Bio-Rad Criterion TBE-Urea Precast Gels User Manual

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Criterion™ Precast Gels

Instruction Manual and Application Guide

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Bio-Rad Technical Support

For help and technical advice, please contact the Bio-Rad Technical Support department. In the United States, the Technical Support department is open Monday–Friday, 5:00 am–5:00 pm, Pacific Time.

Phone: 1-800-424-6723

Fax: 1-510-741-5802

Email: LSG_TechServ_US@bio-rad.com (for U.S. and international customers)

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Legal Notices

No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage or retrieval system, without permission in writing from Bio-Rad Laboratories.

Bio-Rad reserves the right to modify its products and services at any time. This user guide is subject to change without notice.

Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors, or for any damages resulting from the application or use of this information.

Brij and Tween are trademarks of ICI Americas, Inc. Coomassie is a trademark of BASF Aktiengesellschaft. Ficoll is a trademark of Amersham Pharmacia Biotech. StrepTactin is a trademark of Institut für Bioanalytik GmbH. 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. SYBR is a trademark of Invitrogen Corporation. SYPRO is a trademark of Molecular Probes, Inc. Bio-Rad is licensed to sell SYPRO products for research use only, under U.S. Patent 5,616,502. Triton is a trademark of Union Carbide.

Criterion™ TGX Stain-Free™ and Criterion Stain Free™ precast gels are covered by U.S. Patent No. 7,569,130.

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. patents 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.

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Contents

Chapter 1: Criterion™ Precast Gels................................................... 1

1.1 Introduction ................................................................... 1

1.2 Gel Formulations ............................................................... 2

1.3 Comb Configurations ........................................................... 2

1.4 Specifications ................................................................. 2

1.5 Storage Conditions ............................................................ 3

1.6 Important Notes ............................................................... 3

Chapter 2: Setup and Basic Operation ............................................... 4

2.1 Workflow Overview ............................................................. 4

2.2 Required Materials ............................................................. 5

2.3 Setting Up and Running Criterion Gels in the Criterion Cell ............................... 5

2.4 Removing the Gel .............................................................. 5

Chapter 3: SDS-PAGE............................................................. 7

3.1 Introduction ................................................................... 7

3.2 Criterion Gel Selection Guide for SDS-PAGE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3.2.1 Criterion™ TGX™ and Criterion™ TGX Stain-Free™ Gels .............................. 8

3.2.2 Criterion Tris-HCl and Criterion Stain Free™ Gels................................... 9

3.2.3 Criterion™ XT Bis-Tris Gels .................................................. 10

3.2.4 Criterion XT Tris-Acetate Gels ................................................ 11

3.3 SDS-PAGE Buffers ............................................................ 12

3.3.1 Running Buffers........................................................... 12

3.3.2 Sample Buffers ........................................................... 12

3.4 Sample Preparation............................................................ 12

3.5 Running Conditions ............................................................ 13

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Chapter 4: Native PAGE .......................................................... 14

4.1 Introduction .................................................................. 14

4.2 Criterion Gel Selection Guide for Native PAGE ....................................... 14

4.2.1 Criterion TGX and Criterion TGX Stain-Free Gels.................................. 14

4.2.2 Criterion Tris-HCl and Criterion Stain Free Gels ................................... 15

4.2.3 Criterion XT Tris-Acetate Gels ................................................ 15

4.3 Native PAGE Buffers ........................................................... 15

4.4 Sample Preparation............................................................ 16

4.5 Running Conditions ............................................................ 16

Chapter 5: Criterion Stain Free System .............................................. 17

5.1 Introduction .................................................................. 17

5.2 Criterion Stain Free Workflow .................................................... 18

5.3 Electrophoresis with Criterion TGX Stain-Free Gels .................................... 18

5.4 Using the Gel Doc™ EZ Imager .................................................. 18

Chapter 6: Peptide Analysis ....................................................... 19

6.1 Introduction .................................................................. 19

6.2 Criterion Tris-Tricine/Peptide Gels ................................................ 19

6.2.1 Gel Composition .......................................................... 19

6.2.2 Gel Selection Guide........................................................ 19

6.3 Tris-Tricine/Peptide Buffers ...................................................... 19

6.4 Sample Preparation............................................................ 20

6.5 Running Conditions ............................................................ 20

Chapter 7: Isoelectric Focusing (IEF)................................................ 21

7.1 Introduction .................................................................. 21

7.2 Criterion IEF Gels ............................................................. 21

7.2.1 Gel Composition .......................................................... 21

7.2.2 Gel Selection Guide........................................................ 21

7.3 IEF Buffers................................................................... 21

7.4 Sample Preparation............................................................ 22

7.5 Running Conditions ............................................................ 22

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Chapter 8: Protease Analysis by Zymogram PAGE .................................... 23

8.1 Introduction .................................................................. 23

8.2 Criterion Zymogram Gels........................................................ 23

8.2.1 Gel Composition .......................................................... 23

8.2.2 Gel Selection Guide........................................................ 23

8.3 Zymogram Buffers............................................................. 23

8.4 Sample Preparation............................................................ 24

8.5 Running Conditions ............................................................ 24

Chapter 9: Nondenaturing Nucleic Acid PAGE ........................................ 25

9.1 Introduction .................................................................. 25

9.2 Criterion TBE Gels............................................................. 25

9.2.1 Gel Composition .......................................................... 25

9.2.2 Gel Selection Guide........................................................ 25

9.3 Nondenaturing Nucleic Acid PAGE Buffers .......................................... 25

9.4 Sample Preparation............................................................ 26

9.5 Running Conditions ............................................................ 26

Chapter 10: Denaturing Nucleic Acid PAGE .......................................... 27

10.1 Introduction ................................................................. 27

10.2 Criterion TBE-Urea Gels ....................................................... 27

10.2.1 Gel Composition ......................................................... 27

10.2.2 Gel Selection Guide....................................................... 27

10.3 TBE-Urea Buffers ............................................................ 27

10.4 Sample Preparation........................................................... 27

10.5 Running Conditions ........................................................... 28

Chapter 11: 2-D Electrophoresis ................................................... 29

11.1 Introduction ................................................................. 29

11.2 Equilibration................................................................. 29

11.3 Agarose Overlay ............................................................. 29

11.4 Second-Dimension Electrophoresis............................................... 29

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Chapter 12: Detection............................................................ 30

12.1 SDS-PAGE and Native PAGE Detection ........................................... 30

12.2 Peptide Gel Staining .......................................................... 31

12.3 IEF Gel Staining.............................................................. 31

12.4 Zymogram Gel Staining........................................................ 32

12.5 TBE Gel Staining ............................................................ 32

12.6 TBE-Urea Gel Staining ....................................................... 32

Chapter 13: Blotting ............................................................. 33

13.1 Introduction ................................................................. 33

13.2 Transfer.................................................................... 33

13.2.1 Transfer Buffers .......................................................... 33

13.2.2 Wet Transfer Using the Criterion Blotter ....................................... 33

13.2.3 Transfer Using the Trans-Blot® Turbo™ System.................................. 34

13.2.4 Semi-Dry Transfer Using the Trans-Blot® SD Cell ................................ 36

13.3 Total Protein Blot Stains ....................................................... 36

13.4 Immunodetection ............................................................ 37

Chapter 14: Troubleshooting ...................................................... 38

Appendix A: Quick Start Guide .................................................... 40

Appendix B: Buffers ............................................................. 42

Appendix C: Related Literature .................................................... 45

Appendix D: Ordering Information .................................................. 46

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Criterion™ Precast Gels

1.1 Introduction

Criterion precast gels are an effective system for performing polyacrylamide gel electrophoresis (PAGE). These 13.3 x 8.7 cm gels are wider and longer than traditional mini format gels, and their innovative, easy-to-use design produces excellent resolution while accommodating more samples per gel. Designed for use with the Criterion family of vertical electrophoresis cells, which includes the Criterion (2-gel capacity) and Criterion™ Dodeca™ (12-gel capacity) cells, Criterion precast gels allow separation of more samples than mini format gels and provide signiﬁcant cost and time savings. Some of the unique features provided are:

Integrated buffer chamber that eliminates buffer leaks

Capacity for up to 26 samples per gel

Compatibility with multichannel pipets (12+2 and 26-well)

Outlined and numbered wells that simplify sample loading and identiﬁcation

Patented1 J-foot design that eliminates post-run gel processing steps and improves gel

drying and blotting results

Criterion™ TGX Stain-Free™ formulations for rapid gel imaging without staining

Integrated buffer chamber

Gel type, expiration date, and catalog and lot numbers

Outlined and numbered wells

U.S. patent 6,093,301.

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Criterion Precast Gels

1.2 Gel Formulations

Criterion precast gels are available in a range of formulations for virtually every electrophoresis application (Table 1.1). All Criterion gels are composed of polyacrylamide with a bisacrylamide crosslinker, and they are available in a selection of single percentages and gradients.

Table 1.1. Criterion precast gel formulations.

