein assay.
MicroRotofor Cell Lysis Kit
(Plant)
54
ool protein precipitation and wash
C
solutions to –20°C. Chill a mortar with
liquid nitrogen.
2
3
entrifuge cells (~5 x 107) for 3 min at
C
5,000 x g and resuspend the pellet
in an equal volume of 37°C PBS and
centrifuge again. Repeat two more
times to remove all interfering material
(extracellular proteases and growth
media).
Add 200 µl of hot (95°C) SDS sample
solubilization buffer to the pellet and
vortex thoroughly.
Sonicate the sample solution 10 times
for 1 sec each at ~60 W and ~20 kHz.
Incubate at 95°C for 5 min.
Remove salt and other contaminants by one of the
following approaches:
■■
■■
Buffer exchange — use Bio-Spin® or Micro
Bio-Spin™ columns, which are filled with size
exclusion media equilibrated in Tris buffer. These
columns accommodate a sample volume 50–100 μl
and remove compounds <6 kD within 10 min.
Mix the purified sample with 2x SDS-PAGE
sample buffer
recipitation — use the ReadyPrep™ 2-D cleanup
P
kit (based on an acetone/TCA precipitation) for
simultaneous removal of interfering substances and
concentration of dilute samples (<50 ng/ml)
n
Reproducible lysis and
protein solubilization of
bacteria and yeast is
challenging because the
cells may release proteases
and other enzymes into the
growth medium. Wash the
cultures thoroughly with
isotonic buffers and take
precautions to inactivate the
proteolytic activity after cell
lysis. Extensive disruption
of microbial cells is required,
usually with the help of a
French press, bead impact
instruments, or sonicator
Reagents
■■
■■
■■
5
M ortar and pestle
Links
hill a mortar with liquid nitrogen,
C
then grind small tissue pieces in
the presence of liquid nitrogen to a
fine powder.
Tips
4
Cool
the sample to 20°C and dilute with
~250 µl 2x SDS-PAGE sample buffer.
Incubate for another 20 min at room
temperature.
Equipment
■■
5
Centrifuge the sample solution at 20°C
for 30 min at 14,000 x g and harvest the
supernatant.
S DS sample
solubilization buffer
S DS-PAGE sample
buffer (2x)
P hosphate buffered
saline (PBS)
■■
Centifuge
Sonicator
Links
6
Perform the protein assay. The protein
concentration should be ~5 µg/µl.
MicroRotofor Cell Lysis Kit
(Bacteria)
MicroRotofor Cell Lysis Kit
(Yeast)
SDS-PAGE Sample Buffer (2x)
Bio-Spin and Micro Bio-Spin
Columns
ReadyPrep 2-D Cleanup Kit
55
Electrophoresis Guide
Methods
Protocols
Protocols
Sample Quantitation (RC DC Protein Assay)
Handcasting Polyacrylamide Gels
The RC DC protein assay is based on a modification of the Lowry protocol (Lowry et al. 1951), and is both reducing agent compatible (RC)
and detergent compatible (DC). Protein quantitation can be performed in complex mixtures including Laemmli buffer. It involves addition of
detection reagents to a protein solution and subsequent measurement of absorbance at 750 nm with a spectrophotometer. Comparison to a
standard curve provides a relative measurement of protein concentration.
Single-Percentage Gels
Tips
n
n
Prepare a standard curve
each time the assay is
performed
Standard Assay Protocol (5 ml)
1
For best results, prepare
the standards in the same
buffer as the sample
2
Add
20 μl of DC Reagent S to each
1 ml of DC Reagent A needed. This
solution is referred to as Reagent A'.
Each standard or sample assayed
requires 510 μl Reagent A'.
repare 3–5 dilutions of a protein
P
standard (0.2–1.5 mg/ml protein).
1
Microfuge Tube Assay Protocol (1.5 ml)
1
2
General Tips for Handcasting
n
Prepare the resolving and stacking gel solutions without APS or TEMED.
(Tables 1 and 2; consult the instruction manual for the system you are
using for more details.)
Table 1. Volume of resolving gel solution required to fill a gel cassette. Volumes
listed are required to completely fill a gel cassette. Amounts may be adjusted depending
on the application (with or without comb, with or without stacking gel, etc.).
Add 5 μl of DC Reagent S to each 5 μl
of DC Reagent A needed. This solution
is referred to as Reagent A'. Each
standard or sample assayed requires
127 μl Reagent A'.
PROTEAN ® II xi Cell
SpacerMini-PROTEAN ®*Criterion™
16 cm
20 cm
(Gel Thickness) Cell
Cell
0.5 mm
0.75 mm
1.0 mm
1.5 mm
3.0 mm
repare 3–5 dilutions of a protein
P
standard (0.2–1.5 mg/ml protein).
—
4.2 ml
5.6 ml
8.4 ml
—
—
—
15.0 ml —
—
12.8 ml
19.2 ml
25.6 ml
38.4 ml
76.8 ml
16.0 ml
24.0 ml
32.0 ml
48.0 ml
96.0 ml
*1
0 ml of monomer solution is sufficient for two stacking gels of any thickness.
3
TABLE OF CONTENTS
4
Pipet 100 µl of protein standard or
sample into clean tubes. Add 500 µl
of RC Reagent I into each tube and
vortex. Incubate the tubes for 1 min at
room temperature.
dd 500 µl of RC Reagent II to each
A
tube and vortex. Centrifuge the tubes
at 15,000 x g for 3–5 min.
3
4
ipet 25 µl of protein standard or
P
sample into clean microcentrifuge
tubes. Add 125 µl of RC Reagent I into
each tube and vortex. Incubate the
tubes for 1 min at room temperature.
Table 2. Recipes for stacking and resolving gels. Adjust amounts as needed for
the format you are using (see Table 1).
6
dd 510 µl of Reagent A' to each tube
A
and vortex. Incubate tubes at room
temperature for 5 min, or until the
precipitate is dissolved. Vortex.
7
dd 4 ml of DC Reagent B to each tube
A
and vortex immediately. Incubate at
room temperature for 15 min.
Links
Criterion Cell
Mini-PROTEAN Cell
PROTEAN II xi Cell
RC DC Protein Assay
SmartSpec™
Plus
Spectrophotometer
Discard the supernatant by inverting the
tubes on clean, absorbent tissue paper.
Allow the liquid to drain completely from
the tubes.
30% Acrylamide/bis
0.5M Tris-HCl, pH 6.8
1.5M Tris-HCl, pH 8.8
10% SDS
diH2O
TEMED
10% APS
Add 125 µl of RC Reagent II into each
tube and vortex. Centrifuge the tubes
at 15,000 x g for 3–5 min.
6
Discard the supernatant by inverting
the tubes on clean, absorbent tissue
paper. Allow the liquid to drain
completely from the tubes.
Add 127 µl of Reagent A' to each tube
and vortex. Incubate tubes at room
temperature for 5 min, or until the
precipitate is dissolved. Vortex.
2
4%
n
7.5%12%
Proper degassing and filtering of the
casting solution is critical for both
reproducibility of the polymerization
(oxygen removal) and the avoidance of
problems related to mass spectrometry
(keratin contamination)
n
X%
3.75 ml
—
3.75 ml
150 µl
7.28 ml
7.5 µl
75 µl
6.0 ml
—
3.75 ml
150 µl
5.03 ml
7.5 µl
75 µl
0.33 x X ml
—
3.75 ml
150 µl
11.03–(0.33 x X) ml
7.5 µl
75 µl
15 ml
15 ml
15 ml
15 ml
egas the solution under a vacuum for at least 15 min. While solutions
D
are degassing, assemble the glass cassette sandwich.
Use only high-quality reagents,
especially acrylamide monomers,
to avoid polymerization problems
n
Resolving Gel
1.98 ml
3.78 ml
—
150 µl
9 ml
15 µl
75 µl
For casting multiple gels, use the MiniPROTEAN 3 multi-casting chamber
(catalog #165-4110), PROTEAN II
multi-gel casting chamber (catalog
#165-2025), or PROTEAN Plus multicasting chamber (catalog #165-4160)
A temperature of 23–25°C is best
for degassing and polymerization;
equilibrate the stock solutions to
room temperature
APS/TEMED-initiated reactions should
proceed for at least 2 hr to ensure
maximum reproducibility of pore size
n
Make fresh APS solution every day
for best performance
n
nReplace TEMED every three
months because it is subject to
oxidation, which causes the
gradual loss of catalytic activity
The glass plates must be clean and
free of chips. Clean glass plates with
ethanol and lint-free cloths before use
n
3
Place a comb into the assembled gel sandwich. With a marker, place
a mark on the glass plate 1 cm below the teeth of the comb. This will
be the level to which the separating gel is poured. Remove the comb.
The height of the stacking gel
should be at least 2x the height of
the sample in the well. This ensures
band sharpness, even for diluted
protein samples
Product Links:
n
Store gels flat in the fridge at 4°C.
Do not freeze. Wrap handcast gels
tightly in plastic wrap with combs
still inserted
n
7
Add 1 ml of DC Reagent B to each
tube and vortex immediately. Incubate
at room temperature for 15 min.
8
ead absorbance of each sample at 750 nm. The
R
absorbances are stable for at least 1 hr.
9
lot absorbance measurements as a function of
P
concentration for the standards.
10
56
5
Stacking Gel
Total volume
5
n
Acrylamide and bisacrylamide are
neurotoxins when in solution. Avoid
direct contact with the solutions
and clean up spills
Interpolate the concentration of the protein samples from
the plot and sample absorbance measurements.
nRun handcast gels with discontinuous
buffer systems right after gel casting
because the buffer discontinuity
(pH and ionic strength) gradually
disappears during gel storage. SDSPAGE gels are not stable at pH 8.8 over
a longer time period
n
For more information about acrylamide
polymerization, refer to Acrylamide
Polymerization – A Practical Approach,
bulletin 1156
57
Electrophoresis Guide
Methods
Protocols
Protocols
Handcasting Polyacrylamide Gels
Handcasting Polyacrylamide Gels
Single-Percentage Gels (contd.)
Gradient Gels
Pour the Stacking Gel
Pour the Resolving Gel
Tips
n
n
TABLE OF CONTENTS
n
When pouring the resolving
gel solution, pour the
solution down the middle of
the outside plate of the gel
sandwich or down the side
of one of the spacers. Pour
smoothly to prevent it from
mixing with air
For the overlay solution,
water, n-butanol, or t-amyl
alcohol can also be used.
With n-butanol or t-amyl
alcohol, the overlay solution
can be applied rapidly
because very little mixing
will occur. If using water
to overlay, use a needle
and syringe and a steady,
even rate of delivery to
prevent mixing
Do not allow alcohols to
remain on the gels for more
than 1 hr or dehydration of
the top of the gel will occur.
It is sometimes convenient
to cast the separating
portion of the discontinuous
gel the afternoon before
casting the stacking gel
and running the gel. If the
stacking gel is to be cast
the following day, place
approximately 5 ml of 1:4
diluted running gel buffer on
top of each separating gel
after rinsing with deionized
water to prevent dehydration
of the separating gel
1
2
3
dd the APS and TEMED to the
A
degassed resolving gel solution, and
pour the solution to the mark, using a
glass pipet and bulb.
Using a Pasteur pipet and bulb,
immediately overlay the monomer
solution with water-saturated n-butanol.
Allow the gel to polymerize 45–60 min.
The gel is polymerized once you see
a line form between the stacking and
the resolving gel. Pour off the overlay
solution and rinse the top of the gel
with diH2O.
1
2
3
Dry the area above the separating
gel with filter paper before pouring
the stacking gel.
Place the comb in the cassette and
tilt it so that the teeth are at a slight
(~10°) angle. This prevents air from
becoming trapped under the comb
while the acrylamide solution is
being poured.
dd the APS and TEMED to the
A
degassed resolving gel solution,
and pour the solution down the
spacer nearest the upturned side
of the comb. Pour until all the teeth
are covered by the solution.
Alternative Casting Procedure
It is possible to cast separation and stacking
gels one after another, with no intermediate
step requiring overlay solution (water-saturated
n-butanol). Recalculate your gel casting recipes
so that the separation gel solution contains 25%
(w/v) glycerol. Due to the significant difference
in density, the two solutions won’t mix when the
stacking gel solution is carefully poured on top of
the resolving gel solution.
4
Resolving gel
1
etermine the volume of acrylamide
D
to prepare (≥40 ml is required for
the Model 485 gradient former).
Prepare the required volume (+5 ml) of
acrylamide. Table 3 provides estimated
volumes for the casting of 12 miniformat gels. Assemble the stack of MiniPROTEAN 3 cassettes as described
in the Mini-PROTEAN 3 multi-casting
chamber instruction manual. Then,
flow water through the stopcock and
measure the volume required to fill the
cassettes. Disassemble the chamber
and dry all components.
2
3
Table 3. Volume of acrylamide required for
12 mini-format gels. Prepare the amount listed
below plus an additional 5 ml.
