Protocol (50 prep) - Norgen Biotek Corp.

3430 Schmon Parkway
Thorold, ON, Canada L2V 4Y6
Phone: 866-667-4362  (905) 227-8848
Fax: (905) 227-1061
Email: techsupport@norgenbiotek.com
RNA/DNA/Protein Purification Kit
Product Insert
Product # 24000
Norgen’s RNA/DNA/Protein Purification Kit provides a rapid method for the isolation and
purification of total RNA, genomic DNA and proteins sequentially from a single sample of cultured
animal cells, small tissue samples, blood, bacteria, yeast, fungi or plants. The total RNA,
genomic DNA and proteins are all column purified in less than 30 minutes using the same
column. This kit is ideal for researchers who are interested in studying the genome, proteome
and transcriptome of a single sample, such as for studies of gene expression including gene
silencing experiments or mRNA knockdowns, studies involving biomarker discovery, studies in
epigenetics, and for characterization of cultured cell lines.
Norgen’s RNA/DNA/Protein
Purification Kit is especially useful for researchers who are isolating macromolecules from
precious, difficult to obtain or small samples such as biopsy materials or single foci from cell
cultures, as it eliminates the need to fractionate the sample. Furthermore, analysis will be more
reliable since the RNA, DNA and proteins are derived from the same sample, thereby eliminating
inconsistent results. The purification procedure is very rapid, allowing for the isolation of total
RNA, genomic DNA and proteins from a single sample in less than 30 minutes. The purified
macromolecules are of the highest purity and can be used in a number of different downstream
applications.
Norgen’s Purification Technology
RNA and DNA Purification
Purification is based on spin column chromatography using Norgen’s proprietary resin as the
separation matrix. The process involves first lysing the cells or tissue of interest with the provided
Buffer SK (please see the flow chart on page 4). The Buffer SK contains detergents, as well as
large amounts of a chaotropic denaturant that will rapidly inactivate RNases and proteases that
are present. Ethanol is then added to the lysate, and the solution is loaded onto a spin-column.
Norgen’s resin binds nucleic acids in a manner that depends on ionic concentrations, thus only
the genomic DNA and RNA will bind to the column while the proteins are removed in the
flowthrough. Next, the bound RNA is washed with the provided Wash Solution A to remove
impurities, and the purified RNA is eluted with the Elution Solution A. The remaining bound
genomic DNA is then washed with the provided Wash Solution EI to remove any remaining trace
levels of RNA, and the gDNA is then eluted with the Elution Buffer F.
The kit purifies all sizes of RNA, from large mRNA and ribosomal RNA down to microRNA
(miRNA) and small interfering RNA (siRNA). The purified RNA is of the highest integrity, and can
be used in a number of downstream applications including real time PCR, reverse transcription
PCR, Northern blotting, RNase protection and primer extension, and expression array assays.
The genomic DNA is of the highest quality, and can be used in PCR reactions, sequencing,
Southern blotting and SNP analysis.
Protein Purification
The proteins that are present from the initial flowthrough can now be loaded directly onto an SDSPAGE gel for visual analysis. Alternatively, the protein samples can be further purified using the
spin columns provided with the kit. After the RNA and gDNA has been eluted from the column,
the flowthrough is then pH adjusted and loaded back onto the column in order to bind the proteins
that are present. The bound proteins are washed with the provided wash buffer, and are then
eluted such that they can be used in downstream applications. The purified proteins can be used
in a number of downstream applications including SDS-PAGE analysis, Western blots and mass
spectrometry.
1
Specifications
Kit Specifications
Maximum Column Binding Capacity
50 g for RNA
20 g for DNA
200 g for protein
Maximum Column Loading Volume
650 L
Size of RNA Purified
All sizes, including small RNA
(<200 nt)
Size of DNA Purified
≥ 30 kb
Maximum Amount of Starting Material:
Animal Cells
Animal Tissues
Blood
Bacteria
Yeast
Fungi
Plant Tissues
3 x 10 cells
10 mg (for most tissues)
100 L
9
1 x 10 cells
8
1 x 10 cells
50 mg
50 mg
Time to Complete 10 Purifications
30 minutes
Average Yields*
6
HeLa Cells (1 x 10 cells)
6
HeLa Cells (1 x 10 cells)
6
HeLa Cells (1 x 10 cells)
15 g RNA
8 g DNA
150 g protein
6
* average yields will vary depending upon a number of factors including species, growth conditions used and
developmental stage.
