Multiple Mini-Format 2-D Electrophoresis using SE 600 Standard

Multiple Mini-Format 2-D Electrophoresis using SE 600 Standard
application note
2-D Electrophoresis
Multiple Mini-Format 2-D Electrophoresis
SE 600 Standard Vertical Unit
Keywords: 2-D Electrophoresis, 7 cm IPG Drystrip
Two-dimensional (2-D) electrophoresis is a powerful and
widely used method for the analysis of complex protein
mixtures. With the recent improvements to and uses for
this technique, the need for higher throughput has
increased. This application note describes a method for
performing the second-dimension separation for two to eight
mini-format 2-D gels simultaneously in a single vertical
electrophoresis unit. The procedure yields high-quality
separations, using 7 cm Immobiline™ DryStrip IPG gel
strips and the SE 600 Dual Vertical Gel unit. This
arrangement simplifies and improves differential comparisons. Using a third glass plate and additional spacers for
the SE 600, a “club sandwich” assembly can be formed
which produces two identical gels in a single gel space.
Thus eight second-dimension separations can be performed
on one unit: two IPG strips per gel, two gels per sandwich,
and two sandwiches per unit. At approximately three hours
per run, 16 mini-format 2-D separations can be completed
in a normal workday on a single SE 600 system.
Casting gels
1.1 Assemble the SE 600 vertical slab gel unit in the dual
gel casting stand using 18 × 8 cm glass plates (80-6186-59).
For running eight 2-D mini-gels simultaneously, use the
glass plate club sandwich dividers (80-6186-78). The
divider plates allow two gels to be cast in a single sandwich.
Be sure to use the 8 cm × 1 cm × 1 mm (80-6443-09)
or 8 cm × 1 cm × 1.5 mm (80-6443-28) spacers.
1.2 Cast the gels following the instructions provided in the
SE 600 Series User Manual (80-6353-79) or 2-D Electrophoresis Using Immobilized pH Gradients: Principles
& Methods (80-6429-60, “2-D Principles handbook”).
Appropriate volumes of acrylamide are listed in Table 1.
80-6445-94/Rev. B/9-99
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Fig 1 SE 600 and clamp assembly
Products used
SE 600 Dual Cooled Vertical Unit
Glass plates, 18 × 8 cm (2/pk)
Glass plate, club sandwich divider,
notched, 18 × 8 cm
Clamp assembly, 8 cm (2/pk)
Spacer, 1.0 mm, 1 cm wide, 8 cm long (2/pk)
Spacer, 1.5 mm, 1 cm wide, 8 cm long (2/pk)
EPS 601 Power Supply
Plastic ruler
MW markers, 2 512 –16 949 range
MW markers, 14 400 – 94 000 range
IEF Sample Application Pieces (200/pk)
PlusOne™ Reagents
Urea, 500 g
Tris, 500 g
SDS, 100 g
Glycerol (87%), 1 litre
Bromophenol blue
Glycine, 500 g
Agarose M, 10 g
Agarose NA, 10 g
Dithiothreitol (DTT), 1 g
Acrylamide IEF 40% solution, 1 000 ml
N,N’-methylenebisacrylamide, 25 g
Ammonium persulphate, 25 g
2-D Electrophoresis
Equilibrate the IPG strip
IPG strips are run and equilibrated for application to
the second dimension as described in the 2-D Principles
handbook. Soak strips for 15 min in equilibration solution (solution A) containing 1% (w/v) DTT followed by
15 min more in equilibration solution containing 2.5% (w/v)
iodoacetamide. Two 7-cm-long IPG strips can be equilibrated simultaneously in a 15 ml conical centrifuge tube
using 6 ml of equilibration solution.
Apply the equilibrated IPG strip
3.1 Place the IPG strip.
Dip the IPG strip in the SDS electrophoresis buffer (solution B) to lubricate it. Position the first IPG strip between
the plates on the surface of the second-dimension gel
with the plastic backing against one of the glass plates.
Be sure to place the strip as far as possible to one side
of the gel. With a thin plastic ruler (80-6223-83), gently
push the IPG strip down so its entire lower edge is in
contact with the top surface of the slab gel. Ensure that
no air bubbles are trapped between the IPG strip and the
slab gel surface or between the gel backing and the glass
plate. Repeat this procedure, placing the second strip
next to the first and leaving a space of approximately
1 cm between the strips.
3.2 Optional: Apply molecular weight marker proteins.
The markers are applied in 0.5% agarose (M or NA) to a
paper IEF sample application piece in a volume of 15 to
20 µl. For less volume cut the sample application piece
proportionally. Add 0.5% agarose to the appropriate
volume of marker solution and heat at 100 ºC for approximately 5 min. Place the IEF application piece on a glass
plate and pipette the marker solution onto it, then pick
up the application piece with forceps and apply to the
top surface of the gel in the space between the two IPG
strips. The markers should contain 200 to 1 000 ng of
each component for Coomassie staining and about 10 to
50 ng of each component for silver staining.
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3.3 Seal the IPG strip in place.