Spacer Plates
Volume Required for 12 Gels
Volume
to Prepare
0.75 mm
1.0 mm
1.5 mm
80 ml
100 ml
140 ml
85–90 ml
105–110 ml
145–150 ml
6
Allow the gel to polymerize
30–45 min.
5
Combine all reagents except the initiators,
and degas the solution for 15 min.
emove the comb by pulling it
R
straight up slowly and gently. Rinse
the wells completely with diH2O.
6
Just prior to pouring, add TEMED and
APS to both solutions and mix gently.
Pour the appropriate monomer solutions
into the gradient chambers. (Consult
the gradient former instruction manual
for complete instructions.) Pour the light
solution into the mixing chamber labeled
“light,” and the heavy solution in the
reservoir chamber labeled “heavy.”
X = 7.3 ml
1.5 M Tris-HCl stock buffer,
pH 8.8
(1.5 M)(X ml) = (0.375 M)(55 ml)
X = 13.8 ml
Water
(55 ml) – (7.3 ml + 13.8 ml) = X
X = 34 ml
10% APS
(500 µl)/(100 ml) = (X µl)/(55 ml)
X = 275 µl
TEMED
10% APS volume; (275 µl)/10 = X
X = 27.5 µl
Heavy Solution (20%)
Links
Polyacrylamide Gel
Reagents
58
30% Acrylamide stock
(30%)(X ml) = (20%)(55 ml)
X = 36.7 ml
1.5 M Tris-HCl stock buffer,
pH 8.8
(1.5 M)(X ml) = (0.375 M)(55 ml)
X = 13.8 ml
Water
(55 ml) – (36.7 ml + 13.8 ml) = X
X = 4.5 ml
APS
(500 µl)/(100 ml) = (X µl)/(55 ml)
X = 275 µl
TEMED
10% APS volume; (275 µl)/10 = X
X = 27.5 µl
Determine the heavy and light acrylamide
formulations using the chart on the
right. (see Table 4) Reassemble the
multi-casting chamber.
Place the gradient former on a magnetic
stir plate and add a magnetic stir bar to
the mixing chamber labeled “light.” Attach
the luer fitting to the stopcock valve on
the inlet port. Run a piece of Tygon tubing
(1/8" ID Tygon tubing works well) from the
gradient former to the luer fitting on the
multi-casting chamber.
Table 4. Preparation of light and heavy
acrylamide solutions.
30% Acrylamide stock
(30%)(X ml) = (4%)(55 ml)
Determine the chamber volumes. To
create a linear gradient, the volume in
each chamber is half the total gel volume
required (or 20 ml, whichever is greater).
As an example, casting twelve 1.0 mm
gels requires 100 ml, so prepare 105 ml
(step 1). Divide that volume by two to
determine the volume required for each
chamber of the gradient former (52.5 ml
each for the light and heavy chambers).
4
Light Solution (4%)
5
Stacking gel
Realign the comb in the sandwich
and add monomer to fill the
cassette completely. An overlay
solution is not necessary for
polymerization when a comb
is in place.
This protocol is for preparing 12 mini-format linear gradient gels. It requires the Model 485 gradient former and
Mini-PROTEAN 3 multi-casting chamber. For other protocols, refer to the instruction manual for the gradient
former you are using.
Tips
n
If gravity flow isn’t fast
enough, use a peristaltic
pump to pump the entire set
of gradients within 10 min. If
it is not possible to complete
the operation in 10 min from
the time initiators are added,
then it might be necessary
to reduce the amount
of initiators (use half the
amount of TEMED) to slow
polymerization. The gradient
should be poured as quickly
as possible, without mixing
the gradient solution in the
casting chamber
Links
7
Turn on the stirring bar in the mixing
chamber, open the tubing clamp of the
gradient maker and the stopcock valve of
the casting chamber, and pour the gels.
Mini-PROTEAN 3
Multi-Casting Chamber
Model 485 Gradient Former
59
Electrophoresis Guide
Methods
Protocols
Protocols
Performing Electrophoresis
Performing Electrophoresis
General Protocol: SDS-PAGE
The following is a generalized protocol for running a Mini-PROTEAN® TGX™ gel in the Mini-PROTEAN Tetra cell. For detailed instructions,
refer to the Mini-PROTEAN precast gels instruction manual and application guide (bulletin #1658100).
1
Prepare buffers:
a.Running buffer (1x): Dilute 100 ml of 10x stock
with 900 ml diH2O.
Tips for Electrophoresis
■■
2
TABLE OF CONTENTS
b.Fill the inner and outer buffer chambers with running buffer. Fill
the upper (inner) buffer chamber of each core with 200 ml of
1x running buffer. Fill the lower (outer) buffer chamber to the
indicator mark for 2 gels (550 ml) or 4 gels (800 ml) with 1x of
running buffer. At runs >200 V, fill the outer buffer chamber to
the 4-gel (800 ml) mark.
■■
■■
■■
■■
■■
3
Prepare samples as indicated in the table below.
Component
Sample
ReducingNonreducing
5 µl
5 µl
Laemmli sample buffer
4.75 µl
5 µl
b-mercaptoethanol
0.25 µl
—
10 µl
10 µl
Total volume
■■
specified in the protocol and do not titrate to a pH. The ion
balance is set by the concentration of reagents; adjusting
the pH alters this balance and leads to undesirable results
b.Sample buffer: Use Laemmli sample buffer.
Prepare gels and assemble the electrophoresis cell:
a.Remove the comb and tape from the gels and assemble the
electrophoresis cell.
When preparing running buffers, make the solution as
Tips for Sample Loading
the sample complexity and sensitivity of the staining
technique. Using 15–20 µg protein per lane for mini- or
midi-format gels is a good starting point for complex
protein samples when staining with Bio-Safe™ Coomassie
stain. Determine the optimum protein load by running a
dilution series of the sample
Do not reuse running buffers
se 5–10 V per cm of gel for about 10 min during sample
U
entry (or until the sample has concentrated at the starting
point of the separation gel). Then continue with the voltage
setting recommended in the instruction manual for the
electrophoresis system you are using
se the voltage setting recommended in the instruction
U
manual for the electrophoresis system you are using;
excessive voltage leads to decreased band resolution,
band smiling, and lane distortions
hen running multiple cells, use the same voltage for
W
multiple cells as you would for one cell. Be aware that
the current drawn by the power supply will double with
two – compared to one – cells. Use a power supply that
can accommodate this additive current and set the current
limit high enough to permit this additive function
■■
■■
■■
■■
■■
o maximize reproducibility, maintain the temperature
T
of the electrophoresis buffer at 15°C with the help of a
recirculating cooler
■■
■■
4
Heat samples at 90–100°C for 5 min (or at 70°C for 10 min).
Load the appropriate volume of your protein sample on the gel.
5
Connect the electrophoresis cell to the power supply and perform
electrophoresis according to the following conditions:
Run conditions: 200 V
Run time: 31–39 min
Expected current (per gel): Initial 35–50 mA
Final 20–31 mA
Links
Running Buffer
6
Laemmli Sample Buffer
60
entrifuge the sample solution for 10–15 min at
C
>12,000 x g at 20°C before loading to remove insoluble
material that may clog the pores of the acrylamide gel
o avoid edge effects, add 1x sample buffer to unused
T
wells and never overfill wells
oad samples either before or after placing the
L
electrophoresis modules into the tank. Both methods
produce acceptable results. In both cases, fill both the
assembly (inner chamber) and the tank (outer chamber)
with buffer
dd running buffer to the cathode buffer reservoir first
A
and then apply the sample on the stacking gel under the
electrode buffer. Sample buffer must contain glycerol to
stabilize the sample application zone in the sample well
of the gel
se pipet tips designed for protein sample loading for
U
best results. For example, Bio-Rad’s Prot/Elec™ tips fit
easily between vertical slab gel plates of 0.75 mm while
maintaining a large bore for fast flow of sample
oad samples slowly to allow them to settle evenly on the
L
bottom of the well. Be careful not to puncture the bottom
of the well with the syringe needle or pipet tip
If using Bio-Rad’s patented sample loading guide, place it
between the two gels in the electrode assembly. Sample
loading guides are available for 9, 10, 12, and 15-well
formats. Use the sample loading guide to locate the
sample wells. Insert the Hamilton syringe or pipet tip into
the slots of the guide and fill the corresponding wells
fter electrophoresis is complete, turn the power supply off and
A
disconnect the electrical leads. Pop open the gel cassettes and
remove the gel by floating it off the plate into water.
Links
b-Mercaptoethanol
PowerPac Basic
Power Supply
■■
or best resolution, load a concentrated sample rather
F
than a diluted amount
These conditions are for Tris-HCl SDS-PAGE gels. If using
Bio-Rad’s Mini-PROTEAN TGX gels, the gels can be run
at 300 V to decrease the run time.
Mini-PROTEAN TGX
Precast Gels
Mini-PROTEAN Tetra Cell
The total protein amount loaded per lane depends on
7
Stain and image the gel, using one of the protocols on the
following pages as examples.
Prot /Elec Tips
61
Electrophoresis Guide
TIPS
nAlways wear gloves during
the staining process. Try to
avoid touching the gels with
your fingers. Wet gloves
with water or buffer before
handling the gel to keep the
gel from sticking and tearing
nUse clean and dust-free
containers for gel staining.
If possible, place a lid on
the container to avoid
contamination of the
staining solution
nGently agitate the container
on a horizontal shaker,
making sure the gel is
completely covered with
stain solution all the time
Methods
Protocols
Silver Staining (Bio-Rad Silver Stain)
Total Protein Staining
General protocols are described below for Mini-PROTEAN gels. For more details, refer to the instruction manual
for the stain you are using.
Bio-Safe™ Coomassie Stain
3
1
2
3
ash gels three times for 5 min each
W
in 200 ml diH2O per gel.
emove all water from staining container
R
and add 50 ml of Bio-Safe Coomassie
stain (or enough to completely cover
gel). Agitate for 1 hr.
Gels stained with fluorescent
dyes can be counterstained
with colloidal Coomassie
for further reference. In
fact, doing so enhances
sensitivity of the colloidal
Coomassie stain
Oriole™ Fluorescent Gel Stain
1
n
nFor long term-storage,
shrink-wrap the stained gels
in a 10% glycerol solution
(storage at 4°C) or dry them
with a GelAir™ drying system
within 60 min
2
3
1
2
If using the 5 L configuration, prepare
Oriole stain solution by adding
400 ml of methanol to the 1 L bottle
of diluents. Then add 10 ml of Oriole
fluorescent gel stain concentrate and
mix well by shaking.
Place gel in a staining tray with 50 ml of
Oriole fluorescent gel stain. Cover the
tray, place on a rocker, and agitate
gently for ~1.5 hr.
Transfer the gel to diH2O prior to
imaging. Destaining is not necessary.
3
4
Place gel in a staining tray with 100 ml of
fixing solution (40% ethanol, 10% acetic
acid). Cover the tray, place on a rocker,
and agitate gently for at least 2 hr.
our off the fix solution and add 50 ml of
P
1x stain solution (dilute 1 part Flamingo
fluorescent gel stain with 9 parts diH2O).
Cover the tray, place on a rocker or
shaker and agitate gently. Stain for at
least 3 hr.
(Optional) Carefully pour off the stain
solution and replace with an equal
volume of 0.1% (w/v) Tween 20. Cover
the tray, place on a rocker or shaker
and agitate gently for 10 min.
Rinse gel with diH2O prior to imaging.
<0.5 mm Gel
0.5–1.0 mm Gel
>1.0 mm Gel
1
Fixative
40% methanol/10% acetic acid
400 ml
30 min
30 min
60 min
2
Fixative
10% ethanol/5% acetic acid
400 ml
15 min
15 min
130 min
400 ml
15 min
15 min
130 min
4
Oxidizer
200 ml
3 min
5 min
10 min
diH2O
400 ml
2 min
5 min
10 min
6
400 ml
2 min
5 min
10 min
7
(Repeat washes 5–7 times until all the
yellow color is gone from the gel)
400 ml
2 min
5 min
10 min
8
Silver reagent
200 ml
15 min
20 min
30 min
diH2O
400 ml
—
1 min
2 min
5
9
11
200 ml
~5 min
~5 min
~5 min
12
200 ml
—
~5 min
~5 min
13
400 ml
~5 min
~5 min
~5 min
Stop
5% acetic acid
Molecular Weight Estimation
Run the standards and samples on an SDS-PAGE gel.
Process the gel with the desired stain and then destain to
visualize the protein bands. Determine the Rf graphically
or using Quantity One® analysis software (or equivalent).
GelAir Drying System
62
1
2
3
4
5
6
7
8
Precision Plus Protein
Unstained Standards
Criterion Tris-HCl Precast Gels
Bio-Safe Coomassie Stain
Top of resolving gel
MW, kD
250
Figures 1 and 2 illustrate the procedure.