Kit Components
Component
Used For
Product # 24000 (50 samples)
Buffer SK
RNA Lysis
40 mL
Wash Solution A
RNA Wash
38 mL
Elution Solution A
RNA Elution
6 mL
Wash Solution EI
gDNA Wash
15 mL
Elution Buffer F
gDNA Elution
15 mL
Wash Solution C
Binding Buffer A
Protein Wash
Protein Binding
30 mL
8 mL
Elution Buffer C
Protein Elution
8 mL
Protein Neutralizer
Protein Eluent Neutralization
4 mL
Protein Loading Dye
SDS-PAGE Gel Loading
2 mL
Mini Spin Columns
50
Collection Tubes
200
Product Insert
1
2
Advantages
 Fast and easy processing using rapid spin-column format
 All columns for RNA, DNA and protein purification provided
 Sequentially isolate nucleic acids and proteins from a single lysate – no need to split the
lysate
 Isolate total RNA, from large rRNA down to microRNA (miRNA)
 No phenol or chloroform extractions
 Isolate high quality total RNA
 Isolate high quality genomic DNA with a molecular weight ≥ 30 kb
 High yields of isolated proteins
Storage Conditions and Product Stability
All solutions should be kept tightly sealed and stored at room temperature. These reagents
should remain stable for at least 1 year in their unopened containers. The Protein Loading Dye
should be stored at -20°C after the addition of DL-Dithiothreitol (DTT).
Precautions and Disclaimers
This kit is designed for research purposes only. It is not intended for human or diagnostic use.
Ensure that a suitable lab coat, disposable gloves and protective goggles are worn when working
with chemicals. For more information, please consult the appropriate Material Safety Data
Sheets (MSDSs). These are available as convenient PDF files online at www.norgenbiotek.com.
Blood of all human and animal subjects is considered potentially infectious. All necessary
precautions recommended by the appropriate authorities in the country of use should be taken
when working with whole blood.
Customer-Supplied Reagents and Equipment
You must have the following in order to use the RNA/DNA/Protein Purification Kit:
For All Protocols
 Benchtop microcentrifuge
 -mercaptoethanol (Optional)
 96 - 100% ethanol
 Isopropanol
 DL-Dithiothreitol (DTT)
®
 Molecular biology grade water (Milli-Q water)
 1.7 mL microcentrifuge tubes
For Animal Cell Protocol
 PBS (RNase-free)
For Animal Tissue Protocol
 Liquid nitrogen
 Mortar and pestle
 70% ethanol
3
For Bacterial Protocol
 Lysozyme-containing TE Buffer:
o For Gram-negative bacteria, 1 mg/mL lysozyme in TE Buffer
o For Gram-positive bacteria, 3 mg/mL lysozyme in TE Buffer
For Yeast Protocol
 Resuspension Buffer with Lyticase:
o 50 mM Tris pH 7.5
o 10 mM EDTA
o 1 M Sorbital
o 1 unit/L Lyticase
For Fungi Protocol
 Liquid nitrogen
 Mortar and pestle
 70% ethanol
For Plant Protocol
 Liquid nitrogen
 Mortar and pestle
 70% ethanol
Working with RNA
RNases are very stable and robust enzymes that degrade RNA. Autoclaving solutions and
glassware is not always sufficient to actively remove these enzymes. The first step when
preparing to work with RNA is to create an RNase-free environment. The following precautions
are recommended as your best defense against these enzymes.

The RNA area should be located away from microbiological work stations

Clean, disposable gloves should be worn at all times when handling reagents, samples,
pipettes, disposable tubes, etc. It is recommended that gloves are changed frequently to
avoid contamination

There should be designated solutions, tips, tubes, lab coats, pipettes, etc. for RNA only

All RNA solutions should be prepared using at least 0.05% DEPC-treated autoclaved
water or molecular biology grade nuclease-free water

Clean all surfaces with commercially available RNase decontamination solutions

When working with purified RNA samples, ensure that they remain on ice during
downstream applications
4
Flow Chart
Procedure for Purifying Total RNA and Proteins using Norgen’s RNA/DNA/Protein Purification Kit
A. Purification of RNA and DNA
Lyse cells or tissue using Buffer SK
Bind RNA and
DNA to column
B. Purification of Proteins
SPIN
Flowthrough
(Proteins)
Wash
Bind Proteins to
Column
Adjust pH
SPIN
SPIN
Wash
Elute RNA
SPIN
SPIN
RNA
Elute Proteins
Wash DNA
SPIN
SPIN
Elute gDNA
SPIN
Proteins
gDNA
5
Procedures
All centrifugation steps are carried out in a benchtop microcentrifuge. Various speeds are
required for different steps, so please check your microcentrifuge specifications to ensure that it is
capable of the proper speeds. All centrifugation steps are performed at room temperature. The
correct rpm can be calculated using the formula:
RPM =
RCF
(1.118 x 10-5) (r)
where RCF = required gravitational acceleration (relative centrifugal force in units of g); r = radius
of the rotor in cm; and RPM = the number of revolutions per minute required to achieve the
necessary g-force.
IMPORTANT NOTE:
This procedure is written in three steps. Section 1 contains the protocols to isolate total
RNA from different types of starting materials. Please ensure that the proper protocol is
followed for your sample. Section 2 contains the protocol to isolate genomic DNA from
the sample, and Section 3 contains the protocol to isolate total proteins from the sample.