Application Gel Formulation Sample Buffer Running Buffer

SDS-PAGE Criterion Tris-HCl Laemmli Tris/glycine/SDS Criterion Stain Free Criterion TGX Criterion TGX Stain-Free Criterion™ XT Bis-Tris XT XT MOPS or XT MES Criterion XT Tris-acetate XT XT Tricine

Native PAGE Criterion Tris-HCl Native Tris/glycine Criterion Stain Free Criterion TGX Criterion TGX Stain-Free Criterion XT Tris-acetate

Peptide analysis Criterion Tris-Tricine Tricine Tris/Tricine/SDS

Isoelectric focusing (IEF) Criterion IEF IEF Anode and cathode buffers

Protease detection Criterion zymogram Zymogram Tris/glycine/SDS

dsDNA separation Criterion TBE Nucleic acid Tris/boric acid/EDTA (TBE)

ssDNA and RNA separation Criterion TBE-urea TBE-urea TBE

™

1.3 Comb Configurations

Comb Type Well Volume

12+2 we ll1 45 μl with two 15 μl reference wells

18-well 30 μl

26-well1 15 μl

Prep+2 well 800 μl with two 15 μl reference wells

IPG+1 well 11 cm ReadyStrip™ IPG strip (450 μl) with one 15 μl reference well

1.4 Specifications

Gel material Polyacrylamide

Gel dimensions (W x L) 13.3 x 8.7 cm

Gel thickness 1.0 mm

Resolving gel height 6.5 cm

Cassette dimensions (W x L) 15.0 x 10.6 cm

Cassette material Styrene copolymer

Comb material Polycarbonate

Running buffer 460 ml (per gel)

Multichannel pipet compatible.

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Instruction Manual and Application Guide

1.5 Storage Conditions

Table 1.2. Storage conditions for Criterion precast gels. Store gels flat. Shelf life is from date of manufacture; expiration dates

are printed on the cassettes.

Storage Temperature Gel Formulation Shelf Life

Ambient Criterion XT Bis-Tris 12 months

2–8°C Criterion TGX 12 months Criterion TGX Stain-Free 12 months Criterion Tris-HCl 12 weeks Criterion Stain-Free 12 weeks Criterion XT Tris-acetate 8 months Criterion Tris-Tricine 12 weeks Criterion IEF 24 weeks Criterion zymogram 8 weeks Criterion TBE 12 weeks Criterion TBE-urea 8 weeks

1.6 Important Notes

Use each Criterion precast gel as soon as possible after removing it from the storage pouch.

Improper storage of Criterion precast gels can produce numerous artifacts.

Store gels ﬂat

Avoid prolonged storage at temperatures above those recommended

Do not freeze gels

If you suspect your gels have been stored improperly, discard them

Do not run more than one gel type in the same apparatus at the same time. Different gel percentages and formulations have different conductivities and different run times.

Use unstained standards with Criterion TGX Stain-Free and Criterion Stain Free gels, as some

™

prestained standards are not detected by the Gel Doc

EZ imager. To monitor electrophoresis, use

10 µl of a 1:1 mixture of Precision Plus Protein™ unstained and prestained standards.

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Setup and Basic

Operation

2.1 Workflow Overview

Prepare sample and running buffers

Assemble Electrophoresis Cell

Prepare and Load Samples

Prepare Buffers

Prepare Gels and

Dilute in sample buffer

Perform Electrophoresis

SDS-PAGE (Chapter 3)

Native PAGE (Chapter 4)

Peptide Analysis (Chapter 6)

Isoelectric Focusing (Chapter 7)

Protease Analysis (Chapter 8)

Nondenaturing Nucleic Acid PAGE (Chapter 9)

Denaturing Nucleic Acid PAGE (Chapter 10)

2-D Electrophoresis (Chapter 11)

Analyze the Separation

Blot the Gels (Optional)

(Chapter 12)

(Chapter 13)

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Instruction Manual and Application Guide

2.2 Required Materials

Criterion™ precast gels

Criterion or Criterion™ Dodeca™cell

PowerPac™ Basic or PowerPac HC power supply (or equivalent)

Sample buffer

Running buffer (460 ml per gel)

2.3 Setting Up and Running Criterion Gels in the Criterion Cell

1. Each Criterion gel is packaged in a plastic storage tray. Remove the cover of the tray by lifting the corner tab and pulling it diagonally across the package. Remove the gel from the package.

2. Remove the comb and rinse the wells with deionized water (diH2O) or running buffer.

3. Remove the tape from the bottom of the cassette by pulling the tab across the gel.

4. Insert the cassette into one of the slots in the Criterion cell tank so that the integrated upper buffer chamber faces the center of the cell (A).

5. Fill each integrated upper buffer chamber with 60 ml running buffer.

6. Fill each half of the lower buffer tank with 400 ml running buffer to the marked ﬁll line.

Integrated upper buffer chamber

7. Load samples using a syringe or a pipet with gel-loading tips.

Optional: place a sample loading guide on the

outer edge of the cassette to help align pipet tips with the wells (this is particularly useful when using multichannel pipets).

8. Place the lid on the tank, aligning the color-coded banana plugs with corresponding jacks on the lid. See Chapters 3–10 for power supply settings.

2.4 Removing the Gel

1. After electrophoresis is complete, turn off the power supply and disconnect the electrical leads.

2. Remove the lid from the tank and remove the gel(s) from the cell. Pour off and discard the upper running buffer.

3. Invert the cassette and place the integral buffer chamber over the cassette-opening tool built into the Criterion cell lid (B).

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Criterion Precast Gels

4. Press down ﬁrmly to break the seals on both sides of the cassette. The cassette splits open approximately ¹/3 of the way. Alternatively, open the gel cassette by sliding the tapered back of the comb into the slits on either side of the cassette.

5. Pull the two halves of the cassette apart from the top to completely expose the gel (C).

6. Remove the gel by either ﬂoating the gel into a ﬁxing or staining solution or by carefully lifting the bottom edge of the gel from the cassette.

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SDS-PAGE

3.1 Introduction

Criterion™ precast gels provide versatile systems for the separation of proteins by either molecular weight (SDS-PAGE) or mass-to-charge ratio (native PAGE). (See Chapter 4 for native PAGE applications and protocols.) This versatility is possible because Criterion gels are made without SDS, allowing the sample buffer and running buffer to determine the separation mechanism.

SDS-PAGE relies on a discontinuous buffer system. Two ions differing in electrophoretic mobility form a moving boundary when voltage is applied. Proteins have an intermediate mobility that causes them to concentrate, or stack, into a narrow zone at the beginning of electrophoresis. As that zone moves through the gel, the sieving effect of the polyacrylamide gel matrix causes proteins of different molecular weights to move at different rates. This stacking effect is responsible for the high resolving power of SDS-PAGE: the sample is loaded in a relatively broad zone, and the moving boundary concentrates the proteins into sharp bands prior to separation.

Protein samples for SDS-PAGE are prepared using SDS and usually a thiol reducing agent such as β-mercaptoethanol or dithiothreitol (DTT). SDS forms complexes with proteins, giving them a rodlike shape and similar mass-to-charge ratio. The reducing agent disrupts disulﬁde bonds between and within proteins, allowing complete denaturation and dissociation. Heat treatment in the presence of SDS and reducing agent effectively eliminates the effects of native charge and higher order structure on electrophoretic mobility, so the migration distance depends primarily on molecular weight.

Molecular weight is estimated by plotting the logarithm of protein molecular weight vs. the relative mobility (R or by using the point-to-point semilog interpolation method in Quantity One® or Image Lab™ software. Refer to bulletins 3133 and 3144 for more information.

) of the protein (Rf = distance migrated by the protein/distance migrated by the dye front)

3.2 Criterion Gel Selection Guide for SDS-PAGE

A number of Criterion gel types are available for SDS-PAGE (Table 3.1) in both single and gradient polyacrylamide percentages. Use the protein migration charts and tables to select the gel type that offers optimum resolution of your sample:

Use single-percentage gels to separate bands of similar molecular weight. Optimum

separation occurs in the lower half of the gel, so use a percentage in which the protein migrates to the lower half of the gel

Use gradient gels to separate samples containing a broad range of molecular weights.

Gradient gels allow resolution of both high and low molecular weight bands on the same gel. Larger pore sizes at the top of the gel permit resolution of larger molecules, and smaller pore sizes toward the bottom of the gel restrict excessive separation of small molecules

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Criterion Precast Gels

Table 3.1. Criterion precast gels for SDS-PAGE.

Gel Formulation Gels Description

TGX (Laemmli-like) Criterion™ TGX™ Laemmli-like, extended shelf life gels

Criterion™ TGX Stain-Free™ Laemmli-like, extended shelf life gels with trihalo compounds for rapid ﬂuorescence detection

Tris-HCl (Laemmli) Criterion Tris-HCl Tris-HCl Laemmli gels

Criterion Stain Free™ Tris-HCl Laemmli gels with trihalo compounds for rapid ﬂuorescence detection

Bis-Tris Criterion™ XT Bis-Tris Based on a Bis-Tris HCl buffer system (pH 6.4); use these gels with Criterion XT MES buffer for optimum resolution of small proteins

Bis-Tris Criterion XT Bis-Tris Based on a Bis-Tris HCl buffer system (pH 6.4); use these gels with Criterion XT MOPS buffer for optimum resolution of midsized proteins

Tris-acetate Criterion XT Tris-acetate Based on a Tris-acetate buffer system (pH 7.0)

3.2.1 Criterion TGX and Criterion TGX Stain-Free Gels

Criterion TGX (Tris-Glycine eXtended shelf life) gels are Laemmli-like gels with a proprietary modiﬁcation that extends their shelf life to 12 months and enhances separation characteristics relative to conventional gel types. The TGX formulation yields Laemmli-like separation patterns with short run times and exceptionally straight lanes and sharp bands. TGX gels offer excellent staining quality, greater transfer efﬁciency, and molecular weight estimation without the need for special, expensive buffers.