Embedding the IPG strips in agarose prevents them from
moving or floating in the electrophoresis buffer. Prepare
agarose sealing solution (solution C). Melt each aliquot
as needed in a 100 °C heat block (each gel will require
0.5 to 1 ml). It takes approximately 10 min to fully melt
the agarose. (Tip: An ideal time to prepare and melt the
agarose is during the IPG strip equilibration-step 2.) Allow
the agarose to cool to 40 to 50 °C and then slowly pipette
onto the top of the gel the amount required to seal the
IPG strip in place. Pipetting slowly avoids introducing
bubbles. Allow a minimum of 1 min for the agarose to
cool and solidify.
3.4 Finish assembling the electrophoresis unit (see the
SE 600 Series User Manual 80-6353-79) and add SDS
electrophoresis buffer (solution B). This method will
require a total of 5 litres of buffer (4.5 litres for the
anode and 0.5 litre for the cathode).
Electrophoresis conditions
Electrophoresis is performed at constant current in two
steps. Start at 15 mA/gel for an initial migration and
stacking period of 15 min, then increase to 30 mA/gel for
a period of approximately 3 h. Currents up to 50% higher
may be used during the second separation phase if only
two gels per unit are being run (no club sandwich dividers)
and the unit is being cooled with a thermostatic circulator.
Stop the electrophoresis when the dye front is approximately 1 mm from the bottom of the gel.
Cooling is optional; however, temperature control
improves gel-to-gel reproducibility, especially if the ambient temperature of the laboratory fluctuates significantly.
Do not cool SDS-containing gels below 15 ºC.
After electrophoresis remove gels from their cassettes in
preparation for staining or blotting. Notch or mark each gel
at the upper corner nearest the pointed end of the IPG strip
to identify the acidic end of the first-dimension separation.
2-D Electrophoresis
This multiple mini-format method produces high-quality
2-D separations (Fig 2) and allows for two to eight
mini-format 2-D gels to be run on a single SE 600 unit.
Differential comparisons are improved by this method by
minimizing gel-to-gel variations. In addition, this method
allows for increased throughput with minimal equipment.
At approximately three hours per second-dimension run,
16 mini-format 2-D separations can be run in a normal
workday on a single SE 600 system.
For more-detailed information and troubleshooting of 2-D
electrophoresis, see the 2-D Principles handbook.
Table 1. Volumes of Acrylamide Required for
Mini-Format 2-D Gels
Total Volume (ml)
Number of 16 × 8 cm Gels
1.5-mm-thick spacers
1-mm-thick spacers
Solutions required
A. SDS equilibration buffer1
(50 mM Tris-Cl pH 8.8, 6M urea, 30% glycerol, 2% SDS,
bromophenol blue, 200 ml)
Fig 2 Multiple Mini-Format 2-D Gel. E. coli extract (24 µg),
pH 3-10 NL first dimension; 1-mm thick 12.5% acrylamide
second dimension
1.5 M Tris-Cl, pH 8.8
(solution D)
50 mM
6.7 ml
Urea (FW 60.06)
72.02 g
Glycerol (87% v/v)
30% (v/v)
69 ml
SDS (FW 288.38)
2% (w/v)
Bromophenol blue
(a few grains)
Double-distilled H2O
to 200 ml
This is a stock solution. Prior to use, DTT or iodoacetamide is added. See section 2.
Store in 40 ml aliquots at –20 ºC.
B. SDS electrophoresis buffer1
(25 mM Tris, 192 mM glycine, 0.1% SDS, 5 litres)
Tris base (FW 121.1)
25 mM
15.1 g
Glycine (FW 75.07)
192 mM
72.1 g
SDS (FW 288.38)
0.1% (w/v)
5.0 g
Double distilled H2O
to 5 000 ml
Because you do not need to titrate this buffer to a specific pH, it can be made up
directly in large reagent bottles marked at 5 litres. 20 litres can be made up at a time.
Store at room temperature.
(continued on page 4)
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2-D Electrophoresis
Solutions required
C. Agarose sealing solution
SDS electrophoresis buffer
(solution B)
100 ml
Agarose (NA or M)
0.5 g
Bromophenol blue
a few grains
Add all ingredients into a 500 ml Erlenmeyer flask. Swirl to
disperse. Heat in a microwave oven on low until the agarose is
completely dissolved. Do not allow the solution to boil over.
Dispense 2 ml aliquots into screw-cap tubes and store at room
D. 1.5 M Tris-Cl, pH 8.8
Tris base (FW 121.1)
1.5 M
181.5 g
Double-distilled H2O
750 ml
HCl (FW 36.46)
adjust to pH 8.8
Double-distilled H2O
to 1 000 ml
Filter solution through a 0.45 µm filter. Store at 4 °C.
For more information, visit the Amersham Phamacia Biotech Website:
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All goods and services are sold subject to the terms and conditions of sale of the company within the Amersham
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© 1999 Amersham Biosciences UK Limited. All rights reserved.
Amersham Biosciences UK Limited Amersham Place Little Chalfont Buckinghamshire England HP7 9NA
Amersham Biosciences AB SE-751 84 Uppsala Sweden
Amersham Biosciences 800 Centennial Avenue PO Box 1327 Piscataway NJ 08855 USA
Amersham Biosciences Europe GmbH Munzinger Strasse 9 D-79111 Freiburg Germany
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