The same protocols for Section 2 and Section 3 will apply to all the different starting
materials.
Section 1. Total RNA Purification from Various Cell Types
Notes Prior to Use for all Total RNA Purification Procedures
 The steps for preparing the lysate are different depending on the starting material
(Step 1). However, the subsequent steps are the same in all cases (Steps 2 – 6).
 Please ensure that the correct procedure for preparing the lysate from your starting
material is followed.
 All centrifugation steps are carried out in a benchtop microcentrifuge at 14,000 x g
(~ 14,000 RPM) except where noted. All centrifugation steps are performed at room
temperature.
 A variable speed centrifuge should be used for maximum kit performance. If a variable
speed centrifuge is not available a fixed speed centrifuge can be used, however reduced
yields may be observed.
 Ensure that all solutions are at room temperature prior to use.
 Prepare a working concentration of the Wash Solution A by adding 90 mL of 96 - 100%
ethanol (provided by the user) to the supplied bottle containing the concentrated Wash
Solution A. This will give a final volume of 128 mL. The label on the bottle has a box
that may be checked to indicate that the ethanol has been added.
 Prepare a working concentration of the Wash Solution EI by adding 15 mL of
isopropanol (provided by the user) to the supplied bottle containing the concentrated
Wash Solution EI. This will give a final volume of 30 mL. The label on the bottle has a
box that may be checked to indicate that the ethanol has been added.
 Add 93 mg of DL-Dithiothreitol (DTT, not provided) to the Protein Loading Dye. The
Protein Loading Dye should be stored at -20°C after the addition of DTT. The label on
the bottle has a box that may be checked to indicate that DTT has been added.
 Optional: The use of -mercaptoethanol in lysis is highly recommended for most
tissues, particularly those known to have high RNAse content (ex: pancreas). It is also
recommended for users who wish to isolate RNA for sensitive downstream applications.
Add 10 L of -mercaptoethanol (provided by the user) to each 1 mL of Buffer SK
required. -mercaptoethanol is toxic and should be dispensed in a fume hood.
Alternatively, the Buffer SK can be used as provided.
 It is important to work quickly when purifying RNA.
6
Section 1A. Preparation of Lysate From Various Cell Types
1A. Lysate Preparation from Cultured Animal Cells
Notes Prior to Use
6
 For optimal results, it is recommended that 1 x 10 cells be used for the input. Inputs of
6
up to 3 x 10 cells may be used, however slight cross-contamination of RNA in the
6
genomic DNA fraction may be observed in input ranges over 10 cells.
 A hemocytometer can be used in conjunction with a microscope to count the number of
6
cells. As a general guideline, a confluent 3.5 cm plate of HeLa cells will contain 10 cells.
 Cell pellets can be stored at -70°C for later use or used directly in the procedure.
Determine the number of cells present before freezing.
 Frozen pellets should be stored for no longer than 2 weeks to ensure that the integrity of
the RNA is not compromised.
 Frozen cell pellets should not be thawed prior to beginning the protocol. Add the Buffer
SK directly to the frozen cell pellet (Step 1A(ii) d).
1A (i). Cell Lysate Preparation from Cells Growing in a Monolayer
a. Aspirate media and wash cell monolayer with an appropriate amount of PBS. Aspirate
PBS.
b. Add 350 L of Buffer SK directly to culture plate.
c. Lyse cells by gently tapping culture dish and swirling buffer around plate surface for five
minutes.
d. Transfer lysate to a microcentrifuge tube.
e. Add 200 L of 96 - 100% ethanol (provided by the user) to the lysate. Mix by vortexing
for 10 seconds. Proceed to Step 2.
6
Note: For input amounts greater than 10 cells, it is recommended that the lysate is
passed through a 25 gauge needle attached to a syringe 5-10 times at this point, in order
to reduce the viscosity of the lysate prior to loading onto the column.
1A (ii). Cell Lysate Preparation from Cells Growing in Suspension and Lifted Cells
a. Transfer cell suspension to an RNase-free tube (not provided) and centrifuge at no more
than 200 x g (~2,000 RPM) for 10 minutes to pellet cells.
b. Carefully decant the supernatant to ensure that the pellet is not dislodged. Wash the cell
pellet with an appropriate amount of PBS. Centrifuge at 200 x g (~2,000 RPM) for
another 5 minutes.
c. Carefully decant the supernatant. A few L of PBS may be left behind with the pellet in
order to ensure that the pellet is not dislodged.
d. Add 350 L of Buffer SK to the pellet. Lyse cells by vortexing for 15 seconds. Ensure
that the entire pellet is completely dissolved before proceeding to the next step.
e. Add 200 L of 96 - 100% ethanol (provided by the user) to the lysate. Mix by vortexing
for 10 seconds. Proceed to Step 2.