To determine MW graphically:
Migration distance of
unknown band (45 mm)
150
100
1
2
50
37
Repeat this step for the unknown
bands in the samples.
4
Using a graphing program, plot the log
(MW) as a function of Rf.
5
Generate the equation y = mx + b, and
solve for y to determine the MW of the
unknown protein.
Unknown band
25
20
For each band in the standards,
calculate the Rf value using the
following equation:
3
Migration distance of
dye front (67 mm)
75
Using a ruler, measure the migration
distance from the top of the resolving
gel to each standard band and to the
dye front.
Rf = migration distance of the protein/
migration distance of the dye front
Product Links:
15
10
Fig. 1. Example showing MW determination of an unknown protein. Lane 1, 10 μl of Precision Plus
Protein™ unstained standards; lanes 2–8, a dilution series of an E. coli lysate containing a hypothetical
unknown protein (GFP). Proteins were separated by SDS-PAGE in a Criterion™ 4–20% Tris-HCI gel and
stained with Bio-Safe Coomassie stain. Gel shown is the actual size.
3.0
Oriole Fluorescent
Gel Stain
Silver Stains
Quantity One 1-D Analysis
Software
Protocols
Fluorescent Protein Stains
Flamingo Fluorescent
Gel Stain
Links
10
Developer
200 ml
~30 sec. Develop until solution turns yellow or until
brown precipitate appears.
Mini-PROTEAN Gels
Bio-Safe Coomassie Stain
Duration
Volume
Links
Coomassie Stains
Reagent
log MW
TABLE OF CONTENTS
Fluorescent dyes like
Flamingo and Oriole
fluorescent gel stains have a
higher dynamic range than
Coomassie or silver staining
techniques, making them
suitable for quantitative
protein analysis
Flamingo™ Fluorescent Gel Stain
Rinse in 200 ml diH2O for ≥30 min.
Stained gels can be stored in water.
nUse pure chemicals and
highly purified diH2O
(conductivity <2 μS)
n
Step
Standards
Unknown
2.0
y = –1.9944x + 2.7824
r 2 = 0.997
1.0
0
0
0.2
0.4
0.6
Rf
0.8
1.0
Fig. 2. Determining the MW of an
unknown protein by SDS-PAGE.
A standard curve of the log (MW)
versus Rf was generated using the
Precision Plus Protein standards from
Figure 1. The strong linear relationship
(r2 > 0.99) between the proteins’ MW
and migration distances demonstrates
exceptional reliability in predicting MW.
63
Electrophoresis Guide
Methods
Buffer Formulations
Buffer Formulations
Sample Preparation Buffers
Gel Casting Reagents
Sample Buffers
Acrylamide/Bis (30% T, 2.67% C)
2x SDS-PAGE (Laemmli, 30 ml)
(catalog #161-0737)
62.5 mM Tris-HCl, pH 6.8, 2% SDS, 25% glycerol,
0.01% bromophenol blue, 5% b-mercaptoethanol
(added fresh)
1 M Tris-HCl, pH 7.6 (100 ml)
Tris base
Deionized H2O (diH2O)
Adjust pH to 7.6 with HCl.
diH2O
12.11 g
80 ml
to 100 ml
0.5 M Tris-HCl, pH 6.8 (100 ml)
(catalog #161-0799)
Tris base diH2O
Adjust to pH 6.8 with HCl.
diH2O
Store at 4°C.
6.06 g
~60 ml
to 100 ml
TABLE OF CONTENTS
1.00 g
to 10 ml
1.0% Bromophenol Blue (10 ml) (catalog #161-0404)
Bromophenol blue diH2O
0.5 mM Tris-HCl, pH 6.8 1.0 ml
25% Glycerol 2.0 ml
1.0% Bromophenol blue 0.08 ml
10% SDS 1.6 ml
diH2O
2.92 ml
Store as 1–2 ml aliquots at –70°C and add
b-mercaptoethanol (0.4 ml) or 3% DTT immediately
before use.
Protein Precipitation Solution (100 ml)
20% Trichloroacetic acid (TCA), 0.2% DTT in ice-cold
acetone (–20°C)
10% SDS (10 ml) (catalog #161-0416)
SDS diH2O SDS-PAGE Sample Buffer (2x, 8 ml)
(catalog #161-0737, 30 ml)
62.5 mM Tris-HCl, pH 6.8, 25% glycerol, 2% SDS,
0.01% bromophenol blue
100 mg
to 10 ml
TCA
DTT Acetone
Dissolve
Acetone Store at –20°C.
1g
1g
0.10 g
80 ml
2.5 ml
to 100 ml
Phosphate Buffered Saline (PBS, 1 L)
0.9% (w/v) sodium chloride in 10 mM phosphate
buffer, pH 7.4
NaCl
KCl
Na2HPO4 KH2PO4 diH2O
Adjust pH to 7.4 with HCl or NaOH.
diH2O
64
8.00 g
0.20 g
1.44 g
0.24 g
800 ml
to 1 L
to 100 ml
Wash Solution (100 ml)
0.2% DTT in ice-cold acetone (–20°C)
RIPA Solubilization Buffer (100 ml) 25 mM Tris-HCl pH 7.6, 150 mM NaCl, 5 mM EDTA,
DTT 1% NP-40 or 1% Triton X-100, 1% sodium deoxycholate, Acetone
0.1% SDS
Dissolve
Acetone NaCl
0.88 g
Store at –20°C.
EDTA
0.15 g
NP-40 or Triton X-100
Sodium deoxycholate
SDS diH2O
1 M Tris-HCl, pH 7.6
diH2O
20.00 g
0.20 g 80 ml
0.20 g 80 ml
to 100 ml
Lysis Buffer (50 ml)
2 M thiourea, 7 M urea, 4% (w/v) CHAPS, 1% (w/v) DTT,
2% (v/v) carrier ampholytes (pH 3–10)
Urea Thiourea diH2O
CHAPS
Bio-Lyte® ampholytes DTT diH2O 21.00 g
7.60 g
to 45 ml
2.00 g
1.0 ml
0.50 g
to 50 ml
SDS Sample Solubilization Buffer (50 ml)
1% (w/v) SDS, 100 mM Tris-HCl (pH 9.5)
SDS Tris base diH2O
Titrate to pH 9.5 with diluted HCl.
diH2O
Acrylamide (29.2 g/100 ml)
87.60 g
N'N'-bis-methylene-acrylamide
2.40 g
diH2O
to 300 ml
Filter and store at 4ºC in the dark (30 days).
Premade alternatives:
Catalog #161-0125, 37.5:1 acrylamide/bis powder
Catalog #161-0158, 30% acrylamide/bis solution
1.5 M Tris-HCl, pH 8.8 (150 ml)
(catalog #161-0798, 1 L)
Tris base (18.15 g/100 ml)
diH2O
Adjust to pH 8.8 with 6 N HCl.
diH2O
Store at 4ºC.
27.23 g
80 ml
to 150 ml
0.5 M Tris-HCl, pH 6.8
(catalog #161-0799, 1 L)
Tris base
diH2O
Adjust to pH 6.87 with 6 N HCl.
diH2O
Store at 4ºC.
6.00 g
60 ml
to 100 ml
10% (w/v) SDS (100 ml)
(catalog #161-0416)
SDS
diH2O
Dissolve with gentle stirring
diH2O 10% (w/v) APS (fresh daily)
(catalog #161-0700)
Ammonium persulfate diH2O
10.00 g
90 ml
to 100 ml
0.5 M Tris-HCl, pH 6.8 3.75 ml
50% Glycerol 15.0 ml 1.0% Bromophenol blue 0.3 ml
10% SDS 6.0 ml
diH2O
to 30 ml
Add b-mercaptoethanol (50 μl to 950 μl sample buffer)
before use.
2x Native PAGE (30 ml)
(catalog #161-0738)
62.5 mM Tris-HCl, pH 6.8, 40% glycerol,
0.01% bromophenol blue 0.5 M Tris-HCl, pH 6.8 50% Glycerol 1.0% Bromophenol blue
diH2O
3.75 ml
24.0 ml
0.3 ml
to 30 ml
2x Tricine (30 ml)
(catalog #161-0739)
200 mM Tris-HCl, pH 6.8, 2% SDS, 40% glycerol,
0.04% Coomassie Brilliant Blue G-250,
2% b-mercaptoethanol (added fresh)
0.5 M Tris-HCl, pH 6.8
12.0 ml
50% Glycerol 24.0 ml
10% SDS 6.0 ml
Coomassie Blue G-250 12.00 mg
diH2O to 30 ml
Add b-mercaptoethanol (20 μl to 980 μl sample buffer)
before use.
0.10 g
1 ml
Water-Saturated n-Butanol
n-Butanol
50 ml
diH2O
5 ml
Combine in a bottle and shake. Use the top phase only.
Store at room temperature.
0.50 g
0.60 g
40 ml
to 50 ml
65
Electrophoresis Guide
Methods
Buffer Formulations
Running Buffers
Buffer Components
10x SDS-PAGE (1 L)
(catalog #161-0732)
250 mM Tris, 1.92 M glycine, 1% SDS, pH 8.3 0.5 M Tris-HCl, pH 6.8 (1 L)
(catalog #161-0799)
Tris base Glycine SDS diH2O Do not adjust the pH (~pH 8.3).
30.30 g
144.10 g
10.00 g
to 1 L
SDS diH2O 30.30 g
144.10 g
to 1 L
TABLE OF CONTENTS
10x Tris-Tricine (1 L)
(catalog #161-0744)
1 M Tris, 1 M Tricine, 1% SDS, pH 8.3 Tris base Tricine SDS diH2O Do not adjust the pH (~pH 8.3).
66
60.60 g
~900 ml
to 1 L
10% SDS (250 ml) (catalog #161-0416)
10x Native PAGE (1 L)
(catalog #161-0734)
250 mM Tris, 1.92 M glycine, pH 8.3
Tris base Glycine diH2O Do not adjust the pH (~pH 8.3).
Tris base diH2O Adjust to pH 6.8 with HCl.
diH2O Store at 4°C.
25.00 g
to 250 ml
1.0% Bromophenol Blue (10 ml) (catalog #161-0404)
Bromophenol blue diH2O
100 mg
to 10 ml
121.10 g
179.20 g
10.00 g
to 1 L
67
Electrophoresis Guide
Troubleshooting
TABLE OF CONTENTS
Part III
Troubleshooting
Electrophoresis is a straightforward
technique. However, problems may
occasionally arise during the various
steps in the electrophoresis workflow.
This section highlights potential
problems and their causes, and
provides potential solutions.
68
69
Electrophoresis Guide
Troubleshooting
Sample Preparation
TIPS
ProblemCause
Solution
ProblemCause
Solution
Laemmli sample buffer turns
Sample buffer is too acidic
yellow
Add Tris base until buffer turns
blue again
Swirls in gel
Excess catalysts; polymerization time <10 min
Reduce APS and TEMED by
25% each
Gel inhibition; polymerization time >2 hr
Increase APS and TEMED by
50%; degas
Gel feels soft
Low %T
Use different %T
Poor quality acrylamide or bis
Use electrophoresis-grade reagents
Too little cross-linker
Use correct %C
Gel turns white
Bis concentration too high
Check solutions or weights
Gel brittle
Cross-linker too high
Use correct %C
Sample floats out of well
Sample not dense enough Include 10% glycerol in
sample to make it denser
than surrounding buffer
Pipetting, loading errorPipet sample into well slowly. Do
not squirt sample quickly into well,
as it may bounce off bottom or
sides and flow into next well. Do
not remove pipet tip from well
before last of sample has left tip
• Fragment DNA with ultrasonic
Sample very viscous
High DNA or carbohydrate content
waves during cell lysis and
protein solubilization
•Add
endonucleases
(for example benzonase)
• Precipitate protein with TCA/acetone
(ReadyPrep™ 2-D cleanup kit) to diminish carbohydrate content
Gel Casting and Sample Loading
TABLE OF CONTENTS
ProblemCause
Solution
Leaking during handcasting
Chipped glass plates
Ensure plates are free of flaws
Spacer plate and short plate not level Ensure plates are aligned correctly
•
Casting stand gasket dirty, flawed, or worn out
Poor well formation
Incorrect catalyst used
•
Wash gasket if it is dirty
•Replace
flawed or worn out
casting stand gaskets
Prepare fresh catalyst solution
Increase catalyst concentration
of stacking gel to 0.06% APS
and 0.12% TEMED
•
Monomer solution not degassed
(oxygen inhibits polymerization)
Degas monomer solution immediately
prior to casting stacking gel
Webbing; excess acrylamide behind the comb
Incorrect catalyst concentration
•
Prepare fresh catalyst solution
• Increase catalyst concentration
of stacking gel to 0.06% APS
and 0.12% TEMED
Pressure cams on casting Powder residue has built up at
frame are difficult to close or pivot point of pressure cams
make noise when closed
Rinse or wipe off powder residue
before each use
ProblemCause
Solution
Current zero or less than expected, and samples do not migrate into gel
Tape at the bottom of precast
gel cassette not removed
Remove tape
Insufficient buffer in inner buffer chamber
Fill buffer chamber with
running buffer
Insufficient buffer in outer Fill inner and outer buffer chambers
buffer chamberto ensure wells are completely
covered
Electrical disconnection Gels run faster than expected
Running buffer too concentrated Check buffer composition and type
and gel temperature too high;
incorrect running buffer concentration
or type used
Check electrodes and connections
Too little or too much APS or TEMED Use 0.05% APS and 0.05% TEMED
Failure to degas
Temperature too lowCast at room temperature,
warming glass plates if necessary
Running or reservoir buffer too dilute
Check buffer protocol and
concentrate if necessary
Poor quality acrylamide or bis
Use electrophoresis-grade reagents
Voltage too high
Decrease voltage by 25–50%
Old APS Prepare fresh APS
Gels run slower than expected
Incorrect running buffer composition or type
Check buffer composition
and type
Excessive salt in sample
Desalt sample
Buffer leaking from
Incomplete gasket seal inner chamber
Wet gasket with running buffer
before use
• Ensure that top edge of short plate
Improper assembly of gel into the electrode/companion assembly fits under notch at top of gasket
70
Figure 1 provides an
example of an optimal
gel image, where the
bands are nicely resolved,
each lane is very straight,
and protein bands are
present across the
length of the gel (there
is excellent separation
across the entire
molecular weight range).