These gels are run using standard Laemmli sample buffer and Tris/glycine/SDS running buffer. Two types of TGX formulations are available:

Criterion TGX — Laemmli-like, extended shelf life gels

Criterion TGX Stain-Free — Laemmli-like, extended shelf life gels with trihalo compounds

that allow rapid ﬂuorescent detection of proteins with the Criterion Stain Free system, eliminating staining and destaining steps for faster results (see Chapter 5 for more details)

Gel Composition

Crosslinker 2.6% C

Stacking gel 4% T, 2.6% C

Shelf life ~12 months at 2–8°C; expiration date is printed on each cassette

Gel Percentage Optimum Separation Range

7.5% 40–200 kD

10% 30–150 kD

12% 20 –120 kD

18% 10–50 kD

4–15% 20–250 kD

4–20% 10–200 kD

8–16% 20 –120 kD

10–20% 10–100 kD

Any kD™ 1 10–200 kD

Any kD is a unique single-percentage formulation that provides a broad separation range and short running time.

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Instruction Manual and Application Guide

3.2.2 Criterion Tris-HCl and Criterion Stain Free Gels

These Tris-HCl, Laemmli gels use discontinuous glycinate and chloride ion fronts to form moving boundaries to stack and then separate denatured proteins by size. They are run using standard Laemmli sample buffer and Tris/glycine/SDS running buffer.

Criterion Tris-HCl — Tris-HCl formulation that offer a shelf life of 12 weeks

Criterion Stain Free — Tris-HCl gels with unique trihalo compounds that allow rapid

ﬂuorescent detection of proteins with the Criterion Stain Free system, eliminating staining and destaining steps for faster results (see Chapter 5 for more details)

Gel Composition

Gel buffer 0.375 M Tris-HCl, pH 8.6

Crosslinker 2.6% C

Stacking gel 4% T, 2.6% C

Storage buffer 0.375 M Tris-HCl, pH 8.6

Shelf life ~12 weeks at 2–8°C; expiration date is printed on each cassette

Gel Percentage Optimum Separation Range

5 % 100–250 kD

7.5% 40–200 kD

10% 30–150 kD

12.5% 20 –12 0 kD

15% 10–100 kD

18% 10–50 kD

4–15% 20–250 kD

4–20% 10–200 kD

8–16% 20–120 k D

10–20% 10–100 kD

10.5–14% 25–200 kD

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Criterion Precast Gels

Migration charts for protein standards on Criterion Tris-HCl, Criterion TGX, and TGX Stain-Free gels.

3.2.3 Criterion XT Bis-Tris Gels

Criterion XT Bis-Tris gels are based on a Bis-Tris HCl buffer system (pH 6.4) that uses discontinuous chloride and MES or MOPS ion fronts to form moving boundaries that stack and separate denatured proteins by size. This chemistry of XT Bis-Tris gels allows maximum stability and consistent results with a shelf life of at least 12 months.

Running XT Bis-Tris gels with either XT MES or XT MOPS denaturing running buffer produces different migration patterns. A combination of these two running buffers and three XT Bis-Tris gels can generate up to six different migration patterns for small to midsize proteins.

Gel Composition

Gel buffer Bis-Tris HCl, pH 6.4

Crosslinker 5% C

Stacking gel 4% T, 5% C

Storage buffer Bis-Tris HCl, pH 6.4

Shelf life 12 months at ambient temperature; expiration date is printed on each cassette

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Instruction Manual and Application Guide

Gel Percentage Optimum Separation Range XT MES Buffer XT MOPS Buffer

10% 2.5–200 kD 14–220 kD

12% 1–30 kD 6–66 kD

4–12% 2.5–200 kD 10–300 kD

Migration charts for protein standards on Criterion XT Bis-Tris gels.

3.2.4 Criterion XT Tris-Acetate Gels

Criterion XT Tris-acetate gels are based on a Tris-acetate buffer system (pH 7.0). It uses discontinuous acetate and Tricine ion fronts to form moving boundaries that stack and separate large denatured proteins by molecular weight.

Gel Composition

Gel buffer Tris-acetate, pH 7.0

Crosslinker 3.8% C

Stacking gel 4% T, 3.8% C

Storage buffer Tris-acetate, pH 7.0

Shelf life 8 months at 2–8°C; expiration date is printed on each cassette

Gel Percentage Optimum Separation range

7% 36–200 kD

3–8% 40–400 kD

Migration charts for protein standards on Criterion XT Tris-Acetate gels.

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Criterion Precast Gels

3.3 SDS-PAGE Buffers

Table 3.2. Recommended Criterion precast gels and buffers for SDS-PAGE.

Gel Type Sample Buffer Running Buffer

Criterion TGX Laemmli (catalog #161-0737) Tris/glycine/SDS Criterion TGX Stain-Free Optional: 2-mercaptoethanol (catalog #161-0732) Criterion Tris-HCl (catalog #161-0710) or DTT Criterion Stain Free (catalog #161-0611)

Criterion XT Bis-Tris XT sample buffer (catalog #161-0791) XT MES (catalog #161-0789) Optional: XT reducing agent XT MOPS (catalog #161-0788) (catalog #161-0792)

Criterion XT Tris-acetate XT Tricine (catalog #161-0790)

3.3.1 Running Buffers

See Appendix B for buffer formulations. Do not adjust pH.

Tris/glycine/SDS (1x) 25 mM Tris, 192 mM glycine, 0.1% SDS (pH 8.3) Dilute 100 ml 10x stock (catalog #161-0732) with 900 ml diH2O

XT MES (pH 6.4) Dilute 50 ml 20x stock (catalog #161-0789) with 950 ml diH2O

XT MOPS (pH 6.9) Dilute 50 ml 20x stock (catalog #161-0788) with 950 ml diH2O

XT Tricine (pH 8.2) Dilute 50 ml 20x stock (catalog #161-0790) with 950 ml diH2O

3.3.2 Sample Buffers

Laemmli 62.5 mM Tris-HCl, pH 6.8, 2% SDS, 25% glycerol, 0.01% (catalog #161-0737) bromophenol blue, 5% β-mercaptoethanol or 100 mM DTT (added fresh)

XT Use XT sample buffer (catalog #161-0791) and XT reducing agent (catalog #161-0792)

3.4 Sample Preparation

1. Determine the appropriate concentration of sample to load (depends on the load volume and the detection method used; see Chapter 12 for approximate stain sensitivities).

2. Dilute the sample with at least an equivalent volume of sample buffer with added reducing agent. For nonreducing conditions, omit the reducing agent.

TGX and Tris-HCl Gels XT Gels (Bis-Tris and Tris-Acetate)

4.75 μl Laemmli sample buffer 5 μl XT sample buffer

0.25 μl β-mercaptoethanol 1 μl XT reducing agent

5 μl sample 1–14 μl sample

10 μl total volume Make up to 20 μl total volume with diH2O

3. Heat the diluted sample at 90–95°C for 5 min, or at 70°C for 10 min.

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Instruction Manual and Application Guide

3.5 Running Conditions

Run conditions and times are approximate. Conditions may vary depending on water and buffer conductivity, which vary from one lab setting to the next. Multiply current by the number of gels run.

Table 3.3. Running conditions for SDS-PAGE with Criterion gels in the Criterion cell. Do not run different gel formulations at the same time.

TGX Tris-HCl Bis-Tris Tris-Acetate

Running buffer Tris/glycine/SDS Tris/glycine/SDS XT MOPS XT MES XT Tricine

Standard Conditions

Power conditions 200 V constant 200 V constant 200 V constant 200 V constant 150 V constant

Expected current (per gel)

Initial 55–80 mA 90–120 mA 165–175 mA 185–200 mA 170–180 mA

Final 33– 43 mA 35–55 mA 60–70 mA 90–110 mA 85–95 mA

Run time 42–45 min 50–55 min 60 min 45 min 65 min

High Voltage (Rapid) Conditions

Power conditions 300 V constant — — — —

Expected current (per gel)

Initial 89–135 mA — — — —

Final 66–99 mA — — — —

Run time 20–26 min — — — —

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Native PAGE

4.1 Introduction

In native PAGE, proteins are prepared in nonreducing, nondenaturing sample buffer, which maintains native structure and mass-to-charge ratios. Separation is also performed in the absence of SDS and reducing agents. Though native PAGE uses the same moving boundary described for SDS-PAGE (see Section 3.1), protein mobility depends on a number of factors besides molecular weight, including the shape and charge of the protein. Protein-protein interactions may be retained during native PAGE, so some proteins may separate as multisubunit complexes. Consequently, native PAGE is not suitable for molecular weight determination.

The nonreducing and nondenaturing environment of native PAGE allows protein separation with retention of biological activity. Because native structure is retained, native PAGE can allow resolution of proteins with the same molecular weight.

4.2 Criterion™ Gel Selection Guide for Native PAGE

Table 4.1. Criterion precast gels for SDS-PAGE.

Gel Formulation Gels Description

Laemmli-like Criterion™ TGX™ Laemmli-like, extended shelf life gels

Criterion™ TGX Stain-Free™ Laemmli-like, extended shelf life gels with trihalo compounds for rapid ﬂuorescence detection

Tris-HCl (Laemmli) Criterion Tris-HCl Tris-HCl Laemmli gels

Criterion Stain Free™ Tris-HCl Laemmli gels with trihalo compounds for rapid ﬂuorescence detection

Tris-acetate Criterion™ XT Tris-acetate Based on a Tris-acetate buffer system (pH 7.0)

4.2.1 Criterion TGX and Criterion TGX Stain-Free Gels

Criterion TGX (Tris-Glycine eXtended shelf life) gels are Tris-HCl, Laemmli-like gels with a proprietary modiﬁcation that extends their shelf life to 12 months and enhances separation characteristics relative to conventional gel types. The TGX formulation yields Laemmli-like separation patterns with exceptionally straight lanes and sharp bands and has excellent staining quality and transfer efﬁciency.