6
Note: For input amounts greater than 10 cells, it is recommended that the lysate is
passed through a 25 gauge needle attached to a syringe 5-10 times at this point, in order
to reduce the viscosity of the lysate prior to loading onto the column
7
1B. Lysate Preparation from Animal Tissues
Notes Prior to Use



RNA in animal tissues is not protected after harvesting until it is disrupted and
homogenized. Thus it is important that the procedure is carried out as quickly as
possible, particularly the Cell Lysate Preparation step.
Fresh or frozen tissues may be used for the procedure. Tissues should be flash-frozen in
liquid nitrogen and transferred immediately to a -70°C freezer for long-term storage.
Tissues may be stored at -70°C for several months. Do not allow frozen tissues to thaw
prior to grinding with the mortar and pestle in order to ensure that the integrity of the RNA
is not compromised.
The maximum recommended input of tissue varies depending on the type of tissue being
used. Please refer to Table 1 below as a guideline for maximum tissue input amounts. If
your tissue of interest is not included in the table below we recommend starting with an
input of no more than 10 mg.
Table 1. Recommended Maximum Input Amounts of Different Tissues
Tissue
Maximum Input Amount
Brain
25 mg
Heart
5 mg
Kidney
10 mg
Liver
10 mg
Lung
10 mg
Spleen
10 mg
1B. Cell Lysate Preparation from Animal Tissues
a. Excise the tissue sample from the animal.
b. Determine the amount of tissue by weighing. Please refer to Table 1 for the
recommended maximum input amounts of different tissues. For tissues not included in
the table, we recommend starting with an input of no more than 10 mg.
c. Transfer the tissue into a mortar that contains an appropriate amount of liquid nitrogen to
cover the sample. Grind the tissue thoroughly using a pestle.
d. Allow the liquid nitrogen to evaporate, without allowing the tissue to thaw.
e. Add 600 L of Buffer SK to the tissue sample and continue to grind until the sample has
been homogenized. Homogenize by passing the lysate 5-10 times through a 25 gauge
needle attached to a syringe.
f. Using a pipette, transfer the lysate into an RNase-free microcentrifuge tube (not
provided).
g. Spin lysate for 2 minutes to pellet any cell debris. Transfer the supernatant to another
RNase-free microcentrifuge tube (not provided). Note the volume of the
supernatant/lysate.
h. Add an equal volume of 70% ethanol (provided by the user) to the lysate (100 L of
ethanol is added to every 100 L of lysate). Mix by vortexing for 10 seconds. Proceed to
Step 2.
8
1C. Lysate Preparation from Blood
Notes Prior to Use
 Blood of all human and animal subjects is considered potentially infectious. All
necessary precautions recommended by the appropriate authorities in the country of use
should be taken when working with whole blood.
 It is recommended that no more than 100 L of blood be used in order to prevent
clogging of the column.
 We recommend the use of this kit to isolate RNA from non-coagulating fresh blood using
EDTA as the anti-coagulant.
1C. Cell Lysate Preparation from Blood
a. Transfer up to 100 L of non-coagulating blood to an RNase-free microcentrifuge tube
(not provided).
b. Add 350 L of Buffer SK to the blood. Lyse cells by vortexing for 15 seconds. Ensure
that mixture becomes transparent before proceeding to the next step.
c. Add 200 L of 96 - 100% ethanol (provided by the user) to the lysate. Mix by vortexing
for 10 seconds. Proceed to Step 2.
1D. Lysate Preparation from Bacteria
Notes Prior to Use
 Prepare the appropriate lysozyme-containing TE Buffer as indicated in Table 1. This
solution should be prepared with sterile, RNAse-free TE Buffer, and kept on ice until
needed. These reagents are to be provided by the user.
9
 It is recommended that no more than 10 bacterial cells be used in this procedure.
Bacterial growth can be measured using a spectrophotometer. As a general rule, an E.
9
coli culture containing 1 x 10 cells/mL has an OD600 of 1.0.
 For RNA isolation, bacteria should be harvested in log-phase growth.
 Bacterial pellets can be stored at -70°C for later use, or used directly in this procedure.
 Frozen bacterial pellets should not be thawed prior to beginning the protocol. Add the
Lysozyme-containing TE Buffer directly to the frozen bacterial pellet (Step 1Dc).
1D. Cell Lysate Preparation from Bacteria
a. Pellet bacteria by centrifuging at 14,000 x g (~14,000 RPM) for 1 minute.
b. Decant supernatant, and carefully remove any remaining media by aspiration.
c. Resuspend the bacteria thoroughly in 100 L of the appropriate lysozyme-containing TE
Buffer (see Table 1) by vortexing. Incubate at room temperature for the time indicated in
Table 1.
d. Add 300 L of Buffer SK and vortex vigorously for at least 10 seconds.
e. Add 200 L of 96 - 100% ethanol (provided by the user) to the lysate. Mix by vortexing
for 10 seconds. Proceed to Step 2.