Electrophoresis
Gel does not polymerize
Degas monomer solutions 10–15 min
Fig. 1. Schematic of protein
migration during SDS-PAGE.
•Ensure
that top of short plate
touches the green gasket
71
Electrophoresis Guide
Troubleshooting
Electrophoresis
Evaluation of Separation
(contd.)
ProblemCause
Solution
ProblemCause
Leaking from upper buffer chamber Upper buffer chamber overfilled
(Mini-PROTEAN® Tetra cell)
Keep buffer level below top of
spacer plate
•
• Use electrophoresis-grade reagents
Diffuse or broad bands Poor quality acrylamide or
bis-acrylamide, incomplete • Check polymerization conditions
polymerization
Improper assembly
nsure that U-shaped electrode
E
core gasket is clean, free of cuts,
and lubricated with buffer
• Ensure that short plate is
under notch on gasket
Total Protein Staining
TABLE OF CONTENTS
ProblemCause
Solution
Bands not visible No protein in gel
Stain with another method to
confirm there is protein
Imaging system malfunctioning Check instrument manual for
troubleshooting, or contact
imaging instrument manufacturer
Incorrect imaging parameters were used
Check instrument manual
Poor staining sensitivity
Dirty staining trays Old SDS or sample buffer Gel temperature too high Prepare fresh solutions
Use external cooling during run or
run more slowly
• Check buffer composition; buffer
Bands “smile” across gel, band
Excess heating of gel; center of
pattern curves upward at both
gel runs hotter than either end not mixed well, or buffer in upper
sides of gel chamber too concentrated
• Prepare new buffer, ensuring
thorough mixing, especially when
diluting 5x or 10x stock
Power conditions excessive
Do not exceed recommended
running conditions. Decrease power
power setting from 200 V to 150 V
or fill lower chamber to within 1 cm
of top of short plate
Clean staining trays and other
equipment with laboratory
glassware cleaner
Insufficient buffer
Fill inner and outer buffer
chambers to ensure that wells
are completely covered
Insufficient stain volume
Follow recommendations for stain
volume (appropriate to gel size)
Smiling or frowning bands within
gel lane
Load less protein
Increase staining time
Sample preparation/buffer issues
Minimize salts, detergents, and
solvents in sample preparation
and sample buffers
Use correct voltage
Insufficient staining time
Reuse of staining solution
Repeat staining protocol with fresh
staining solution
High or uneven background
Dirty equipment or staining trays
staining
Clean staining trays and other
equipment with laboratory
glassware cleaner
Overloaded proteins
Incorrect running conditions
Skewed or distorted bands, Excess salt in samples
lateral band spreading
Remove salts from sample by
dialysis or desalting column prior
to sample preparation
Ionic strength of sample lower than
that of gel
Use same buffer in samples as
in gel
• Wash gel in water or respective
destaining solution for ≥30 min
Insufficient sample buffer or wrong
formulation
Check buffer composition and
dilution instructions
Reagent impurities
Use high-purity water and reagents
for staining
Diffusion prior to turning on current
Minimize time between sample
application and power startup
Speckles or blotches in gel
image
•
• Restrict duration of incubation
Too much time in staining solution
in staining solutions as
recommended in protocol
Particulate material from reagents,
staining tray, dust, or gloves
Clean staining trays thoroughly
• Limit time that gels and staining
solution are exposed to open air
• Use dust-free gloves and handle
gels only by edges
Uneven staining
Gel shrinkage
72
Solution
Insufficient shaking during staining
Gel dehydrated
• Increase %T of stacking gel to
Diffusion during migration through
stacking gel 4.5% or 5% T
• Increase current by 25% during
stacking
Uneven gel interface
•
Decrease polymerization rate
•
Overlay gels carefully
Agitate gel during staining
Transfer gel to water for rehydration
Rinse wells after removing comb to
remove residual acrylamide
•
73
Electrophoresis Guide
Troubleshooting
Evaluation of Separation
(contd.)
ProblemCause
Solution
Vertical streaking •
Overloaded samples
Dilute sample
• Selectively remove predominant
protein in sample (fractionate)
• Reduce voltage by 25% to minimize
streaking
• Centrifuge samples to remove
Sample precipitation particulates prior to sample loading
•
Fuzzy or spurious artifactual
bands
Concentration of reducing agent too low
Use 5% BME or 1% DTT
Protein bands do not migrate
down as expected
Bands of interest may be neutral or positively charged in buffer used;
pl of bands must be ~2 pH units
more negative than pH of
running buffer
Use SDS-PAGE or a different
buffer system in native PAGE
or IEF
Dilute sample in sample buffer
TABLE OF CONTENTS
74
75
Electrophoresis Guide
Appendices
TABLE OF CONTENTS
Part IV
Appendices
76
77
Electrophoresis Guide
Appendices
%CCross-linker concentration; weight percentage of cross-linker in a polyacrylamide gel
CathodeNegatively charged electrode. Positively charged molecules (cations) move toward
the cathode, which is usually colored black
%TMonomer concentration (acrylamide + cross-linker) in a gel (in g/100 ml). Gels can
be made with a single, continuous %T through the gel (single-percentage gels), or
with a gradient of %T through the gel (gradient gels)
CHAPS
Zwitterionic detergent (having both positively and negatively charged groups
with a net charge of zero) that is widely used for protein solubilization for IEF and
2-D electrophoresis; 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate
2-D electrophoresisTwo-dimensional electrophoresis. Proteins are separated first according to
isoelectric point (pI) by isoelectric focusing (IEF) and then according to size by
SDS-PAGE, yielding a two-dimensional protein map of spots
Comb Object used to cast wells in an agarose or acrylamide gel. In PAGE applications,
square-bottom combs are inserted into the gel sandwich before polymerization to
form square-bottomed wells
2-MercaptoethanolReducing agent necessary for cleavage of intra- and inter-molecular disulfide bonds
to achieve complete protein unfolding and to maintain proteins in a fully reduced
state. Also known as b-mercaptoethanol or BME
Continuous buffer
Gel-based electrophoresis system that uses the same buffer (at constant pH) in system
the gel, sample, and electrode reservoirs. Typically a single-percentage gel is used, and the sample is loaded directly into the part of the gel in which separation occurs. Continuous systems are not common in protein separations; they are used mostly for nucleic acid analysis
Glossary
AcrylamideMonomer used with a cross-linker to form the matrix used for separating proteins or
small DNA molecules
Ammonium persulfate
(APS)
Initiator used with TEMED (catalyst) to initiate the polymerization of acrylamide and bisacrylamide in making a polyacrylamide gel; (NH4)2S2O8
AmpholyteAmphoteric molecule (containing both acidic and basic groups) that exists mostly
as a zwitterion in a certain pH range. Ampholytes are used to establish a stable pH
gradient for use in isoelectric focusing
TABLE OF CONTENTS
AnodePositively charged electrode. Negatively charged molecules (anions) move toward
the anode, which is usually colored red
Anionic dye Negatively charged compound used as a stain; used in blotting to stain proteins
immobilized on membranes such as nitrocellulose or PVDF
Antibody Immunoglobulin; protein produced in response to an antigen, which specifically
binds the portion of the antigen that initiated its production
Antigen Foreign molecule that specifically binds with an antibody
Assay Analysis of the quantity or characteristics of a substance
Background Nonspecific signal or noise that can interfere with the interpretation of valid signals
Criterion™ cells,
Family of Bio-Rad products used for midi-format vertical electrophoresis;
blotters, and gelsincludes the Criterion and Criterion™ Dodeca™ cells, Criterion blotter, and Criterion
precast gels
Cross-linker Molecule (for example, bis-acrylamide) used to link polymerizing monomer
molecules together to form the gel, a netlike structure. Holes in the nets are called
pores, and pore size is determined in part by the cross-linker concentration. Pores
may or may not sieve the macromolecules
DC™ assay kit
Bio-Rad’s detergent-compatible protein assay kit
Discontinuous
Gel-based electrophoresis system that uses different buffers and sometimes
buffer systemdifferent buffer compositions to focus and separate components of a sample.
Discontinuous systems typically focus the proteins into tighter bands than
continuous gel systems, allowing larger protein loads
Bio-Spin® columnsFamily
Dithiothreitol (DTT)Reducing agent necessary for cleavage of intra- and inter-molecular disulfide
bonds to achieve complete protein unfolding and to maintain all proteins in a fully
reduced state
Bis or bis-acrylamide
A common cross-linker used with acrylamide to form a support matrix;
N,N'-methylene-bis-acrylamide
ElectroelutionTechnique that applies the principles of electrophoresis to enable recovery (elution)
of molecules such as proteins from gels and gel slices
Blocking reagent Protein used to saturate unoccupied binding sites on a blot to prevent nonspecific
binding of antibody or protein probes to the membrane
Electrophoresis
of Bio-Rad sample preparation products that includes the Bio-Spin 6 and
Micro Bio-Spin™ 6 columns used for buffer exchange and desalting applications
Blot Immobilization of proteins or other molecules onto a membrane, or a membrane that
has the molecules adsorbed onto its surface
Blue native PAGEDiscontinuous electrophoretic system that allows high-resolution separation of
membrane protein complexes in native, enzymatically active states. Membrane
protein complexes are solubilized by neutral, nondenaturing detergents like
n-dodecyl-b-D-maltoside. After addition of Coomassie (Brilliant) Blue G-250, which
binds to the surface of the proteins, separation of the negatively charged complexes
according to mass is possible
Bromophenol blue
Common tracking dye used to monitor the progress of electrophoresis
Carrier ampholytesHeterogeneous mixture of small (300–1,000 Da) polyamino-polycarboxylate buffering
compounds that have closely spaced pI values and high conductivity. Within an
electric field, they align according to pI to establish the pH
78
Coomassie Anionic dye used in the total protein staining of gels and blots that comes in two
(Brilliant) Blueforms: Coomassie (Brilliant) Blue G-250 differs from Coomassie (Brilliant) Blue R-250 by the addition of two methyl groups
Movement of charged molecules in a uniform electric field
GlycerolSmall nonionic molecule used in vertical gel electrophoresis to increase the density
of the sample buffer so that it sinks to the bottom of the sample well; also used to
help keep proteins soluble, especially in isoelectric focusing
GlycineAmino acid used as the trailing ion in discontinuous electrophoresis
Gradient gel Gel with gradually changing monomer concentration (%T) in the direction of
migration. In SDS-PAGE, gradients are used to separate wider molecular weight
ranges than can be separated with single-percentage gels
Immobilized pH
gradient (IPG)
Strips in which buffering groups are covalently bound to an acrylamide gel matrix, resulting in stable pH gradients except the most alkaline (>12) pH values. This eliminates problems of gradient instability and poor sample loading capacity associated with carrier ampholyte–generated pH gradients
79
Electrophoresis Guide
Appendices
Immunoassay Test for a substance by its reactivity with an antibody
Immunoblotting Blot detection by antibody binding
Immunodetection Detection of a molecule by its binding to an antibody
ImmunoglobulinAntibody; protein produced in response to an antigen, which specifically binds the
portion of the antigen that initiated its production
Ion front Group of ions moving together during electrophoresis, marking the movement of the
buffer from the upper buffer reservoir. Due to their small size, they are not hindered
by a sieving matrix and move together primarily because of their charge
Ionic strength Measure of the ionic concentration of a solution that affects its resistance
Isoelectric focusing
(IEF)
Electrophoresis technique that separates proteins according to their isoelectric
point (pI)
Isoelectric point (pI)pH value at which a molecule carries no electrical charge, or at which the negative
and positive charges are equal
Ligand Molecule that binds another in a complex
MicroRotofor ™ cells and kits
Family of Bio-Rad sample preparation products, including the MicroRotofor
liquid-phase IEF cell and MicroRotofor cell lysis kits
TABLE OF CONTENTS
Monomer Unit that makes up a polymer (acrylamide is a monomer that is polymerized into
polyacrylamide)
Mini-PROTEAN ®
Family of Bio-Rad products used for mini-format vertical electrophoresis;
cells and gelsincludes the Mini-PROTEAN Tetra and Mini-PROTEAN® 3 Dodeca™ cells, and
Mini-PROTEAN precast gels
Native PAGE Version of PAGE that retains native protein configuration, performed in the absence
of SDS and other denaturing agents
Ohm’s LawDescribes the mutual dependence of three electrical parameters (V, volts;
I, ampere; R, ohm): V = I x R
PAGE Polyacrylamide gel electrophoresis, a common method of separating proteins
Protein standards Mixtures of well-characterized or recombinant proteins used to monitor separation
and estimate the size and concentration of the proteins separated in a gel
Prestained standards Mixture of molecular weight marker proteins that have covalently attached dye
molecules, which render the bands visible during electrophoresis and transfer
RC DC™ assay kit
Bio-Rad’s reductant- and detergent-compatible protein assay kit
Resolving gel Portion of a discontinuous electrophoresis gel that separates the different bands
from each other
Rf value Relative distance a protein has traveled compared to the distance traveled by the ion
front. This value is used to compare proteins in different lanes and even in different
gels. It can be used with standards to generate standard curves, from which the
molecular weight or isoelectric point of an unknown may be determined
Running bufferBuffer that provides the ions for the electrical current in an electrophoresis run.