These gels are run using native sample buffer and Tris/glycine running buffer.

Two types of TGX formulations are available:

Criterion TGX — Laemmli-like gels with the TGX formulation

Criterion TGX Stain-Free — Laemmli-like, extended shelf life gels that include unique trihalo

compounds that allow rapid ﬂuorescent detection of proteins with the Criterion Stain Free system, eliminating staining and destaining steps for faster results (see Chapter 5 for more details)

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Page 21

Instruction Manual and Application Guide

Gel Composition

Crosslinker 2.6% C

Stacking gel 4% T, 2.6% C

Shelf life ~12 months at 2–8°C; expiration date is printed on each cassette

4.2.2 Criterion Tris-HCl and Criterion Stain Free Gels

These Tris-HCl Laemmli gels are run using native sample buffer and Tris/glycine running buffer.

Criterion Tris-HCl — Tris-HCl, Laemmli-like formulation that offer a shelf life of 12 weeks

Criterion Stain Free — Tris-HCl, Laemmli-like gels with unique trihalo compounds that allow

rapid uorescent detection of proteins with the Criterion Stain Free system, eliminating

staining and destaining steps for faster results (see Chapter 5 for more details)

Gel Composition

Gel buffer 0.375 M Tris-HCl, pH 8.6

Crosslinker 2.6% C

Stacking gel 4% T, 2.6% C

Storage buffer 0.375 M Tris-HCl, pH 8.6

Shelf life ~12 weeks at 2–8°C; expiration date is printed on each cassette

4.2.3 Criterion XT Tris-Acetate Gels

Criterion XT Tris-acetate gels can also be used to separate proteins by their charge-to-mass ratio (under native PAGE conditions). Separation by native PAGE with XT Tris-acetate gels uses discontinuous acetate and Tricine ion fronts to form moving boundaries to stack and separate proteins by both size

and charge.

Gel Composition

Gel buffer Tris-acetate, pH 7.0

Crosslinker 3.8% C

Stacking gel 4% T, 3.8% C

Storage buffer Tris-acetate, pH 7.0

Shelf life 8 months at 2–8°C; expiration

date is printed on each cassette

4.3 Native PAGE Buffers

See Appendix B for buffer formulations. Do not adjust pH unless instructed to do so.

Running buffer (1x) 25 mM Tris, 192 mM glycine Dilute 100 ml 10x stock (catalog #161-0734) with 900 ml diH2O

Sample buffer 62.5 mM Tris-HCl, pH 6.8, 25% glycerol, 0.01% bromophenol blue (catalog #161-0738)

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Criterion Precast Gels

4.4 Sample Preparation

In the absence of SDS, the net charge of a polypeptide is determined by its amino acid composition and the pH of the sample buffer. Only polypeptides with a net negative charge migrate into Criterion gels under native conditions. Most polypeptides have an acidic or slightly basic pI (~3–8). These proteins can be separated using the following standard protocol:

1. Determine the protein concentration and load volume of your sample based on the detection method used (see Chapter 12 for approximate stain sensitivities).

2. Dilute the sample in twice the volume of native sample buffer (DO NOT HEAT SAMPLES).

For example, combine: 5 μl sample

10 μl native sample buffer (catalog #161-0738)

15 μl total volume

Strongly basic proteins (pl >8.5) have a net positive charge and will not enter a Criterion gel under native conditions. To allow polypeptides with a net positive charge to migrate into a native Criterion gel, change the polarity of the electrodes by reversing the color-coded jacks when connecting to the power supply.

4.5 Running Conditions

Running conditions for native PAGE are similar to the standard running conditions used for SDS-PAGE (see Section 3.5). If high temperature is a concern, run native PAGE at lower voltage; at lower voltages, runs require more time to complete.

Table 4.1. Running conditions for native PAGE for Criterion gels in the Criterion cell.

Laemmli/Laemmli-like Tris-Acetate

Running buffer Native Native

Power conditions 200 V constant 200 V constant

Expected current (per gel)

Initial 90 –120 mA 70–80 mA

Final 35–55 mA 25–35 mA

Run time 55 min 75 min

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Page 23

Criterion Stain Free™

System

5.1 Introduction

The Criterion Stain Free system, which comprises the Gel Doc™ EZ imager, Image Lab™ software, and Criterion™ TGX Stain-Free™ and Criterion Stain Free precast gels, eliminates the time-consuming staining and destaining steps required by other protein detection methods. Criterion TGX (Tris-Glycine eXtended shelf life) Stain-Free gels include a proprietary modiﬁcation that extends their shelf life to 12 months and enhances separation characteristics relative to conventional gel types. Criterion TGX Stain-Free and Criterion Stain Free gels also include unique trihalo compounds that allow rapid ﬂuorescent detection of proteins with the Gel Doc EZ imager — without staining.

The trihalo compounds in the gels react with tryptophan residues in a UV-induced reaction to produce ﬂuorescence, which can be easily detected by the Gel Doc EZ imager 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 cannot be detected using this system. The sensitivity of the Criterion 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%.

Molecular weights of proteins are estimated by a regression method using Image Lab software. The software generates a standard curve using the molecular weight and relative mobility (R proteins (Rf = distance migrated by the protein/distance migrated by the dye front). The standard curve is then used to estimate the molecular weights of sample proteins.

Beneﬁts of the Criterion Stain Free system include:

Elimination of staining and destaining steps for faster results

Automated gel imaging and analysis

No background variability within a gel or between gels (as is often seen with standard

Coomassie staining)

Reduced organic waste by not requiring acetic acid and methanol for staining or destaining

Visualization of transferred (blotted) proteins on low-ﬂuorescence PVDF membranes

) of standard

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Criterion Precast Gels

5.2 Criterion Stain Free Workflow

Perform Electrophoresis

SDS-PAGE (Chapter 3)

Native PAGE (Chapter 4)

2-D Electrophoresis (Chapter 11)

Activate/Image Gels

(Chapter 5)

Stain the Gels for Total Protein

(Chapter 12)

Blot the Gels

(Chapter 13)

Analyze the Separation

5.3 Electrophoresis with Criterion TGX Stain-Free Gels

Criterion TGX Stain-Free gels (and Criterion Stain Free gels) are made and packaged without SDS, so they can be used for both SDS and native PAGE applications. To perform electrophoresis with these gels, prepare the sample and running buffers, set up the Criterion cell, and perform the run as directed in Chapters 2–4.

Use unstained standards with Criterion TGX Stain-Free and Criterion Stain Free gels, as some prestained standards are not detected by Stain-Free technology. To monitor electrophoresis, use 10 µl of a 1:1 mixture of Precision Plus Protein

™

unstained

and Precision Plus Protein All Blue protein standards.

5.4 Using the Gel Doc EZ Imager

Image Criterion TGX Stain-Free and Criterion Stain Free gels and blots in the Gel Doc EZ imager. The imager activates the reaction between the proteins and trihalo compounds in the gel to enable visualization.

Immediately place the gel in the tray of the imager; no ﬁxation or rinsing steps are required.

Prolonged rinsing may diminish image quality and lead to gel deformation

If desired, stain the gel with any TGX-compatible stains after imaging. Certain stains, if used

prior to imaging, eliminate detection capability

Refer to the Gel Doc EZ Stain-Free Sample Tray Instruction Manual (bulletin 10019634) for detailed instructions.

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Page 25

Peptide Analysis

6.1 Introduction

Criterion™ Tris-Tricine/peptide gels are optimized for separating peptides and proteins with molecular weight <10,000. Peptide-SDS complexes move more slowly through these gels, allowing the faster SDS micelles that normally interfere with peptide separations to separate completely from peptides. This enables resolution of distinct peptide bands.

6.2 Criterion Tris-Tricine/Peptide Gels

6.2.1 Gel Composition

Gel buffer 1.0 M Tris-HCl, pH 8.45

Crosslinker 2.6% C

Stacking gel 4% T, 2.6% C

Storage buffer 1.0 M Tris-HCl, pH 8.45

Shelf life ~12 weeks at 2–8°C; expiration date is printed on each cassette

6.2.2 Gel Selection Guide

Criterion Tris-Tricine/peptide gels are available in either a single percentage or a linear gradient format.

Gel Percentage Optimum Separation Range

16.5% 1.5–30 kD

10–20% 1–40 kD

6.3 Tris-Tricine/Peptide Buffers

See Appendix B for buffer formulations. Do not adjust pH unless instructed to do so.

Running buffer (1x) 100 mM Tris, 100 mM Tricine, 0.1% SDS Dilute 100 ml 10x stock (catalog #161-0744) with 900 ml diH2O

Sample buffer 200 mM Tris-HCl, pH 6.8, 2% SDS, 40% glycerol, 0.04% Coomassie (catalog #161-0739) Brilliant Blue G-250, 2% β-mercaptoethanol or 100 mM DTT (added fresh)

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Criterion Precast Gels

6.4 Sample Preparation

1. Determine the appropriate concentration of sample to load (depends on the load volume and the detection method used; see Chapter 12 for approximate stain sensitivities).

2. Dilute the sample with at least an equivalent volume of sample buffer (catalog #161-0739) and reducing agent (β-mercaptoethanol, for example). Heat the diluted sample at 90–95°C for 5 min, or at 70°C for 10 min.