Table 1: Incubation Time for Different Bacterial Strains
Bacteria Type
Lysozyme Concentration
in TE Bufffer
Incubation Time
Gram-negative
Gram-positive
1 mg/mL
3 mg/mL
5 min
10 min
9
1E. Lysate Preparation from Yeast
Notes Prior to Use
 Prepare the appropriate amount of Lyticase-containing Resuspension Buffer, considering
that 500 L of buffer is required for each preparation. The Resuspension Buffer should
have the following composition: 50 mM Tris, pH 7.5, 10 mM EDTA, 1M Sorbital, 0.1% mercaptoethanol and 1 unit/L Lyticase. This solution should be prepared with sterile,
RNAse-free reagents, and kept on ice until needed. These reagents are to be provided
by the user.
7
 It is recommended that no more than 10 yeast cells or 1 mL of culture be used for this
procedure.
 For RNA isolation, yeast should be harvested in log-phase growth.
 Yeast can be stored at -70°C for later use, or used directly in this procedure.
 Frozen yeast pellets should not be thawed prior to beginning the protocol. Add the
Lyticase-containing Resuspension Buffer directly to the frozen yeast pellet (Step 1Ec).
1E. Cell Lysate Preparation from Yeast
a. Pellet yeast by centrifuging at 14,000 x g (~14,000 RPM) for 1 minute.
b. Decant supernatant, and carefully remove any remaining media by aspiration.
c. Resuspend the yeast thoroughly in 500 L of Lyticase-containing Resuspension Buffer
o
by vortexing. Incubate at 37 C for 10 minutes.
d. Pellet the spheroplasts at 200 x g (~2,000 RPM) for 3 minutes. Decant supernatant.
e. Add 350 L of Buffer SK and vortex vigorously for at least 10 seconds.
f. Add 200 L of 96 - 100% ethanol (provided by the user) to the lysate. Mix by vortexing
for 10 seconds. Proceed to Step 2.
1F. Lysate Preparation from Fungi
Notes Prior to Use



Fresh or frozen fungi may be used for this procedure. Fungal tissue should be flashfrozen in liquid nitrogen and transferred immediately to a -70°C freezer for long-term
storage. Fungi may be stored at -70°C for several months. Do not allow frozen tissues
to thaw prior to grinding with the mortar and pestle in order to ensure that the integrity of
the RNA is not compromised.
It is recommended that no more than 50 mg of fungi be used for this procedure in order
to prevent clogging of the column.
It is important to work quickly during this procedure.
1F. Cell Lysate Preparation from Fungi
a. Determine the amount of fungi by weighing. It is recommended that no more than 50 mg
of fungi be used for the protocol.
b. Transfer the fungus into a mortar that contains an appropriate amount of liquid nitrogen to
cover the sample. Grind the fungus thoroughly using a pestle.
Note: At this stage the ground fungus may be stored at -70°C, such that the RNA
purification can be performed at a later time.
c. Allow the liquid nitrogen to evaporate, without allowing the tissue to thaw.
d. Add 600 L of Buffer SK to the tissue sample and continue to grind until the sample has
been homogenized.
e. Using a pipette, transfer the lysate into an RNase-free microcentrifuge tube (not
provided).
10
f.
Spin lysate for 2 minutes to pellet any cell debris. Transfer the supernatant to another
RNase-free microcentrifuge tube. Note the volume of the supernatant/lysate.
g. Add an equal volume of 70% ethanol (provided by the user, 100 L of ethanol is added to
every 100 L of lysate). Vortex to mix. Proceed to Step 2.
1G. Lysate Preparation from Plant
Notes Prior to Use


6
The maximum recommended input of plant tissue is 50 mg or 5 x 10 plant cells.
Both fresh and frozen plant samples can be used for this protocol. Samples should be
flash-frozen in liquid nitrogen and transferred immediately to a -70°C freezer for long-term
storage. Do not allow frozen tissues to thaw prior to grinding with the mortar and pestle
in order to ensure that the integrity of the RNA is not compromised.
1G. Cell Lysate Preparation from Plant
6
a. Transfer ≤50 mg of plant tissue or 5 x 10 plant cells into a mortar that contains an
appropriate amount of liquid nitrogen to cover the sample. Grind the sample into a fine
powder using a pestle in liquid nitrogen.
Note: If stored frozen samples are used, do not allow the samples to thaw before
transferring to the liquid nitrogen.
b. Allow the liquid nitrogen to evaporate, without allowing the tissue to thaw.
c. Add 600 L of Buffer SK to the tissue sample and continue to grind until the sample has
been homogenized.
d. Using a pipette, transfer the lysate into an RNase-free microcentrifuge tube (not
provided).
e. Spin lysate for 2 minutes to pellet any cell debris. Transfer the supernatant to another
RNase-free microcentrifuge tube. Note the volume of the supernatant/lysate.
f. Add an equal volume of 70% ethanol (provided by the user, 100 L of ethanol is added to
every 100 L of lysate). Vortex to mix. Proceed to Step 2.