It may also contain denaturing agents. The running buffer provides the trailing ions in
discontinuous electrophoresis
Sample buffer Buffer in which a sample is suspended prior to loading onto a gel. SDS-PAGE
sample buffer typically contains denaturing agents (including reducing agents and
SDS), tracking dye, and glycerol
SDS-PAGE Separation of molecules by molecular weight in a polyacrylamide gel matrix in the
presence of a denaturing detergent, sodium dodecyl sulfate (SDS). SDS denatures
polypeptides and binds to proteins at a constant charge-to-mass-ratio. In a sieving
polyacrylamide gel, the rate at which the resulting SDS-coated proteins migrate in
the gel is relative only to their size and not to their charge or shape
Secondary antibody Reporter antibody that binds to a primary antibody; used to facilitate detection
Sodium dodecyl sulfate (SDS)
Anionic detergent that denatures proteins and binds to polypeptides in a constant weight ratio of 1:4 (SDS:polypeptide)
Spacers Small blocks set between the two glass plates at the sides of a gel cassette,
which create a space between the glass plates in which to pour the slab gel
monomer solution
PolyacrylamideAnticonvective sieving matrix used in gel electrophoresis. Polyacrylamide gels are
cast using mixtures of acrylamide monomers with a cross-linking reagent, usually
N,N'-methylenebisacrylamide (bis), both solubilized in buffer
Stacking gel Portion of a discontinuous electrophoresis gel that concentrates the components of
the sample to create a very thin starting zone; bands are then separated from each
other in the resolving gel
Polyacrylamide gel Electrophoresis technique that uses polyacrylamide as the separation medium
electrophoresis (PAGE)
Stain-free technologyProtein detection technology involving UV-induced haloalkane modification of protein
tryptophan residues. Continued exposure to UV light causes fluorescence of the
modified proteins, which are then detected by a CCD imager. Sensitivity of this
technique is generally equal to or better than Coomassie staining
PowerPac™
power supplies
Family of Bio-Rad power supplies
Power supply Instrument that provides the electric power to drive electrophoresis and
electrophoretic blotting experiments
Stained standardsMixture of molecular weight marker proteins that have covalently attached dye
molecules; the bands are visible during electrophoresis and transfer
Precision Plus Protein™ Bio-Rad’s family of recombinant protein standards
standards
Standard Collection of molecules with known properties, such as molecular weight or
isoelectric point. Often used to create standard curves, from which properties of an
unknown may be determined
Preparative
electrophoresis
Electrophoresis techniques that separate large volumes of protein samples (nanogram to gram quantities of protein), generally for the purposes of purification
or fractionation (to reduce sample complexity)
TEMED
Used with APS (initiator) to catalyze the polymerization of acrylamide and
bisacrylamide in making a polyacrylamide gel; N,N,N',N'-tetramethylethylenediamine
Primary antibody Antibody that binds a molecule of interest
TGX™ gels
Bio-Rad’s Tris-glycine extended shelf life precast gels
PROTEAN® cellsFamily of Bio-Rad products used for large-format vertical electrophoresis;
includes the PROTEAN II xi, PROTEAN II XL, and PROTEAN Plus® Dodeca™ cells
80
81
Electrophoresis Guide
Appendices
Total protein stain Reagent that binds nonspecifically to proteins; used to detect the entire protein
pattern on a blot or gel
TricineOrganic compound used in SDS-PAGE as a buffer component to replace glycine
and improve resolution of small (down to 1–5 kD) proteins
Tris
Organic component of buffer solutions that has an effective pH range of 7.0–9.2; tris(hydroxymethyl) aminomethane
Transfer Immobilization of proteins or other molecules onto a membrane by electrophoretic
or passive means
Triton X-100Nonionic detergent widely used for protein solubilization (for IEF and 2-D
electrophoresis)
References and Related Reading
References
Sample preparation and protein assay
Berkelman T (2008). Quantitation of protein in samples prepared for 2-D electrophoresis. Methods Mol Biol 424, 43–49.
Bradford MM (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye
binding. Anal Biochem 72, 248–254.
Cañas B et al. (2007). Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 1153, 235–258.
Chen Y et al. (2008). Sample preparation. J Chromatogr A 1184, 191–219.
Damerval C et al. (1988). Two-dimensional electrophoresis in plant biology. Advances in Electrophoresis 2, 236–340.
Drews O et al. (2004). Setting up standards and a reference map for the alkaline proteome of the Gram-positive bacterium Lactococcus lactis.
Proteomics 4, 1293–1304.
Evans DR et al. (2009). Concentration of proteins and removal of solutes. Methods Enzymol 463, 97–120.
Goldberg S (2008). Mechanical/physical methods of cell disruption and tissue homogenization. Methods Mol Biol 424, 3–22.
Tween 20 Nonionic detergent; used in blot detection procedures as a blocking reagent or in
wash buffers to minimize nonspecific binding and background
Harder A et al. (1999). Comparison of yeast cell protein solubilization procedures for two-dimensional electrophoresis. Electrophoresis 20,
826–829.
Unstained standards Mixture of molecular weight marker proteins that do not have covalently attached
dye molecules; the bands are invisible during electrophoresis and transfer, but are
useful for molecular weight determination
Lowry OH et al. (1951). Protein measurement with the Folin phenol reagent. J Biol Chem 193, 265–275.
UreaChaotrope usually included at rather high concentrations (9.5 M) in sample
solubilization buffers for denaturing IEF and 2-D PAGE
TABLE OF CONTENTS
Western blotting Immobilization of proteins onto a membrane and subsequent detection by
protein-specific binding and detection reagents
Zymogram PAGEElectrophoresis technique used to detect and characterize collagenases and
other proteases within the gel. Gels are cast with gelatin or casein, which
acts as a substrate for the enzymes that are separated in the gel under
nonreducing conditions
Huber LA et al. (2003). Organelle proteomics: implications for subcellular fractionation in proteomics. Circ Res. 92, 962–968.
Luche S et al. (2003). Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis.
Proteomics 3, 249–253.
Noble JE and Bailey MJ (2009). Quantitation of protein. Methods Enzymol 463, 73–95.
Poetsch A and Wolters D (2008). Bacterial membrane proteomics. Proteomics 8, 4100–4122.
Posch A et al. (2006). Tools for sample preparation and prefractionation in two-dimensional gel electrophoresis. In Separation Methods in
Proteomics, Smejkal GB ed. (Boca Raton: CRC Press), 107–133.
Rabilloud T (1996). Solubilization of proteins for electrophoretic analyses. Electrophoresis 17, 813–829.
Rhodes DG and Laue TM (2009). Determination of protein purity. Methods Enzymol 463, 677–689.
Sapan CV et al. (1999). Colorimetric protein assay techniques. Biotechnol Appl Biochem 29, 99–108.
Smith PK et al. (1985). Measurement of protein using bicinchoninic acid. Anal Biochem 150, 76-85.
Vuillard L et al. (1995). Enhancing protein solubilization with nondetergent sulfobetaines. Electrophoresis 16, 295-297.
Electrophoresis
Andrews AT (1986). Electrophoresis: theory, techniques and biochemical and clinical applications (New York: Oxford University Press).
Bjellqvist B et al. (1982). Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys
Methods 6, 317–339.
Davis BJ (1964). Disc electrophoresis. II. Method and application to human serum proteins. Ann NY Acad Sci 121, 404–427.
Dunn MJ (1993). Gel electrophoresis: Proteins (Oxford: BIOS Scientific Publishers Ltd.).
Fenselau C (2007). A review of quantitative methods for proteomic studies. J Chromatogr B Analyt Technol Biomed Life Sci 855, 14–20.
Garfin DE (1990). One-dimensional gel electrophoresis. Methods Enzymol 182, 425–441.
Garfin DE (2009). One-dimensional gel electrophoresis. Methods Enzymol 463, 497–513.
Goldenberg DP and Creighton TE (1984). Gel electrophoresis in studies of protein conformation and folding. Anal Biochem 138, 1–18.
Hames BD (1998). Gel electrophoresis of proteins: A practical approach, 3rd ed. (Oxford: Oxford University Press).
Laemmli UK (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.
McLellan T (1982). Electrophoresis buffers for polyacrylamide gels at various pH. Anal Biochem 126, 94–99.
Niepmann M (2007). Discontinuous native protein gel electrophoresis: pros and cons. Expert Rev Proteomics 4, 355–361.
Nijtmans LG et al. (2002). Blue Native electrophoresis to study mitochondrial and other protein complexes. Methods 26, 327–334.
O'Farrell PH (1975). High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250, 4007–4021.
Ornstein L (1964). Disc electrophoresis I: background and theory. Ann NY Acad Sci 121, 321–349.
Rabilloud T (2010). Variations on a theme: changes to electrophoretic separations that can make a difference. J Proteomics 73, 1562–1572.
Reisinger V and Eichacker LA (2008). Isolation of membrane protein complexes by blue native electrophoresis. Methods Mol Biol 424, 423–431.
Schägger H and von Jagow G (1987). Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the
range from 1 to 100 kDa. Anal Biochem 166, 368–379.
Vavricka SR et al. (2009). Serum protein electrophoresis: an underused but very useful test. Digestion 79, 203–210.
Westermeier R (2004). Isoelectric focusing. Methods Mol Biol 244, 225–232.
Wheeler D et al. (2004). Discontinuous buffer systems operative at pH 2.5 - 11.0, 0 degrees C and 25 degrees C, available on the Internet.
Electrophoresis 25, 973–974.
Zewert TE and Harrington MG (1993). Protein electrophoresis. Curr Opin Biotechnol 4, 3–8.
82
83
Electrophoresis Guide
Appendices
Staining
Agrawal GK and Thelen JJ (2009). A high-resolution two dimensional Gel- and Pro-Q DPS-based proteomics workflow for phosphoprotein
identification and quantitative profiling. Methods Mol Biol 527, 3–19.
Product Information
BulletinTitle
Fernandez-Patron C et al. (1992). Reverse staining of sodium dodecyl sulfate polyacrylamide gels by imidazole-zinc salts: sensitive detection of
unmodified proteins. Biotechniques 12, 564-573.
1069
Gottlieb M and Chavko M (1987). Silver staining of native and denatured eucaryotic DNA in agarose gels. Anal Biochem 165, 33-37.
5517MicroRotofor™ Lysis Kits Flier
Colorimetric Protein Assays
2826SmartSpec™ Plus Spectrophotometer Brochure
2414
The Little Book of Standards
2998
Protein Standards Application Guide
Lee C et al. (1987). Copper staining: a five-minute protein stain for sodium dodecyl sulfate-polyacrylamide gels. Anal Biochem 166, 308-312.
2317
Ready-to-Run Buffers and Solutions Brochure
Merril CR (1987). Detection of proteins separated by electrophoresis. Adv Electrophoresis 1, 111–139.
5535Mini-PROTEAN® Tetra Cell Brochure
Merril CR et al. (1981). Ultrasensitive stain for proteins in polyacrylamide gels shows regional variation in cerebrospinal fluid proteins. Science
211, 1437–1438.
5871Mini-PROTEAN® TGX™ Precast Gels Product Information Sheet
Hart C et al. (2003). Detection of glycoproteins in polyacrylamide gels and on electroblots using Pro-Q Emerald 488 dye, a fluorescent periodate
Schiff-base stain. Electrophoresis 24, 588–598.