For example, combine: 5 μl sample

4.75 μl Tricine sample buffer (catalog #161-0739)

0.25 μl β-mercaptoethanol (catalog #161-0710)

10 μl total volume

6.5 Running Conditions

Power conditions 125 V constant

Starting current 140–150 mA/gel

Final current 60–70 mA/gel

Run time 120 min

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Page 27

Isoelectric Focusing

(IEF)

7.1 Introduction

Isoelectric focusing (IEF) separates proteins by their net charge rather than molecular weight. Criterion™ IEF gels are cast with Bio-Rad’s Bio-Lyte® ampholytes, amphoteric molecules that generate a pH gradient across the gels. Proteins migrate to their isoelectric point (pI), the pH at which the protein has no net charge. Criterion IEF gels contain no denaturing agents, so IEF is performed under native conditions.

7.2 Criterion IEF Gels

7.2.1 Gel Composition

Gel buffer 2% ampholyte, pH 3–10 or 5–8

Crosslinker 3.0% C

Stacking gel None

Storage buffer diH2O

Shelf life ~24 weeks at 2–8°C; expiration date is printed on each cassette

7.2.2 Gel Selection Guide

IEF gel pH Range

5–8 5–8.0

3–10 4–8 .5

7.3 IEF Buffers

See Appendix B for buffer formulations. Do not adjust pH unless instructed to do so.

Running buffers:

IEF cathode buffer (1x) 20 mM lysine (free base), 20 mM arginine (free base) Dilute 100 ml 10x stock (catalog #161-0762) with 900 ml diH2O

IEF anode buffer (1x) 7 mM phosphoric acid Dilute 100 ml 10x stock (catalog #161-0761) with 900 ml diH2O

Sample buffer 50% glycerol

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Page 28

Criterion Precast Gels

7.4 Sample Preparation

1. Determine the appropriate concentration of sample to load (depends on the load volume and the detection method used).

2. Dilute the sample with at least an equivalent volume of sample buffer.

For example, combine: 5 μl sample

5 μl sample buffer

10 μl total volume

7.5 Running Conditions

Power conditions (stepwise) 100 V constant 60 min 250 V constant 60 min 500 V constant 30 min

Starting current 5–25 mA/gel

Final current 5–25 mA/gel

Run time 150 min

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Page 29

Protease Analysis by

Zymogram PAGE

8.1 Introduction

Criterion™ zymogram gels are used to test for proteolytic activity. Gels are cast with gelatin or casein, which acts as a substrate for proteases that are separated in the gel under nonreducing conditions. Proteases are detected by ﬁrst 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.

8.2 Criterion Zymogram Gels

8.2.1 Gel Composition

Gel buffer 0.375 M Tris-HCl, pH 8.6

Crosslinker 2.6% C

Stacking gel 4% T, 2.6% C

Storage buffer 0.375 M Tris-HCl, pH 8.6, 0.2% NaN

Shelf life ~8 weeks at 2–8°C; expiration date is printed on each cassette

8.2.2 Gel Selection Guide

Zymogram Gel Optimum Separation Range

10% with gelatin 30–150 kD

12.5% with casein 20–120 kD

8.3 Zymogram Buffers

See Appendix B for buffer formulations. Do not adjust pH unless instructed to do so.

Running buffer (1x) 25 mM Tris, 192 mM glycine, 0.1% SDS Dilute 100 ml 10x stock (catalog #161-0732) with 900 ml diH2O

Sample buffer 62.5 mM Tris-HCl, pH 6.8, 4% SDS, 25% glycerol, 0.01% Coomassie (catalog #161-0764) Brilliant Blue G-250

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Page 30

Criterion Precast Gels

8.4 Sample Preparation

1. Determine the appropriate protein concentration of your sample based on the detection method and load volume used. (See Chapter 12 for approximate stain sensitivities.)

2. Dilute 1 part sample with 1 part sample buffer. Do not heat the samples.

8.5 Running Conditions

Power conditions 125 V constant

Starting current 90–120 mA/gel

Final current 35–55 mA/gel

Run time 90 min

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Page 31

Nondenaturing Nucleic

Acid PAGE

9.1 Introduction

Criterion™ TBE gels are used to separate small double-stranded DNA (dsDNA) fragments, particularly PCR products. DNA molecules have nearly uniform mass-to-charge ratios, allowing nondenaturing nucleic acid PAGE to separate dsDNA by mass using a continuous TBE buffer system.

9.2 Criterion TBE Gels

9.2.1 Gel Composition

Gel buffer 89 mM Tris, 89 mM boric acid, 2 mM EDTA, pH 8.3

Crosslinker 3.3% C

Stacking gel 4% T, 3.3% C

Storage buffer 89 mM Tris, 89 mM boric acid, 2 mM EDTA

Shelf life ~12 weeks at 2–8°C; expiration date is printed on each cassette

9.2.2 Gel Selection Guide

Gel Percentage Optimum Separation Range

5% 200–2,000 bp

10% 50–1,500 bp

15% 20–1,000 bp

4–20% 10–2,000 bp

9.3 Nondenaturing Nucleic Acid PAGE Buffers

See Appendix B for buffer formulations. Do not adjust pH unless directed to do so.

Running buffer (1x) 89 mM Tris, 89 mM boric acid, 2 mM EDTA Dilute 100 ml 10x stock (catalog #161-0733) with 900 ml diH2O

Sample buffer (5x) 50 mM Tris-HCl, pH 8.0, 5 mM EDTA, 25% glycerol, 0.2% bromophenol (catalog #161-0767) blue, 0.2% xylene cyanole FF

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Criterion Precast Gels

9.4 Sample Preparation

Determine the DNA concentration of your sample based on the detection method used. (See Chapter 12 for approximate stain sensitivities.) Dilute 4 parts sample with 1 part sample buffer.

9.5 Running Conditions

Table 9.1. Running conditions for nondenaturing nucleic acid PAGE with Criterion gels in the Criterion cell.

5% and 10% Gels 15% and 4–20% Gels

Power conditions 100 V constant 150 V constant

Expected current (per gel)

Initial 20–25 mA 27–35 mA

Final 14–18 mA 20–35 mA

Run time 90 min 90 min

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Page 33

Denaturing Nucleic

Acid PAGE

10.1 Introduction

Criterion™ TBE-urea gels are used for separation of small RNA and single-stranded DNA (ssDNA) fragments. Applications include oligonucleotide analysis, RNase protection assays, and northern blotting.

10.2 Criterion TBE-Urea Gels

10.2.1 Gel Composition

Gel buffer 89 mM Tris, 89 mM boric acid, 2 mM EDTA, 7 M urea, pH 8.3

Crosslinker 3.3% C

Stacking gel 4% T, 3.3% C

Storage buffer 89 mM Tris, 89 mM boric acid, 2 mM EDTA, pH 8.3

Shelf life ~8 weeks at 2–8°C; expiration date is printed on each cassette

10.2.2 Gel Selection Guide

Gel Percentage Optimum Separation Range

5% 50–1,000 nt

10% 25–300 nt

15% 10–50 nt

10.3 TBE-Urea Buffers

See Appendix B for buffer formulations. Do not adjust pH unless directed to do so.

Running buffer (1x) 89 mM Tris, 89 mM boric acid, 2 mM EDTA Dilute 100 ml 10x stock (catalog #161-0733) with 900 ml diH2O

Sample buffer (5x) 89 mM Tris, 89 mM boric acid, 2 mM EDTA, pH 8.0, 12% Ficoll, (catalog #161-0768) 0.01% bromophenol blue, 0.02% xylene cyanole FF, 7 M urea

10.4 Sample Preparation

Determine the desired ssDNA or RNA concentration for your sample based on the detection method used. Dilute 4 parts sample with 1 part sample buffer.

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Criterion Precast Gels

10.5 Running Conditions

Table 10.1. Running conditions for denaturing nucleic acid PAGE with Criterion gels in the Criterion cell.

5% Gels 10% Gels 15% Gels

Power conditions 200 V constant 200 V constant 200 V constant

Expected current (per gel)

Initial 40–45 mA 20–33 mA 18–22 mA

Final 20 –25 mA 14–18 mA 10–15 mA

Run time 90 min 90 min 90 min

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Page 35

2-D Electrophoresis

11.1 Introduction

Criterion™ precast gels are available for second-dimension PAGE in 2-D electrophoresis workﬂows. The IPG-well gels accommodate 11 cm IPG strips. Criterion™ Any kD™ gels are particularly well suited for 2-D electrophoresis applications.

The transition from ﬁrst- to second-dimension gel electrophoresis involves:

Equilibration of the resolved IPG strips in a reducing buffer containing SDS

Placing the IPG strip on top of the second-dimension gel

11.2 Equilibration

Equilibration ensures that proteins in the IPG strips are coated with SDS and that cysteines are reduced and alkylated. Use the equilibration protocols (bulletin 4110009) and buffers in the ReadyPrep™ 2-D starter kit (catalog #163-2105), or other protocols and buffers used with Tris-HCl gels.

11.3 Agarose Overlay

Place the equilibrated IPG strip into the IPG well of the Criterion gel and overlay it with molten agarose to ensure good contact between the strip and gel.

Criterion TGX™ and Tris-HCl gels: prepare 0.5% low-melt agarose (catalog #161-3111),

0.003% bromophenol blue (catalog #161-0404) in 1x Tris/glycine/SDS running buffer. (Alternatively, use ReadyPrep overlay agarose, catalog #163-2111)

Criterion™ XT gels: prepare 0.5% low-melt agarose (catalog #161-3111), 0.001% bromophenol blue (catalog #161-0404) in appropriate 1x XT running buffer

1. Following equilibration, place the IPG strip, gel side up, on the back plate of the Criterion gel, above the IPG well. The “+” and pH range on the IPG strip should be on the left.