Section 1B: Total RNA Purification from All Types of Lysate
Note: The remaining steps of the procedure for the purification of total RNA are the same from
this point forward for all the different types of lysate.
2. Binding RNA to Column
a. Assemble a column with one of the provided collection tubes
b. Apply up to 600 L of the lysate with the ethanol onto the column and centrifuge for 1
minute at ≥ 3,500 x g (~6,000 RPM).
Note: Ensure the entire lysate volume has passed through into the collection tube by
inspecting the column. If the entire lysate volume has not passed, spin for an
additional minute at 14,000 x g (~14,000 RPM).
c.
Retain the flowthrough for Protein Purification (Section 2). The flowthough
contains the proteins and should be stored on ice or at -20°C until the Protein
Purification protocol is carried out.
d. Depending on your lysate volume, repeat steps 2b and 2c if necessary. The
flowthroughs should be combined and retained in the same microcentrifuge tube.
e. Reassemble the spin column with a new collection tube.
11
3. RNA Wash
a. Apply 400 L of Wash Solution A to the column and centrifuge for 1 minute.
Note: Ensure the entire wash solution has passed through into the collection tube by
inspecting the column. If the entire wash volume has not passed, spin for an
additional minute.
b. Discard the flowthrough and reassemble the column with the collection tube.
c. Wash column a second time by adding another 400 L of Wash Solution A and
centrifuge for 1 minute.
d. Discard the flowthrough and reassemble the spin column with its collection tube.
e. Spin the column for 2 minutes in order to thoroughly dry the resin. Discard the collection
tube.
4. RNA Elution
a. Place the column into a fresh 1.7 mL microcentrifuge tube (provided by the user).
b. Add 50 L of Elution Solution A to the column.
c. Centrifuge for 1 minute at 14,000 x g (~14,000 RPM). Note the volume eluted from the
column. If the entire volume has not been eluted, spin the column at 14,000 x g (~14,000
RPM) for 1 additional minute.
Note: For maximum RNA recovery, it is recommended that a second elution be
performed into a separate microcentrifuge tube (Repeat Steps 4b and 4c). For
samples that are known to contain large amounts of RNA a second elution is
necessary to prevent RNA carryover in the gDNA elution. Please consult Table 1
nd
below to determine if a 2 elution is recommended.
Table 1. Recommendations for a 2
Starting Material
HeLa Cells
Bacteria
Yeast
Brain Tissue
Heart Tissue
Liver Tissue
Lung Tissue
Spleen Tissue
Arabidopsis Leaves
Blood
d.
nd
RNA Elution for Different Starting Materials
2
nd
Elution Recommended?
Optional
Yes
Yes
Optional
Optional
Yes
Yes
Yes
Yes
Optional
Retain the column for Genomic DNA Isolation and/or Protein Purification. Proceed
to Section 2 for DNA Purification. If genomic DNA isolation is not required, proceed
directly to Section 3 for Protein Purification.
5. Storage of RNA
The purified RNA sample may be stored at –20°C for a few days. It is recommended that
samples be placed at –70°C for long term storage.
12
Section 2: Genomic DNA Purification from All Types of Lysate
Note: The following steps of the procedure for the purification of genomic DNA are the same for
all the different types of lysate.
6. Genomic DNA Wash
a. Reassemble the column from Step 4d with a new collection tube. Apply 500 L of Wash
Solution EI to the column and centrifuge for 2 minutes.
b. Discard the flowthrough and reassemble the spin column with its collection tube.
c. Spin the column for 2 minutes in order to thoroughly dry the resin. Discard the collection
tube.
7. Genomic DNA Elution
a. Place the column into a fresh 1.7 mL microcentrifuge tube (provided by the user).
b. Add 100 L of Elution Buffer F to the column.
c. Centrifuge for 2 minutes at 200 x g (~2,000 RPM), followed by 1 minute at 14,000 x g
(~14,000 RPM). Note the volume eluted from the column. If the entire volume has not
been eluted, spin the column at 14,000 x g (~14,000 RPM) for 1 additional minute.
Note: For maximum DNA recovery, it is recommended that a second elution be
performed into a separate microcentrifuge tube (Repeat Steps 7b and 7c).
d.
Retain the column for Protein Purification. Proceed to Section 3 for Protein
Purification.
8. Storage of DNA
The purified DNA sample may be stored at 4°C for a few days. It is recommended that
samples be placed at ≤–20°C for long term storage.
Section 3. Procedure to Isolate Total Proteins from All Cell
Types
A. Total Protein Purification from All Cell Types
Notes Prior to Use
 At this point, the proteins that are present in the flowthrough from the RNA Binding Step
(Section 1B, Step 2c) can be processed by one of the following three options:
o Direct running on an SDS-PAGE gel with the provided loading dye for visual
analysis
o Column purification (recommended)
o Acetone precipitation
 Add 93 mg of DL-Dithiothreitol (DTT, not provided) to the Protein Loading Dye. The
Protein Loading Dye should be stored at -20°C after the addition of DTT. The label on
the bottle has a box that may be checked to indicate that DTT has been added
 For direct running on a gel, the provided Protein Loading Dye should be used instead of
regular SDS-PAGE Loading Buffer in order to prevent any precipitates from forming. Add
1 volume of the Protein Loading Dye to the sample and boil for 2 minutes before
loading.