2710Criterion™ Precast Gel System Brochure
Miller I et al. (2006). Protein stains for proteomic applications: which, when, why? Proteomics, 6, 5385–5408.
2911
Criterion XT Precast Gels Product Information Sheet
Neuhoff V et al. (1988). Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at
nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 9, 255–262.
5974
Criterion TGX Stain-Free Precast Gels Product Information Sheet
Oakley BR et al. (1980). A simplified ultrasensitive silver stain for detecting proteins in polyacrylamide gels. Anal Biochem 105, 361–363.
2881PowerPac™ Basic 300 V Power Supply Flier
Rabilloud T et al. (1994). Silver-staining of proteins in polyacrylamide gels: a general overview. Cell Mol Biol 40, 57–75.
2882
PowerPac HC High-Current Power Supply Flier
Simpson RJ (2010). Rapid coomassie blue staining of protein gels. Cold Spring Harb Protoc, pdb prot5413.
2885
PowerPac Universal Power Supply Brochure
Sinha P et al. (2001). A new silver staining apparatus and procedure for matrix-assisted laser desorption/ionization-time of flight analysis of
proteins after two-dimensional electrophoresis. Proteomics 1, 835-840.
3189
PowerPac HV Power Supply Brochure
Steinberg TH (2009). Protein gel staining methods: an introduction and overview. Methods Enzymol 463, 541–563.
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TABLE OF CONTENTS
Yan JX et al. (2000). A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization
and electrospray ionization-mass spectrometry. Electrophoresis 21, 3666–3672.
Bio-Rad Bulletins
Technical Notes
BulletinTitle
1760PROTEAN® II xi and XL Cells Product Information Sheet
2423Bio-Safe™ Coomassie Stain Brochure
5346Flamingo™ Fluorescent Gel Stain Product Information Sheet
5900Oriole™ Fluorescent Gel Stain Product Information Sheet
5888
Bio-Rad Imaging Systems Family Brochure
3096
Expression Proteomics Brochure
2032
Western Blotting Detection Reagents Brochure
5294
MicroRotofor Cell Product Information Sheet
2651
2-D Electrophoresis for Proteomics: A Methods and Product Manual
Instruction Manuals
BulletinTitle
2895
Protein Blotting Guide, A Guide to Transfer and Detection
10007296
Mini-PROTEAN Tetra Cell
1156
Acrylamide Polymerization – a Practical Approach
1658100
Mini-PROTEAN Precast Gels
1909
Modification of Bio-Rad DC™ Protein Assay for Use with Thiols
4006183
Criterion Cell
6001
Rapid Validation of Purified Proteins Using Criterion™ Stain Free™ Gels
4006213
PowerPac Basic Power Supply
5910Mini-PROTEAN® TGX™ Precast Gel: A Gel for SDS-PAGE with Improved Stability — Comparison with Standard Laemmli Gels
4006222
PowerPac HC Power Supply
5911
Mini-PROTEAN TGX Precast Gel: A Versatile and Robust Laemmli-Like Precast Gel for SDS-PAGE
4006223
PowerPac Universal Power Supply
5932
Ready Gel® to Mini-PROTEAN TGX Precast Gels Catalog Number Conversion Chart
4110001
Criterion Gel Application Guide
5934
NuPAGE Bis-Tris Precast Gels (MOPS Buffer) to Mini-PROTEAN TGX Precast Gels Catalog Number Conversion Chart
4110130
Criterion XT Precast Gels
3133
Molecular Weight Determination by SDS-PAGE
4110065
Quick Start™ Bradford Protein Assay
3144
Using Precision Plus Protein™ Standards to Determine Molecular Weight
4110107
RC DC™ Protein Assay
5956
Precision Plus Protein Dual Xtra Standards – New Protein Standards with an Extended Range from 2 to 250 kD
4000126-14 The Discovery Series: Quantity One® 1-D Analysis Software
5763
Molecular Weight Estimation Using Precision Plus Protein™ WesternC™ Standards on Criterion Tris-HCl and Criterion™ XT Bis-Tris Gels
LIT33
Bio-Rad Protein Assay
LIT448
DC Protein Assay
5576Molecular Weight Estimation and Quantitation of Protein Samples Using Precision Plus Protein WesternC Standards,
the Immun-Star™ WesternC™ Chemiluminescent Detection Kit, and the Molecular Imager ® ChemiDoc™ XRS Imaging System
2043
Purification of Proteins from Mycobacterium tuberculosis
2168
Isolation of Hydrophobic C. albicans Cell Wall Protein by In-Line Transfer From Continuous Elution Preparative Electrophoresis
2376
Gel Electrophoresis: Separation of Native Basic Proteins by Cathodic, Discontinuous Polyacrylamide Gel Electrophoresis
5705
Sensitivity and Protein-to-Protein Consistency of Flamingo™ Fluorescent Gel Stain Compared to Other Fluorescent Stains
5754
Comparison of SYPRO Ruby and Flamingo Fluorescent Gel Stains with Respect to Compatibility with Mass Spectrometry
5921Oriole™ Fluorescent Gel Stain: Characterization and Comparison with SYPRO Ruby Gel Stain
84
5989
Imaging Fluorescently Stained Gels with Image lab™ Software
5723
Increase Western Blot Throughput with Multiplex Fluorescent Detection
5294
MicroRotofor Cell Product Information Sheet
85
Electrophoresis Guide
Appendices
Ordering Information
Catalog # Description
Catalog # Electrophoresis Instrumentation
165-8033 ini-PROTEAN Tetra Cell, Mini Trans-Blot
M
Module, and PowerPac Basic Power Supply,
includes 165-8001, 170-3935, and 164-5050
PROTEAN ® Plus Dodeca™ Cells and Systems
165-4150 PROTEAN Plus Dodeca Cell, 100/120 V, includes
electrophoresis buffer tank with built-in ceramic
cooling core, lid, buffer recirculation pump with
tubing, 2 gel releasers
Protein Assay Kits and Instruments
500-0001
Bio-Rad Protein Assay Kit I, includes 450 ml dye
reagent concentrate, bovine b-globulin standard;
sufficient for 440 standard assays or 2,200
microplate assays
165-4140 PROTEAN Plus Dodeca Cell (100/120 V) and
PowerPac HC Power Supply, includes 165-4150
and 164-5052
500-0002
Bio-Rad Protein Assay Kit II, includes 450 ml
dye reagent concentrate, bovine serum albumin
standard; sufficient for 440 standard assays or
2,200 microplate assays
Catalog # Description
Mini-PROTEAN ® Tetra Cells and Systems
165-8000 Mini-PROTEAN Tetra Cell, 10-well, 0.75 mm
thickness; 4-gel system includes 5 combs, 5 sets
of glass plates, 2 casting stands, 4 casting frames,
sample loading guide, electrode assembly,
companion running module, tank, lid with power
cables, mini cell buffer dam
165-8001
Mini-PROTEAN Tetra Cell, 10-well, 1.0 mm
thickness; 4-gel system includes 5 combs, 5 sets
of glass plates, 2 casting stands, 4 casting frames,
sample loading guide, electrode assembly,
companion running module, tank, lid with power
cables, mini cell buffer dam
165-8002
Mini-PROTEAN Tetra Cell, 2 10-well, 0.75 mm
thickness; 2-gel system includes 5 combs, 5 sets of
glass plates, casting stand, 2 casting frames, sample
loading guide, electrode assembly, tank, lid with
power cables, mini cell buffer dam
165-8003
Mini-PROTEAN Tetra Cell, 10-well, 1.0 mm
thickness; 2-gel system includes 5 combs, 5 sets of
glass plates, casting stand, 2 casting frames, sample
loading guide, electrode assembly, tank, lid with
power cables, mini cell buffer dam
165-8004 TABLE OF CONTENTS
ini-PROTEAN Tetra Cell for Mini Precast Gels,
M
4-gel system includes electrode assembly, clamping
frame, companion module, tank, lid with power
cables, mini cell buffer dam
165-8005
Mini-PROTEAN Tetra Cell for Mini Precast Gels,
2-gel system includes electrode assembly, clamping
frame, tank, lid with power cables, mini cell buffer dam
165-8006 Mini-PROTEAN Tetra Cell, 10-well, 1.5 mm
thickness; 4-gel system includes 5 combs, 5 sets
of glass plates, 2 casting stands, 4 casting frames,
sample loading guide, electrode assembly,
companion running module, tank, lid with power
cables, mini cell buffer dam
165-8007
Mini-PROTEAN Tetra Cell, 10-well, 1.5 mm
thickness; 2-gel system includes 5 combs, 5 sets of
glass plates, casting stand, 2 casting frames, sample
loading guide, electrode assembly, tank, lid with
power cables, mini cell buffer dam
165-8025 Mini-PROTEAN Tetra Cell and PowerPac™ Basic
Power Supply, includes 165-8001 and 164-5050
165-8026 ini-PROTEAN Tetra Cell and PowerPac™
M
Universal Power Supply, includes 165-8001
and 164-5070
165-8027 Mini-PROTEAN Tetra Cell and PowerPac™ HC
Power Supply, includes 165-8001 and 164-5052
165-8028 165-8029 ini-PROTEAN Tetra Cell and PowerPac™ HV
M
Power Supply, includes 165-8001 and 164-5056
ini-PROTEAN Tetra Cell and Mini Trans-Blot®
M
Module, includes 165-8001 and 170-3935
165-8030 Mini-PROTEAN Tetra Cell for Mini Precast Gels
and Mini Trans-Blot Module, includes 165-8004
and 170-3935
86
165-8034 Mini-PROTEAN Tetra Cell for Mini Precast Gels,
Mini Trans-Blot Module, and PowerPac Basic
Power Supply, includes 165-8004, 170-3935,
and 164-5050
165-8035 Mini-PROTEAN Tetra Cell, Mini Trans-Blot
Module, and PowerPac HC Power Supply,
includes 165-8001, 170-3935, and 164-5052
165-8036 Mini-PROTEAN Tetra Cell for Mini Precast Gels,
Mini Trans-Blot Module, and PowerPac HC Power
Supply, includes 165-8004, 170-3935, and 164-5052
Mini-PROTEAN ® Dodeca™ Cells and Systems
165-4100
Mini-PROTEAN 3 Dodeca Cell, includes
electrophoresis tank with built-in cooling coil, lid with
power cables, 6 electrophoresis clamping frames,
2 buffer dams, drain line, 2 gel releasers
165-4101
Mini-PROTEAN 3 Dodeca Cell with Multi-Casting
Chamber, same as 165-4100 with multi-casting
chamber, 15 separation sheets, 8 acrylic blocks,
tapered luer connector, stopcock valve
Criterion™ Cells and Systems
165-6001
Criterion Cell, includes buffer tank, lid with power
cables, 3 sample loading guides (12 + 2-well,
18-well, 26-well)
165-6019
Criterion Cell and PowerPac Basic Power Supply,
100–120/220–240 V, includes 165-6001 and 164-5050
™
Criterion
165-4130 Cells and Systems
riterion Dodeca Cell, includes electrophoresis
C
buffer tank with built-in cooling coil, lid with
power cables
165-4139 Criterion Dodeca Cell and PowerPac Universal
Power Supply, includes 165-4130 and 164-5070
165-5133 Criterion Dodeca Cell and 6-Row AnyGel™ Stand,
includes 165-4130 and 165-5131
PROTEAN ® II xi Cells
165-1801 PROTEAN II xi Cell, 16 cm, without spacers and combs
165-1802 PROTEAN II xi Cell, 16 cm, 1.5 mm spacers (4),
15-well combs (2)
165-1803 PROTEAN II xi Cell, 16 cm, 1.0 mm spacers (4),
15-well combs (2)
ROTEAN II xi Cell, 16 cm, 0.75 mm spacers (4),
P
15-well combs (2)
165-1811 PROTEAN II xi Cell, 20 cm, without spacers
and combs
165-1812 PROTEAN II xi Cell, 20 cm, 1.5 mm spacers (4),
15-well combs (2)
165-1813 ROTEAN II xi Cell, 20 cm, 1.0 mm spacers (4),
P
15-well combs (2)
165-1814 PROTEAN II xi Cell, 20 cm, 0.75 mm spacers (4),
15-well combs (2)
ROTEAN Plus Dodeca Cell (100/120 V) and
P
PowerPac Universal Power Supply, includes
165-4150 and 164-5070
165-4144 PROTEAN Plus Dodeca Cell (100/120 V),
Trans-Blot Plus Cell, and PowerPac Universal Power
Supply, includes 165-4150, 170-3990, and 164-5070