2. Using forceps, push the strip into the IPG well, taking care to not trap air bubbles under the strip. Push on the backing of the strip, not on the gel.

3. Using a disposable pipet, add overlay agarose to the IPG well. Fill the well to the top of the inner plate. Dispense rapidly, as overlay agarose solidiﬁes quickly. To avoid bubbles, tilt the cassette slightly to allow bubbles to escape. Push gently on the plastic backing of the strip to free any trapped bubbles.

11.4 Second-Dimension Electrophoresis

Place the cassettes into the Criterion cell and start the run using the run conditions for SDS-PAGE. Use the migration of the bromophenol blue in the overlay agarose to monitor the progress of the run.

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Page 36

Detection

12.1 SDS-PAGE and Native PAGE Detection

Following electrophoresis, either stain the gel or use the Criterion Stain Free™ system to visualize proteins in the gel.

Refer to Table 12.1 for a comparison of total protein stains

For Criterion™ TGX Stain-Free™ and Criterion Stain Free™ gels, immediately place the gel on

the tray of the Gel Doc™ EZ imager; no additional ﬁxation or rinsing steps are required. If desired, stain with any compatible stains (Table 12.1) following imaging. Some stains, if used prior to imaging, can impair imaging quality

Table 12.1. Total protein gel stains for use with Criterion gels.

Stain

Criterion Gels

Coomassie R-250

™

Bio-Safe Coomassie

Zinc stain

Sensitivity

(Lower

Limit)

36 –47 ng ~0.5 Laboratory

8–28 ng ~0.5 Nonhazardous 43 070 51

6–12 ng ~0.2 High contrast, fast,

Optimum

Protein Load

(µg/Band)

Advantages

standard

reversible

Disadvantages

Requires methanol destaining

Negative SDSPAGE stain, must be photographed

Imaging

Photography with white light or transmission densitometry

4006082

literature

Manual

Consult

Silver Stain Plus

Silver stain 0.6–1. 2 n g ~0.01 Stains complex

Dodeca silver stain kit

Oriole ﬂuorescent gel stain

Do not use zinc stain or Oriole ﬂuorescent gel stain to stain native gels.

™

kit

™

0.6–1.2 n g ~0.01 Sensitive, robust, mass spectrometry compatible

proteins (glyco- or lipoproteins)

0. 5–1.2 n g ~0 .1 Convenient staining for a large number of gels

~2 ng ~ 0.1 High sensitivity,

broad dynamic range, simple one-step protocol

Does not stain glycoproteins well

Not mass spectrometry compatible

30 Technical Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com

Fluorescence visualization with UV transillumination

LIT4 42

LIT34

4110 15 0

10017295

Page 37

Instruction Manual and Application Guide

Stain

SYPRO Ruby protein gel stain

Flamingo ﬂuorescent gel stain

Criterion TGX Stain-Free and Criterion Stain Free Gels

Stain Free imaging

™

Sensitivity

(Lower

Limit)

1–10 ng ~ 0.1 Broad dynamic

0.25– 0.5 ng ~0.02 Broad dynamic

2–28 ng ~0.5 Rapid (<5 min),

Optimum

Protein Load

(µg/Band)

Advantages

range

range, mass spectrometry compatible

compatible with blotting and mass spectrometry, simple protocol with no additional reagents

Disadvantages

Requires laseror LED-based imaging instrument for maximum sensitivity

Requires tryptophan residues in proteins for detection

Imaging

Fluorescence visualization with UV, LED, or laser scanning

Fluorescence visualization using Criterion Stain Free imaging system

Manual

400 6173

10003321

10014472

12.2 Peptide Gel Staining

Peptides and small proteins are prone to diffusion and loss during staining. The following protocol includes a ﬁxing step prior to staining to prevent sample loss and is suitable for detection of bands as low as 10–20 ng.

Fixative solution 40% methanol, 10% acetic acid

Stain solution 0.025% (w/v) Coomassie Blue G-250, 10% acetic acid

Destain solution 10% acetic acid

Place gels in ﬁxative solution and equilibrate for 30 min. Stain gels with stain solution for 1 hr. Stain should be used only once; reuse may result in loss of sensitivity. Destain gels three times for 15 min or until the desired background is achieved. Some peptides may not be completely ﬁxed and may diffuse out of the gels if ﬁxing and staining times are greatly exceeded.

12.3 IEF Gel Staining

Samples on IEF gels can be detected using multiple methods. Use Table 12.2 as a guide to selecting an appropriate staining method.

Table 12.2. IEF gel detection methods.

Method

Silver Stain Plus kit 0.6–1.2 ng ~0.01 Sensitive, robust, mass

Silver stain 0.6 –1.2 ng ~0.01 Stains complex proteins

SYPRO Ruby protein gel stain

Flamingo ﬂuorescent gel stain

Sensitivity

(Lower Limit)

1.0 –10 ng ~0.1 Broad dynamic range, mass

0.25– 0.5 ng ~0.2 Broad dynamic range, mass

Optimum

Protein Load

(µg/Band)

Advantages

spectrometry compatible

(glyco- or lipoproteins)

spectrometry compatible

Disadvantages

Requires TCA ﬁxation

Not mass spectrometry compatible

Requires laser- or LEDbased imaging instrument for maximum sensitivity

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Criterion Precast Gels

12.4 Zymogram Gel Staining

Prior to staining zymogram gels, sample proteases must ﬁrst be renatured and allowed to break down the substrate contained in the gel. The following protocol provides basic guidelines for detection. Optimal results should be determined empirically.

Renaturing solution 2.5% Triton X-100

Development solution 50 mM Tris, 200 mM NaCl, 5 mM CaCl2 (anhydrous), 0.02% Brij-35 Adjust to pH 7.5

Staining solution 40% methanol, 10% acetic acid, 0.5% Coomassie Blue R-250

Destaining solution 40% methanol, 10% acetic acid

Place gels in renaturing solution for 30 min at room temperature. Incubate gels in development solution at 37ºC for a minimum of 4 hr. Highest sensitivity is typically achieved with overnight incubation. Optimum conditions should be determined empirically. Stain gels with staining solution for at least 1 hr at room temperature. Destain until clear bands appear against the blue background (~30–60 min).

12.5 TBE Gel Staining

Use Table 12.3 as a guide to selecting an appropriate staining method.

Table 12.3. TBE gel detection methods.

Method

Ethidium bromide 50 ng Classic ﬂuorescent DNA stain Carcinogenic

Silver stain 1–2 ng More sensitive than ethidium bromide Requires multiple steps

SYBR

Green 0.02–2 ng High sensitivity Multiple steps, –20°C storage

Safe 0.5 ng Non-hazardous Multiple steps

SYBR

Sensitivity

(Lower Limit)

Advantages

Disadvantages

12.6 TBE-Urea Gel Staining

Use Table 12.4 as a guide to selecting an appropriate staining method.

Table 12.4. TBE-urea gel detection methods.

Method

Ethidium bromide 10 ng Classic ﬂuorescent DNA stain Carcinogenic

™

Radiant

Silver stain 1–2 ng More sensitive than ethidium bromide Requires multiple steps

Red 10 ng Fast, single-step protocol RNA and ssDNA only

Sensitivity

(Lower Limit)

Advantages

Disadvantages

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Page 39

Blotting

13.1 Introduction

Western blotting is an electrophoretic technique used to move proteins from a gel onto a solid support such as a nitrocellulose or PVDF membrane. The membrane can be used for immunological or biochemical analyses or demonstration of protein-protein or protein-ligand interactions. Below are guidelines for western blotting of Criterion™ precast gels onto nitrocellulose or PVDF membranes using either wet or semi-dry transfer techniques.

Assess transfer efﬁciency using a total protein blot stain such as SYPRO Ruby stain (see Table 12.1). With Criterion PVDF membranes may also be assessed using the Gel Doc™ EZ imager (see Chapter 5; activate the gel before blotting).

™

TGX Stain-Free™ and Criterion Stain Free™ gels, transfer efﬁciency to low-ﬂuorescence

13.2 Transfer

13.2.1 Transfer Buffers

See Appendix B for buffer formulations. Do not adjust pH unless directed to do so.

Towbin buffer (1x) 25 mM Tris, 192 mM glycine, 20% (v/v) methanol (pH 8.3) Dilute 100 ml 10x stock (catalog #161-0734) with 400 ml diH2O. Add 200 ml methanol, then adjust volume to 1 L with diH2O.

Add SDS to 0.1% to promote transfer of high molecular weight proteins.

13.2.2 Wet Transfer Using the Criterion Blotter

1. Equilibrate the gels and membranes (for example, in Towbin buffer) for 15 min prior to blot assembly.

2. Assemble the transfer apparatus:

a) Fill the tank with transfer buffer to ~50% of the ﬁll volume and place a magnetic stir bar inside

the tank.

b) Place the ice block in the pocket in the back of the cell. Flip down the lever to hold the ice

block. Alternatively, connect the optional cooling coil to an appropriate recirculating water chiller and place it in the grooves in the back of the tank.

3. Assemble the cassette:

a) Pour chilled transfer buffer into each compartment of the assembly tray, and then place the

membrane (nitrocellulose, PVDF) into the front (small) compartment of the tray to soak.