 Column purification of the proteins is recommended. For column purification please
follow steps 1 to 4 below.
 For acetone precipitation, please refer to the supplementary protocol provided in the
Appendix below
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1. pH Adjustment of Lysate
a. Transfer 300 L of flowthrough from the RNA Binding Step (Section IB, Step 2c) to a
separate microcentrifuge tube.
Note: To purify the entire flowthrough, adjust the volume according to the note in
step b below.
b. Adjust volume to 600 L with molecular biology grade water.
Note: To purify the entire flowthrough, adjust the volume to 1.2 mL with molecular
biology grade water.
c. Add 24 L (or 48 L for the entire flowthrough) of Binding Buffer A. Mix
contents well.
2. Protein Binding
a. Apply up to 650 L of the pH-adjusted protein sample onto the column, and centrifuge for
2 minutes at 5,200 x g (~8,000 RPM). Inspect the column to ensure that the entire
sample has passed through into the collection tube. If necessary, spin for an additional 3
minutes.
b. Discard the flowthrough. Reassemble the spin column with its collection tube.
Note: You can save the flowthrough in a fresh tube for assessing your protein’s binding
efficiency.
c. Depending on your sample volume, repeat steps 2a and 2b until the entire protein
sample has been loaded onto the column.
3. Column Wash
a. Apply 500 L of Wash Solution C to the column and centrifuge for 2 minutes at 5,200 x
g (8000 RPM).
b. Discard the flowthrough and reassemble the spin column with its collection tube.
c. Inspect the column to ensure that the liquid has passed through into the collection tube.
There should be no liquid in the column. If necessary, spin for an additional minute to
dry.
4. Protein Elution and pH Adjustment
The supplied Elution Buffer C consists of 10 mM sodium phosphate pH 12.5.
a. Add 9.3 L of Protein Neutralizer to a fresh 1.7 mL microcentrifuge tube (provided by
the user).
b. Transfer the spin column from the Column Wash procedure into the Elution Tube.
c. Apply 100 L of the Elution Buffer C to the column and centrifuge for 2 minutes at
5,200 x g (8000 RPM) to elute bound proteins.
Note: Approximately 95% of bound protein is recovered in the first elution. If desired, a
second elution using 50 L of Elution Buffer C may be carried out. This should be collected
into a different tube (to which 4.6 L of Protein Neutralizer is pre-added) to prevent dilution
of the first elution.
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Appendix: Acetone Precipitation Procedure for Proteins
a. Add 4 volumes of ice-cold acetone to the flowthrough from the RNA Binding Step
(Section 1B, Step 2c).
b. Incubate for 15 minutes on ice or at -20°C.
c. Centrifuge for 10 minutes at 14,000 x g (~12,000 RPM). Discard the supernatant and
allow the pellet to air-dry.
Note: At this point the pellet can be washed with 100 L of ice cold ethanol and again airdried.
d. Resuspend the pellet in the buffer of your choice that is suited to your downstream
application.
15
Troubleshooting Guide
Problem
Poor RNA
Recovery
Clogged
Column
Possible Cause
Solution and Explanation
Incomplete lysis of
cells or tissue
Ensure that the appropriate amount of Buffer SK was
used for the amount of cells or tissue.
Column has
become clogged
Do not exceed the recommended amounts of starting
materials. The amount of starting material may need to
be decreased if the column shows clogging below the
recommended levels. See also “Clogged Column”
below.
An alternative
elution solution was
used
It is recommended that the RNA Elution Buffer supplied
with this kit be used for maximum RNA recovery.
Ethanol was not
added to the lysate
Ensure that the appropriate amount of ethanol is added
to the lysate before binding to the column.
Ethanol was not
added to the Wash
Solution A
Ensure that 90 mL of 96 - 100% ethanol is added to the
supplied Wash Solution prior to use.
Low RNA content
in cells or tissues
used
Different tissues and cells have different RNA contents,
and thus the expected yield of RNA will vary greatly from
these different sources. Please check literature to
determine the expected RNA content of your starting
material.
Cell Culture: Cell
monolayer was not
washed with PBS
Ensure that the cell monolayer is washed with the
appropriate amount of PBS in order to remove residual
media from cells.
Yeast: Lyticase
was not added to
the Resuspension
Buffer
Ensure that the appropriate amount of lyticase is added
when making the Resuspension Buffer.
Bacteria and Yeast:
All traces of media
not removed
Ensure that all media is removed prior to the addition of
the Buffer SK through aspiration.
Insufficient
solubilization of
cells or tissues
Ensure that the appropriate amount of lysis buffer was
used for the amount of cells or tissue.