165-5134 ROTEAN Plus Dodeca Cell (100/120 V) and
P
Two 6-Row AnyGel Stands, includes 165-4150
and two 165-5131
Catalog # Description
500-0111
DC™ Protein Assay Kit I, includes 250 ml alkaline
copper tartrate solution, 2 L dilute Folin reagent,
5 ml surfactant solution, bovine b-globulin standard;
sufficient for 450 standard assays
500-0112
DC Protein Assay Kit II, includes 250 ml alkaline
copper tartrate solution, 2 L dilute Folin reagent, 5 ml
surfactant solution, bovine serum albumin standard;
sufficient for 450 standard assays
165-4151 PROTEAN Plus Dodeca Cell, 220/240 V, includes
electrophoresis buffer tank with built-in ceramic
cooling core, lid, buffer recirculation pump with
tubing, 2 gel releasers
500-0120
RC DC™ Protein Assay Reagents Package,
includes 250 ml alkaline copper tartrate solution,
2 L dilute Folin reagent, 5 ml surfactant solution;
sufficient for 450 standard assays
165-4141 PROTEAN Plus Dodeca Cell (220/240 V) and
PowerPac HC Power Supply, includes 165-4151
and 164-5052
500-0121
RC DC Protein Assay Kit I, includes RC reagents
package, DC reagents package, bovine b-globulin
standard; sufficient for 450 standard assays
165-4143 PROTEAN Plus Dodeca Cell (220/240 V) and
PowerPac Universal Power Supply, includes
165-4151 and 164-5070
500-0122
RC DC Protein Assay Kit II, includes RC reagents
package, DC reagents package, bovine serum
albumin standard; sufficient for 450 standard assays
165-4145 ROTEAN Plus Dodeca Cell (220/240 V),
P
Trans-Blot Plus Cell, and PowerPac Universal Power
Supply, includes 165-4151, 170-3990, and 164-5070
165-5135 ROTEAN Plus Dodeca Cell (220/240 V) and
P
Two 6-Row AnyGel Stands, includes 165-4151
and two 165-5131
500-0201
Quick Start™ Bradford Protein Assay Kit 1,
includes 1x dye reagent (1 L), bovine serum albumin
standard (5 x 2 mg/ml); sufficient for 200 standard
assays or 4,000 microplate assays
Dodeca™
165-4138 Criterion Dodeca Cell and PowerPac HC Power
Supply, includes 165-4130 and 164-5052
165-1804 165-4142 Description
Power Supplies
164-5050
PowerPac Basic Power Supply, 100–120/220–240 V
164-5052
PowerPac HC Power Supply, 100–120/220–240 V
164-5056 PowerPac HV Power Supply, 100–120/220–240 V
164-5070 PowerPac Universal Power Supply,
100–120/220–240 V
Sample Preparation Kits
163-2141
MicroRotofor ™ Cell Lysis Kit (Mammal), 15 preps,
includes 50 ml protein solubilization buffer (PSB),
ReadyPrep™ mini grinders (2 packs of 10 each)
163-2142
MicroRotofor Cell Lysis Kit (Plant), 10 preps,
includes 50 ml protein solubilization buffer (PSB),
ReadyPrep 2-D cleanup kit (50 reaction size)
163-2143
icroRotofor Cell Lysis Kit (Yeast), 15 preps,
M
includes 50 ml protein solubilization buffer (PSB),
15 ml yeast suspension buffer, 2 x 0.5 ml lyticase
(1.5 U/µl)
500-0202
Quick Start Bradford Protein Assay Kit 2,
includes 1x dye reagent (1 L), bovine serum albumin
standard set (2 sets of 7 concentration standards,
0.125–2.0 mg/ml, 2 ml)
500-0203
Quick Start Bradford Protein Assay Kit 3,
includes 1x dye reagent (1 L), bovine b-globulin
standard (5 x 2 mg/ml)
500-0204
Quick Start Bradford Protein Assay Kit 4,
includes 1x dye reagent (1 L), bovine b-globulin
standard set (2 sets of 7 concentration standards,
0.125–2.0 mg/ml, 2 ml)
170-2525
170-2502
SmartSpec™ Plus Spectrophotometer
Standard Cuvette, 1–3.5 ml, quartz
170-2511
t rUView™ Cuvettes, pack of 100, individually packaged,
disposable DNase- and RNase-free cuvettes
Sample Preparation Buffers and Reagents
161-0737 Laemmli Sample Buffer, 30 ml
161-0738 Native Sample Buffer, 30 ml
161-0739 Tricine Sample Buffer, 30 ml
163-2144
MicroRotofor Cell Lysis Kit (Bacteria), 15 preps,
includes 50 ml protein solubilization buffer (PSB),
25 ml bacteria suspension buffer, 1 ml lysozyme
(1,500 U/µl)
161-0763
IEF Sample Buffer, 30 ml
161-0764
Zymogram Sample Buffer, 30 ml
161-0791
XT Sample Buffer, 4x, 10 ml
161-0792
XR Reducing Agent, 1 ml
163-2140
161-0719 Tris, 1 kg
732-6221
Micro Bio-Spin™ 6 Columns, includes 25 columns
in Tris buffer, 50 collection tubes
161-0718 Glycine, 1 kg
161-0301 SDS, 100 g
732-6227
Bio-Spin® 6 Columns, includes 25 columns
in Tris buffer, 50 collection tubes
161-0416 SDS Solution, 10% (w/v), 250 ml
166-2404 10% Tween 20, 5 ml
732-6228
Bio-Spin 6 Columns, includes 100 columns
in Tris buffer, 200 collection tubes
161-0710 2-Mercaptoethanol, 25 ml
161-0611 Dithiothreitol, 5 g
161-0404 Bromophenol Blue, 10 g
161-0730 Urea, 250 g
ReadyPrep 2-D Cleanup Kit, 5 preps
87
Electrophoresis Guide
Appendices
Catalog # Description
Protein Standards
Recombinant Prestained Protein Standards
161-0393
Precision Plus Protein All Blue Standards
Value Pack, 5 x 500 µl
161-0373
Precision Plus Protein All Blue Standards, 500 µl
161-0394
Precision Plus Protein Dual Color Standards
Value Pack, 5 x 500 µl
161-0374
Precision Plus Protein Dual Color Standards,
500 µl
161-0397
Precision Plus Protein Dual Xtra Standards
Value Pack, 5 x 500 µl
161-0377
Precision Plus Protein Dual Xtra Standards,
500 µl
161-0395
Precision Plus Protein Kaleidoscope Standards
Value Pack, 5 x 500 µl
161-0375
Precision Plus Protein Kaleidoscope Standards,
500 µl
161-0399
Precision Plus Protein WesternC Standards
Value Pack, 5 x 250 µl
Catalog # Description
Precast Gels
Running Buffers and Reagents
161-0732 10x Tris/Glycine/SDS, 1 L
161-0734 10x Tris/Glycine, 1 L
161-0744
10x Tris/Tricine/SDS, 1 L
161-0788 XT MOPS Running Buffer, 20x, 500 ml
161-0789 XT MES Running Buffer, 20x, 500 ml
161-0790 XT Tricine Running Buffer, 20x, 500 ml
161-0793 T MOPS Buffer Kit, includes 500 ml 20x XT MOPS
X
running buffer, 10 ml 4x XT sample buffer, 1 ml
20x XT reducing agent
161-0796 XT MES Buffer Kit, includes 500 ml 20x XT MOPS
running buffer, 10 ml 4x XT sample buffer, 1 ml
20x XT reducing agent
161-0797 XT Tricine Buffer Kit, includes 500 ml 20x XT
MOPS running buffer, 10 ml 4x XT sample buffer,
1 ml 20x XT reducing agent
161-0761 10x IEF Anode Buffer, 250 ml
161-0762 10x IEF Cathode Buffer, 250 ml
Description
10-Well
30 µl
15-Well
15 µl
Ready Gel® Tris-HCl Gels
5% Resolving Gel
7.5% Resolving Gel
10% Resolving Gel
12% Resolving Gel
15% Resolving Gel
18% Resolving Gel
4–15% Linear Gradient
4–20% Linear Gradient
8–16% Linear Gradient
10–20% Linear Gradient
161-1210
161-1100
161-1101
161-1102
161-1103
161-1216
161-1104
161-1105
161-1222
161-1106
Ready Gel IEF Gels
pH 3–10
pH 5–8
Ready Gel Zymogram Gels
10% Zymogram Gel with Gelatin
12% Zymogram Gel with Casein
Prep+1 Well
450 µl
10-Well
50 µl
12-Well*9-Well*
20 µl
30 µl
161-1211**
161-1118
161-1119
161-1120
161-1121
161-1217**
161-1122
161-1123
161-1223
161-1124
—
161-1136**
161-1137
161-1138
161-1139**
—
161-1140
161-1141
—
161-1142**
161-1213
161-1154
161-1155
161-1156
161-1157
161-1219
161-1158
161-1159
161-1225
161-1160
161-1214**
161-1172
161-1173
161-1174
161-1175
161-1220**
161-1176
161-1177
161-1226
161-1178
—
—
161-1191**
—
—
—
161-1194**
—
—
—
161-1111
161-1112**
161-1129**
—
—
—
161-1165**
—
—
—
—
—
—
—
161-1113
161-1114**
161-1131**
—
—
—
161-1167
161-1168**
161-1185**
—
—
—
—
—
161-0765 Zymogram Renaturation Buffer, 125 ml
161-0766 Zymogram Development Buffer, 125 ml
161-0729 EDTA, 500 g
161-0398
Precision Plus Protein WesternC
(Standards + HRP) Value Pack, 5 x 250 µl
161-0718 Glycine, 1 kg
10-Gels/Box
161-0713 Tricine, 500 g
161-0385
Precision Plus Protein WesternC
(Standards + HRP), 250 µl
161-0719 Tris, 1 kg
10-well
10-well 15-well
30 µl50 µl15 µl
161-0376
Precision Plus Protein WesternC Standards,
250 µl
TABLE OF CONTENTS
Recombinant Unstained Protein Standards
161-0396
Precision Plus Protein Unstained Standards
Value Pack, 5 x 1000 µl
Gel Casting Buffers and Reagents
161-5100
SDS-PAGE Reagent Starter Kit, includes
100 g acrylamide, 5 g bis, 5 ml TEMED,
10 g ammonium persulfate
161-0363
Precision Plus Protein Unstained Standards,
1000 µl
161-0100
161-0120
Acrylamide, 99.9%, 100 g
Acrylamide/Bis Powder, 19:1, 30 g
Natural Prestained SDS-PAGE Protein Standards
161-0324
Kaleidoscope Prestained Standards, 500 µl
161-0122
Acrylamide/Bis Powder, 37.5:1, 30 g
IPG Well
7 cm IPG Strip
—
—
161-1390**
161-1391
—
—
161-1392**
161-1393**
161-1394
161-1395**
Description
Mini-PROTEAN ® TGX™ Resolving Gels
7.5%
456-1023456-1024
10%
456-1033456-1034
12%
456-1043456-1044
4–15%
456-1083456-1084
4–20%
456-1093456-1094
456-9033456-9034
Any kD 161-0140
40% Acrylamide Solution, 500 ml
Mini-PROTEAN ® TGX Stain-Free™ Gels
161-0305
Prestained SDS-PAGE Standards,
low range, 500 µl
161-0144
40% Acrylamide/Bis Solution, 19:1, 500 ml
161-0146
40% Acrylamide/Bis Solution, 29:1, 500 ml
161-0309
Prestained SDS-PAGE Standards,
high range, 500 µl
161-0148
40% Acrylamide/Bis Solution, 37.5:1, 500 ml
161-0154
30% Acrylamide/Bis Solution, 19:1, 500 ml
7.5%
10%
12%
Any kD 161-0318
Prestained SDS-PAGE Standards,
broad range, 500 µl
161-0156
30% Acrylamide/Bis Solution, 29:1, 500 ml
Mini-PROTEAN Tris-Tricine Gels (Pack of 2)
161-0158
30% Acrylamide/Bis Solution, 37.5:1, 500 ml
Natural Unstained SDS-PAGE Protein Standards
161-0303
SDS-PAGE Standards, high range, 200 µl
161-0200
Bis Crosslinker, 5 g
16.5% Resolving Gel
10–20% Resolving Gel
161-0800
TEMED, 5 ml
Mini-PROTEAN TBE Gels (Pack of 2)
161-0304
SDS-PAGE Standards, low range, 200 µl
161-0798
Resolving Gel Buffer, 1.5 M tris-HCl, pH 8.8, 1 L
161-0317
SDS-PAGE Standards, broad range, 200 µl
161-0700
Ammonium Persulfate (APS), 10 g
161-0326
Polypeptide SDS-PAGE Standards, 200 µl
161-0799
Stacking Gel Buffer, 0.5 M tris-HCl, pH 6.8, 1 L
5% TBE Gel
10% TBE Gel
15% TBE Gel
4–20% TBE Gel
456-8023456-8024
456-8033456-8034
456-8043456-8044
456-8123456-8124
456-3063
456-3113
456-5013
456-5033
456-5053*
456-5093*
IPG/Prep
12-well
8+1-well
7cm IPG Strip/450 µl20 µl30 µl
456-1026
456-1036
456-1046
456-1086
456-1096
456-9036
456-1021
456-1031
456-1041
456-1081
456-1091
456-9031
456-1025 456-1029
456-1035 456-1039
456-1045 456-1049
456-1085456-1089
456-1095 456-1099
456-9035 456-9039
456-8026
456-8036
456-8046
456-8126
456-8021
456-8031
456-8041
456-8121
456-8025 456-8029
456-8035 456-8039
456-8045 456-8049
456-8125456-8129
456-3064
456-3114
—
—
—
—
456-3065*
456-3115*
456-3066
456-3116*
456-5014*
456-5034*
456-5054
456-5094*
—
—
—
—
—
—
—
—
456-5015*
456-5035
456-5055*
456-5095*
456-5016
456-5036
456-5056
456-5096*
—
—
—
—
—
456-6055*
456-6036*
456-6056*
Mini-PROTEAN TBE-Urea Gels (Pack of 2)
10% TBE-Urea Gel
15% TBE-Urea Gel
456-6033*
456-6053*
—
—
All formats are available as both ten packs (catalog numbers listed) and two packs. To order as a two pack, add an “S” to the end of the catalog
number for the corresponding ten pack.