Wet PVDF membranes in methanol before soaking in transfer buffer.

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Page 40

Criterion Precast Gels

b) Open the cassette and place it in the back (large) compartment of the tray so the red plate

with the handle is vertical (anode) and the black plate (cathode) is horizontal and submerged in transfer buffer.

c) Assemble the sandwich as shown, placing the gel closest to the black side of the cassette and

the membrane closest to the red plate. Use a blot roller to remove air trapped between the layers of the blot assembly.

Foam pad Filter paper Membrane Gel

Filter paper Foam pad

Assembly of the gel blot sandwich with the Criterion blotter.

4. Place the assembled cassette into the groove in the tank, aligning the red side of the card with the red electrode. Make sure the magnetic stirbar is free to move. Repeat steps 2–4 for a second blot.

5. Add the remaining transfer buffer to the ﬁll level marked on the tank, place the tank on a stir plate, and begin stirring to maintain even buffer temperature and ion concentration during the transfer.

6. Connect the Criterion blotter to a PowerPac™ HC power supply and begin transfer.

For many proteins, excellent transfer efﬁciency is obtained in 30 min at a constant voltage of 100 V. For best results, optimize conditions for proteins of interest. Large proteins (>150 kD) may take 60 min, while smaller proteins (<30 kD) may transfer in 20 min. Refer to the Criterion Blotter Instruction Manual (bulletin

4006190) or the Protein Blotting Guide (bulletin 2895) for additional information.

13.2.3 Transfer Using the Trans-Blot

Turbo™ System

1. Open the transfer pack and assemble the components on the cassette in the order shown. For best

results, use the roller to remove any air trapped between the layers. If using a single mini or midi sandwich, place the sandwich in the middle of the cassette bottom. With two mini gels, place the sandwiches on a midi stack with the foot of each gel facing the center of the stack.

2. Place the lid on the cassette and lock the lid in place by turning the knob clockwise, using the

symbols on the lid as a guide. Slide the cassette into the appropriate bay of the Trans-Blot Turbo cell. Each cassette and bay can hold up to two mini gels or one midi gel (Table 13.1).

3. Start the transfer. With the cassette in the cell, press TURBO and select the gel type. Press A:RUN

or B:RUN to begin the transfer. Press LIST to select a Bio-Rad optimized protocol (Table 13.2) or a user-deﬁned protocol. Press NEW to create and run a new protocol.

4. When transfer completes, RUN COMPLETE appears. Pull the cassette straight out of the slot and

unlock the lid. Disassemble the blotting sandwich.

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Instruction Manual and Application Guide

Cassette top (–) electrode (cathode)

Top ion reservoir stack

Gel

Membrane

Bottom ion reservoir stack

Cassette bottom (+) electrode (anode)

Assembly of the gel blot sandwich with the Trans-Blot Turbo system.

Table 13.1. Placement of cassettes in the Trans-Blot Turbo cell.

Acceptable Unacceptable

Option 1 Option 2 Option 1 Option 2

Upper bay (A) 1 mini gel 2 mini gels -or- 1 midi gel 1 mini gel 2 mini gels -or- 1 midi gel

-a nd/or- - and/or- -and- -and-

Lower bay (B) 1 mini gel 2 mini gels -or- 1 midi gel 2 mini gels -or- 1 midi gel 1 mini gel

Table 13.2. Trans-Blot Turbo transfer protocols.

Protocol Name

STA ND AR D SD Any 30 Up to 1.0 A, 25 V constant Up to 1.0 A, 25 V constant

1.5 MM GEL Any 10 2.5 A constant, up to 25 V 1.3 A constant, up to 25 V

HIGH MW >15 0 10 2.5 A constant, up to 25 V 1.3 A constant, up to 25 V

LOW MW <30 5 2.5 A constant, up to 25 V 1.3 A constant, up to 25 V

MIXED MW 5 –150 7 2.5 A constant, up to 25 V 1.3 A constant, up to 25 V

1 Mini TGX 5–150 3 2.5 A constant, up to 25 V N /A

MW, kD Time, Min

1 Mini Gel

2 Mini Gels or 1 Midi Gel

Refer to the Trans-Blot Turbo Instruction Manual (bulletin 10020688) for complete instructions or the Protein Blotting Guide (bulletin 2895) for additional information.

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Criterion Precast Gels

13.2.4 Semi-Dry Transfer Using the Trans-Blot® SD Cell

1. Equilibrate the gels and membranes (for example, in transfer buffer; see Appendix B for buffer recipes) for 20 min prior to blot assembly.

2. Assemble the blot for transfer using the Trans-Blot SD semi-dry transfer system.

3. Connect the Trans-Blot SD cell to a PowerPac HC power supply and begin transfer at 10–15 V.

For most proteins transferred from Criterion precast gels, optimum transfer efﬁciency is obtained in 30 min; smaller proteins (<30 kD) may transfer more quickly, while proteins >150 kD may show increased transfer efﬁciencies at up to 60 min. Run times longer than 60 min are NOT recommended for semi-dry transfers.

Refer to the Trans-Blot SD Instruction Manual (bulletin

1703940) or the Protein Blotting Guide (bulletin 2895)

for additional information.

(–)

Filter paper

Gel

Membrane

Filter paper

13.3 Total Protein Blot Stains

Total protein staining of a membrane provides an image of the complete protein pattern, which is required for the full characterization of speciﬁc antigens detected in complex protein mixtures. Gels shrink during staining, so comparison of an immunologically probed membrane to a stained gel is not practical. Instead, the exact location of a specifc antigen is determined by comparing two blotted membranes: one that has been probed with an antibody and the other stained for total protein.

Table 13.1. Total protein blot stains.

Method

SYPRO Ruby protein blot stain

Sensitivity

2–8 ng ~0.2 Compatible with

Protein

Load

(μg/Band)

Advantages

mass spectrometry, Edman-based sequencing, and standard immunological procedures

(+)

Assembly of the gel blot sandwich with the Trans-Blot SD cell.

Disadvantages

Multi-step protocol; requires UV, LED, or laser imaging for maximum sensitivity

Imaging

Fluorescence visualization with UV, LED epi-illumination or laser scanning

Colloidal gold stain 1 ng ~ 0.1 Highly sensitive,

single-step protocol

Anionic dyes (amido black, Coomassie R-250, Ponceau S, Fast Green FCF)

100–1,000 ng ~5.0 Inexpensive, rapid Low sensitivity

Incompatible with nylon membranes

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Photography with epi-illumination or reﬂectance densitometry

Page 43

Instruction Manual and Application Guide

To visualize total protein on blots using the Gel Doc EZ imager, refer to Section 5.4.

13.4 Immunodetection

After transfer, blots are ready for downstream processing. While all protein and antibody combinations are different and may require optimization, a general protocol for the immunodetection of a large number of protein and antibody combinations is provided (see Appendix B for buffer formulations).

1. Immediately after transfer, place the membrane into Tris-buffered saline with Tween 20 (TTBS) containing blocking agent (for example, 3% BSA, 5% nonfat dry milk, 1% casein, or 1% gelatin). Incubate at room temperature with agitation for 1 hr.

2. Dilute the primary antibody in blocking solution (suggested dilution is speciﬁed by the manufacturer). Incubate the blot in the primary antibody solution at room temperature and with agitation for 1 hr.

3. Wash the blot with TTBS as directed in the instructions for the detection method to be used (for example, 5 times, 5 min each at room temperature).

4. Dilute the secondary antibody into TTBS as speciﬁed by the manufacturer. Incubate the blot in the secondary antibody solution at room temperature with agitation for 1 hr.

5. Wash the blot with TTBS for 5 min at room temperature with agitation. Pour off the wash solution and repeat 5 times.

6. Follow the directions for the detection kit used to develop the blot. For the Immun-Star™ WesternC™ chemiluminescence kit (catalog #170-5070), mix 3 ml luminol/enhancer with 3 ml peroxide solution to make a 1x working solution for a 7 x 8.5 cm membrane. Incubate the membrane in the solution for 3–5 min. Prior to imaging, drain the excess substrate and place the membrane in a protective sleeve (such as plastic wrap) to prevent drying.

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Page 44

Table 14.1. Troubleshooting electrophoresis and detection with Criterion™ gels. For more troubleshooting tips, refer to the Criterion cell, Criterion blotter, and Trans-Blot® SD cell instruction manuals, or contact Technical Support.