Maximum number
of cells or amount
of tissue exceeds
kit specifications
Refer to specifications to determine if amount of starting
material falls within kit specifications.
Centrifuge
temperature too
low
Ensure that the centrifuge remains at room temperature
throughout the procedure. Temperatures below 20°C
may cause precipitates to form that can cause the
columns to clog.
16
Problem
RNA is
Degraded
Possible Cause
RNase
contamination
RNases may be introduced during the use of the kit.
Ensure proper procedures are followed when working
with RNA. Please refer to “Working with RNA” at the
beginning of this user guide.
Procedure not
performed quickly
enough
In order to maintain the integrity of the RNA, it is
important that the procedure be performed quickly. This
is especially important for the Cell Lysate Preparation
Step in the Animal Tissue protocol, since the RNA in
animal tissues is not protected after harvesting until it is
disrupted and homogenized.
Improper storage of
the purified RNA
For short term storage RNA samples may be stored at
–20°C for a few days. It is recommended that samples
be stored at –70°C for longer term storage.
Frozen tissues or
cell pellets were
allowed to thaw
prior to RNA
isolation
RNA does not
perform well
in
downstream
applications
Solution and Explanation
Do not allow frozen tissues to thaw prior to grinding with
the mortar and pestle in order to ensure that the integrity
of the RNA is not compromised.
Lysozyme or
lyticase used may
not be RNAse-free
Ensure that the lysozyme and lyticase being used with
this kit are RNase-free, in order to prevent possible
problems with RNA degradation.
Tissue samples
were frozen
improperly
Samples should be flash-frozen in liquid nitrogen and
transferred immediately to a -70°C freezer for long-term
storage.
RNA was not
washed twice with
the provided Wash
Solution A
Traces of salt from the binding step may remain in the
sample if the column is not washed twice with Wash
Solution A. Salt may interfere with downstream
applications, and thus must be washed from the column.
Ethanol carryover
Ensure that the dry spin under the RNA Wash procedure
is performed, in order to remove traces of ethanol prior to
elution. Ethanol is known to interfere with many
downstream applications.
Incomplete lysis of
cells or tissue
Ensure that the appropriate amount of Buffer SK was
used for the amount of cells or tissue. Incubate the
Buffer SK for an extra 5 minutes to assist in lysis.
The DNA elution is
incomplete
Ensure that centrifugation at 14,000 x g for 1 minute is
performed following the 2 minute centrifugation at 200
x g. Also, ensure that the entire volume of Elution
Buffer F passed through and is eluted from the column.
Yield of
Genomic
DNA is Low
17
Problem
Possible Cause
Solution and Explanation
Sample is old
Ensure that the sample is not too old, as old samples
often yield only degraded DNA
Sample repeatedly
frozen and thawed
Samples should not be repeatedly frozen and thawed, as
this tends to increase the likelihood of isolating degraded
DNA.
Number of cells or
amount of tissue
used is close to the
maximum
recommended
amount
When the maximum recommended amount of cells or
tissues is used for the procedure, some crosscontamination of RNA in the genomic DNA fraction may
be observed. Reduce the input amount of cells or tissues
below the maximum recommendation in order to avoid
this problem. Recommended amounts of starting
material to use for optimal kit performance are given in
each section of the protocol.
High levels of RNA
in the starting
material
Some sample types, such as bacteria, are known to
contain high levels of RNA. It is recommended that a
second RNA elution be performed in these cases in order
to remove the large amounts of RNA from the column.
An RNase treatment could also be performed in the
gDNA in order to remove the RNA that is present.
Incorrect pH
adjustment of
sample.
Ensure that the pH of the starting protein sample is
adjusted to pH 3.5 or lower after the Binding Buffer A
has been added and prior to binding to the column. If
necessary, add additional Binding Buffer A.
Low protein content
in the starting
materials
Run a 20 L fraction from the flowthrough (after RNA
binding) on a SDS-PAGE gel to estimate the amount of
protein present in the sample. In addition, use the entire
flowthrough in protein purification procedure
Eluted protein
solution was not
neutralized.
Add 9.3 µL of Protein Neutralizer to each 100 µL of
eluted protein in order to adjust the pH to neutral. Some
proteins are sensitive to high pH, such as the elution
buffer at pH 12.5
Eluted protein
was not
neutralized
quickly enough.
If eluted proteins are not used immediately, degradation
will occur. We strongly suggest adding Protein
Neutralizer in order to lower the pH.
Genomic DNA
is Sheared
Contamination
of Genomic
DNA with
RNA
Poor Protein
Recovery
Proteins are
Degraded
18
Related Products
1kb RNA Ladder
UltraRanger 1kb DNA Ladder
RNA/Protein Purification Kit
Product #
15003
12100
24100
Technical Support
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Technical support can also be obtained from our website (www.norgenbiotek.com) or through
email at techsupport@norgenbiotek.com.
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Phone: (905) 227-8848
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