88
89
Electrophoresis Guide
Appendices
Catalog # Description
Criterion™ TGX™ Gels**
7.5%
10%
12%
18%
4–15%
4–20%
8–16%
10–20%
Any kD
12+2 Well**
45 µl 18-Well 30 µl 26-Well*
15 µl
Prep+2 Well**
800 µl
IPG+1 Well**
11 cm IPG Strip
567-1023567-1024567-1025
—
—
567-1033567-1034567-1035
—
—
567-1043567-1044567-1045
—
—
567-1073567-1074567-1075 567-1072567-1071
567-1083567-1084567-1085 567-1082567-1081
567-1093567-1094567-1095 567-1092567-1091
567-1103567-1104567-1105 567-1102567-1101
567-1113567-1114567-1115 567-1112567-1111
567-1123
567-1124
567-1125
567-1122
567-1121
TABLE OF CONTENTS
Criterion™ TGX Stain-Free™
Gels**
7.5% 10% 12% 18% 4–15% 4–20% 8–16% 10–20% Any kD
567-8023
567-8033
567-8043
567-8073
567-8083
567-8093
567-8103
567-8113
567-8123
567-8024
567-8034
567-8044
567-8074
567-8084
567-8094
567-8104
567-8114
567-8124
567-8025
567-8035
567-8045
567-8075
567-8085
567-8095
567-8105
567-8115
567-8125
—
—
—
567-8072
567-8082
567-8092
567-8102
567-8112
567-8122
Criterion XT Bis-Tris Gels***
10% Resolving Gel
12% Resolving Gel
4–12% Resolving Gel
345-0111
345-0117
345-0123
345-0112
345-0118
345-0124
345-0113
345-0119
345-0125
—
345-0115
345-0120†345-0121
345-0126†345-0127
Criterion XT Tris-Acetate Gels
7% Resolving Gel
3–8% Resolving Gel
345-0135
345-0129
345-0136†345-0137†— —
345-0130
345-0131
—
345-0133†
Criterion Tris-HCl Gels
5% Resolving Gel
7.5% Resolving Gel
10% Resolving Gel
12.5% Resolving Gel
15% Resolving Gel
18% Resolving Gel
4–15% Linear Gradient
4–20% Linear Gradient
8–16% Linear Gradient
10–20% Linear Gradient
10.5–14% Linear Gradient
345-0001
345-0005
345-0009
345-0014
345-0019
345-0023
345-0027
345-0032
345-0037
345-0042
345-9949
345-0002
345-0006
345-0010
345-0015
345-0020
345-0024
345-0028
345-0033
345-0038
345-0043
345-9950
—
—
—
567-8071
567-8081
567-8091
567-8101
567-8111
567-8121
—
345-0003†—
345-0007
345-0008
—
345-0011
345-0012†345-0101
345-0016
345-0017†345-0102
345-0021
345-0022†—
345-0025
345-0026†—
345-0029
345-0030†345-0103
345-0034
345-0035
345-0104
345-0039
345-0040†345-0105
345-0044
345-0045†345-0107
345-9951
—
345-0106
Criterion Stain-Free Gels
10% Tris-HCI Gel
4–20% Tris-HCL Gel
8–16% Tris-HCL Gel
345-1012
345-0412
345-8162
345-1018
345-0418
—
—
345-0426
345-8166
Criterion Tris-Tricine Gels
16.5% Tris-Tricine
10–20% Tris-Tricine
345-0063
345-0067
345-0064
345-0068
345-0065†345-0066†
345-0069
—
—
—
—
—
—
345-8161
—
—
See catalog or www.bio-rad.com for a complete listing of
accessories, including available empty gel cassettes and glass plates,
spacers, combs, etc.
165-5131 AnyGel Stand, 6-row, holds 6 PROTEAN® gels,
12 Criterion gels, or 18 Ready Gel® mini gels
165-4131 AnyGel Stand, single-row, holds 1 PROTEAN gel,
2 Criterion gels, or 3 Ready Gel mini gels
165-4122
Model 485 Gradient Former and Mini-PROTEAN
3 Multi-Casting Chamber, includes 165-4120
and 165-4110
165-4123
Model 495 Gradient Former and PROTEAN
Plus Multi-Casting Chamber, includes 165-4121
and 165-4160
Total Protein Gel Stains
161-0786 Bio-Safe™ Coomassie Stain, 1 L
161-0787 Bio-Safe Coomassie Stain, 5 L
161-0435 Coomassie Brilliant Blue R-250 Staining
Solutions Kit, includes 1 L Coomassie Brilliant Blue
R-250 staining solution, 2 x 1 L Coomassie Brilliant
Blue R-250 destaining solution
161-0436 Coomassie Brilliant Blue R-250 Staining Solution, 1 L
161-0438
Coomassie Brilliant Blue R-250 Destaining
Solution, 1 L
161-0400 Coomassie Brilliant Blue R-250, 10 g
161-0406 Coomassie Brilliant Blue G-250, 10 g
161-0443 Silver Stain Kit, includes oxidizer concentrate, silver
reagent concentrate, silver stain developer, stains
20 full size or 48 mini gels
161-0449 161-0496 ilver Stain Plus™ Kit, includes fixative enhancer
S
concentrate, silver complex solution, reduction
moderator solution, image development reagent,
development accelerator reagent, stains 13 full size
or 40 mini gels
Oriole™ Fluorescent Gel Stain, 1x solution, 1 L
161-0492 Flamingo™ Fluorescent Gel Stain, 10x solution,
500 ml
170-3125 SYPRO Ruby Protein Gel Stain, 1x solution, 1 L
161-0440 Zinc Stain and Destain Kit, includes 125 ml of 10x
zinc stain solution A, 125 ml of 10x zinc stain solution
B, 125 ml of 10x zinc destain solution
161-0470 Copper Stain and Destain Kit, includes 125 ml
of 10x copper stain, 125 ml of 10x copper
destain solution
Criterion IEF Gels
pH 3–10
pH 5–8
345-0071
—
—
—
—
Criterion Zymogram Gels
10% Zymogram Gel with Gelatin
12.5% Zymogram Gel with Casein
High-Throughput Stainers
165-3400
Dodeca™ Stainer, large, 100–240 V, includes
13 trays (12 clear, 1 white), 12 tray attachments,
shaking rack, solution tank, lid with shaker motor,
shaker control unit, gel clip
345-0079†345-0080†345-0081†—
345-0082†345-0083†345-0084†—
—
—
165-3401
†345-0072†345-0073†—
345-0076†—
*Multichannel pipet compatible.
**Includes reference well(s).
***Purchase of this product is accompanied by a limited license under U.S. Patent Numbers 6,143,154; 6,096,182; 6,059,948; 5,578,180;
5,922,185; 6,162,338; and 6,783,651 and corresponding foreign patents.
† Please allow up to 2 weeks for delivery.
90
Description
Gel Casting Accessories
odeca Stainer, small, 100–240 V, includes
D
13 trays (12 clear, 1 white), 12 Criterion tray
attachments, shaking rack, solution tank, lid with
shaker motor, shaker control unit, gel clip
Catalog # Description
Imaging Systems
170-7983 GS-800™ USB Calibrated Densitometer,
PC or Mac, 100–240 V
170-8195
Gel Doc™ XR+ System with Image Lab Software,
PC or Mac, includes darkroom, UV transilluminator,
epi-white illumination, camera, cables, Image Lab
software
170-8270
Gel Doc EZ System with Image Lab Software, PC
or Mac, includes darkroom, camera, cables, Image
Lab software; samples trays (#170-8271, 170-8272,
170-8273, or 170-8274) are sold separately; sample
trays are required to use the system
170-8265 ChemiDoc™ XRS+ System with Image Lab
Software, PC or Mac, includes darkroom, UV
transilluminator, epi-white illumination, camera,
power supply, cables, Image Lab™ software
170-8280 ChemiDoc MP System with Image Lab Software,
PC or Mac, includes darkroom, UV transilluminaator,
epi-white illumination, camera, power supply, cables,
ImageLab™ software
170-9460
PharosFX™ Plus System, PC or Mac, 110–240 V,
includes Quantity One® software, sample tray set,
fluorescence filters (170-7866, 170-7896) and
phosphor imaging filters, USB2 cable
170-9450
PharosFX System, PC or Mac, 110–240 V, includes
Quantity One software, sample tray set, fluorescence
filters (170-7866, 170-7896), USB2 cable
170-9400
Personal Molecular Imager ™ (PMI) System, PC
or Mac, 110/240 V, includes Quantity One software,
sample tray set, USB2 cable
Analysis Software
170-9690
Image Lab Software
170-9600
Quantity One 1-D Analysis Software, PC or Mac
170-9630
PDQuest Advanced 2-D Analysis Software
Gel Drying and Electroelution Supplies
165-1771
GelAir™ Drying System, 115 V, 60 Hz, includes
165-1777, 2 drying frames, 16 clamps, assembly
table, 50 precut sheets of cellophane support,
gel drying solution
165-1777
GelAir Dryer, 115 V, gel drying oven only
165-1251Whole Gel Eluter with Harvesting Box, includes lid,
electrodes, elution chamber core, base, roller, ruler,
template, 75 pieces of lower filter paper, 50 pieces
of upper filter paper, 50 sealing strips, 25 pieces
of cellophane, application note; requires a vacuum
source pulling 5" Hg for the harvesting box
165-1256
Mini Whole Gel Eluter with Harvesting Box,
includes lid, electrodes, elution chamber core, base,
roller, ruler, template, 75 pieces of lower filter paper,
50 pieces of upper filter paper, 50 sealing tabs,
25 pieces of cellophane, application note; requires a
vacuum source pulling 5" Hg for the harvesting box
165-2976
Model 422 Electro-Eluter, includes electro-eluter
module, membrane caps (MW cutoff 12,000–15,000),
glass tubes, frits, silicone adaptors, grommets and
stoppers, buffer tank, lid with power cables
91
Electrophoresis Guide
Purchase of Criterion XT Bis-Tris gels, XT MOPS running buffer, XT MES running buffer, XT MOPS buffer kit, and XT MES buffer kit is accompanied
by a limited license under U.S. Patent Numbers 6,143,154; 6,096,182; 6,059,948; 5,578,180; 5,922,185; 6,162,338; and 6,783,651, and
corresponding foreign patents.
LabChip and the LabChip logo are trademarks of Caliper Life Sciences, Inc. Bio-Rad Laboratories, Inc. is licensed by Caliper
Life Sciences, Inc. to sell products using the LabChip technology for research use only. These products are licensed under
U.S. Patent Numbers 5,863,753; 5,658,751; 5,436,134; and 5,582,977, and pending patent applications, and related foreign
patents, for internal research and development use only in detecting, quantitating, and sizing macromolecules, in combination
with microfluidics, where internal research and development use expressly excludes the use of this product for providing medical,
diagnostic, or any other testing, analysis, or screening services, or providing clinical information or clinical analysis, in any event in
return for compensation by an unrelated party.
Precision Plus Protein standards are sold under license from Life Technologies Corporation, Carlsbad, CA, for use only by the buyer of the product.
The buyer is not authorized to sell or resell this product or its components.
StrepTactin is covered by German patent application P 19641876.3. Bio-Rad Laboratories, Inc. is licensed by Institut für Bioanalytik GmbH to sell
these products for research use only.
Bio-Rad Laboratories, Inc. is licensed by Invitrogen Corporation to sell SYPRO products for research use only under U.S. Patent Number
5,616,502.
Coomassie is a trademark of BASF Aktiengesellschaft. Cy is a trademark of GE Healthcare. NuPage, Pro-Q, and SYPRO are trademarks of
Invitrogen Corporation. Strep-tag is a trademark of Institut für Bioanalytik GmbH. Triton is a trademark of Dow Chemical Corporation. Tygon is a
trademark of Saint-Gobain Performance Plastics Corporation.
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