General Troubleshooting Tips

Current is zero or less than expected, and samples do not migrate into gel

Troubleshooting

Problem Cause Solution

Tape at bottom of cassette not removed Remove tape

Insufﬁcient buffer in integral buffer chamber

Fill buffer chamber with running buffer

Insufﬁcient buffer in lower buffer chamber

Electrical disconnection Check electrodes and connections

Gels run faster than expected Running buffer too concentrated or

incorrect

Gel temperature too high Do not exceed recommended running

Bands “smile” across gel: band pattern curves upward at both sides of the gel

Bands “smile” or “frown” within gel lanes

Bands are skewed or distorted; lateral band spreading

Excessive heating of gel Check buffer composition

Insufﬁcient buffer Fill both halves of lower buffer tank with

Protein load too high Load less protein

Sample or buffer preparation issues Minimize salts, detergents, and solvents

Incorrect running conditions Set correct voltage

Too much salt in samples Remove salt from samples (dialysis,

Insufﬁcient or wrong sample buffer Check buffer composition and dilution

Sample precipitation Selectively remove predominant proteins in

Insoluble materials (for example, cell membranes) in samples

Fill both halves of lower buffer tank with 400 ml running buffer when running two gels

Check buffer composition

conditions

Do not exceed recommended running conditions

400 ml running buffer when running two gels

in sample preparation and sample loading buffers

precipitation, or other method)

instructions

sample

Dilute sample in sample buffer

Centrifuge samples to remove particulates prior to sample loading

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Page 45

Instruction Manual and Application Guide

Problem Cause Solution

Artifactual bands at 60 –70 kD

Poor resolution or fuzzy bands Sample volume too high If possible, load a more concentrated

Skin keratin contamination Clean all dishware, and wear gloves while

handling and loading gels

Filter all solutions (0.2–0.45 µm ﬁlter)

sample in a lower sample buffer volume

Not enough running buffer in lower chamber

Diffuse sample loading zone Load sample with a syringe or gel loading

Sample diffusion during staining Fix gel with 40% methanol, 10% acetic acid

Incompatible sample components Minimize salts, detergents, and solvents

Expired gel Use gels before expiration date printed on

Add running buffer to ﬁll line of lower buffer chamber

pipet tip

for 80 min prior to staining

in sample preparation and sample loading buffers

the cassette

Criterion™ TGX Stain-Free™ and Criterion Stain Free™ Gels

Low sensitivity for proteins Low tryptophan content in proteins After activation and imaging, stain gel with

Bio-Safe™ Coomassie or similar to detect missing bands

Uneven sensitivity or fuzzy bands Gel was soaked in water or buffer prior

to activation and imaging

Bands are too light or missing from blot (membrane)

Proteins transferred through membrane Use membrane with smaller pore size

If possible, activate and image gel using the Gel Doc EZ imager immediately after electrophoresis

Decrease transfer time

Decrease voltage

Standards not visible Incorrect standards were used Use unstained standards; some prestained

standards are not detected by the Gel Doc EZ imager. To monitor electrophoresis, use a 1:1 mixture of unstained and prestained standards

Dye front at bottom of gels interfering with detection of proteins

High background or low sensitivity on a blot of a Criterion TGX StainFree or Criterion Stain Free gel (imaged using the Gel Doc EZ imager)

Sample constituents present in gel interfering with imaging

Low tryptophan content in proteins After activation and imaging, stain blot with

Membrane not low-ﬂuorescence PVDF Always use low-ﬂuorescence PVDF

PVDF membrane is dry Wet PVDF membrane brieﬂy in methanol

Dilute sample in gel running buffer prior to loading

Activate and image gel, rinse in ﬁxation solution for 30 min, and repeat imaging

a total protein blot stain to detect missing bands

membranes to blot Criterion TGX Stain-Free or Criterion Stain Free gels

and wash in water for 1 min before imaging

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Page 46

The following instructions are for electrophoresis of Criterion™ precast gels using the Criterion system.

Running buffer (1x) Dilute 100 ml 10x stock (catalog #161-0732) with 900 ml diH2O.

Quick Start Guide

Prepare Buffers

Sample buffer

Remove the comb and tape from the gels and assemble the electrophoresis cell.

Fill the inner and outer buffer chambers with running buffer.

Fill the lower buffer chamber with 400 ml running buffer (to the ﬁll mark).

Use Laemmli sample buffer (catalog #161-0737).

Prepare Gels and

Assemble Electrophoresis Cell

Prepare and Load Samples

Component Reducing Nonreducing

Sample 5 μl 5 μl

Laemmli sample buffer (catalog #161-0737)

β-Mercaptoethanol 0.25 μl —

Total volume 10 μl 10 μl

Heat samples at 90–100°C for 5 min or at 70°C for 10 min.

4.75 μl 5 μl

Load the appropriate amount of sample on the gel.

Perform Electrophoresis

Connect the electrophoresis cell to the power supply and perform electrophoresis according to the conditions in Table A.1.

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Page 47

Table A.1. Running conditions for SDS-PAGE in the Criterion cell. Do not run different gel formulations at the same time.

TGX Tris-HCl Bis-Tris Tris-Acetate

Running buffer Tris/glycine/SDS Tris/glycine/SDS X T MOPS XT MES XT Tricine

Standard Conditions

Power conditions 200 V constant 200 V constant 200 V constant 200 V constant 150 V constant

Expected current (per gel)

Initial 55–80 mA 90–120 mA 165–175 mA 185–200 mA 170–180 mA

Final 33– 43 mA 35–55 mA 60–70 mA 90–110 mA 85–95 mA

Run time 42–45 min 50–55 min 60 min 45 min 65 min

High Voltage (Rapid) Conditions

Power conditions 300 V constant — — — —

Expected current (per gel)

Initial 89–135 mA — — — —

Final 66–99 mA — — — —

Run time 20–26 min — — — —

Table A.2. Standard transfer (blotting) conditions.

Method Membrane Time Voltage

Tank blotting Nitrocellulose (0.45 μm) 20 –60 min 100 V

PVDF (0.2 μm)

Semi-dry blotting Nitrocellulose (0.45 μm) 20–60 min 25 V

PVDF (0.2 μm)

For previously optimized protocols for proteins <30 kD, reduce transfer time by 20%.

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Page 48

Buffers

Running Buffers

10x SDS-PAGE (1 L) 250 mM Tris, 1.92 M glycine, 1% SDS, pH 8.3

(catalog #161-0732) Tris base 30.3 g Glycine 144.1 g SDS 10 g diH2O to 1 L Do not adjust the pH (~pH 8.3)

10x Native PAGE (1 L) 250 mM Tris, 1.92 M glycine, pH 8.3

(catalog #161-0734) Tris base 30.3 g Glycine 144.1 g diH2O to 1 L Do not adjust the pH (~pH 8.3)

10x Tris-Tricine (1 L) 1 M Tris, 1 M Tricine, 1% SDS, pH 8.3 (catalog #161-0744) Tris base 121.1 g Tricine 179.2 g SDS 10 g diH2O to 1 L Do not adjust the pH (~pH 8.3)

10x TBE (1 L) 890 mM Tris, 890 mM boric acid, 20 mM EDTA

(catalog #161-0741) Tris base 107.8 g Boric acid 55.0 g EDTA 5.8 g diH2O to 1 L Do not adjust the pH (~pH 8.3)

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Instruction Manual and Application Guide

Sample Buffers

2x SDS-PAGE (Laemmli, 30 ml) 62.5 mM Tris-HCl, pH 6.8, 2% SDS, 25% glycerol, 0.01% (catalog #161-0737) bromophenol blue, 5% β-mercaptoethanol (added

fresh)

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 β-mercaptoethanol (50 µl to 950 µl sample buffer) before use.

2x Native PAGE (30 ml) 62.5 mM Tris-HCl, pH 6.8, 40% glycerol, 0.01% (catalog #161-0738) bromophenol blue

0.5 M Tris-HCl, pH 6.8 3.75 ml

50% Glycerol 24 ml

1.0% Bromophenol blue 0.3 ml

diH2O to 30 ml

2x Tricine (30 ml) 200 mM Tris-HCl, pH 6.8, 2% SDS, 40% glycerol, 0.04% (catalog #161-0739) Coomassie Brilliant Blue G-250, 2% β-mercaptoethanol (added fresh)

1.0 M Tris-HCl, pH 6.8 6.0 ml

100% Glycerol 12.0 ml 10% SDS 6.0 ml Coomassie Blue G-250 12.0 mg diH2O to 30 ml

 Add β-mercaptoethanol (20 µl to 980 µl sample buffer) before use.

5x Nucleic acid (10 ml) 50 mM Tris-HCl, pH 8.0, 5 mM EDTA, 25% glycerol, 0.2%

(catalog #161-0767) bromophenol blue, 0.2% xylene cyanole FF

Tris base 78.8 mg 50% Glycerol 5 ml EDTA 14.6 mg

1.0% Bromophenol blue 2.0 ml

Xylene cyanole FF 20.0 mg diH2O to 10 ml

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Page 50

Criterion Precast Gels

TBE-urea (30 ml) 89 mM Tris, 89 mM boric acid, 2 mM EDTA, pH 8.0, 12%

(catalog #161-0768) Ficoll, 0.01% bromophenol blue, 0.02% xylene cyanole, Store at 4°C 7 M urea

Tris base 0.32 g Boric acid 0.165 g EDTA 17.5 mg Ficoll 3.6 g Bromophenol blue 3 mg Xylene cyanole FF 6 mg Urea 12.6 g diH2O to 30 ml

Buffer Components

0.5 M Tris-HCl, pH 6.8 (1 L) Tris base 60.6 g

(catalog #161-0799) diH2O ~900 ml Store at 4°C Adjust to pH 6.8 with HCl diH2O to 1 L

10% SDS (250 ml) SDS 25.0 g (catalog #161-0416) diH2O to 250 ml

1.0% Bromophenol blue (10 ml) Bromophenol blue 100 mg

(10 g powder, catalog #161-0404) diH2O to 10 ml

Blotting Buffers

Towbin buffer (1 L) 25 mM Tris, 192 mM glycine, 20% methanol

Dissolve: Tris base 14.4 g Glycine 3.03 g diH2O 500 ml

Then add: Methanol 200 ml diH2O to 1 L

Alternatively, use: 10x Tris/glycine (catalog #161-0734) 100 ml Add 200 ml methanol and diH2O to 1 L as above

Tris-buffered saline with 20 mM Tris, 500 mM NaCl, 0.05% Tween 20 Tween (TTBS, 1 L) Tris base 2.4 g

NaCl 29.2 g 10% Tween 20 5.0 ml diH2O to 1 L

Alternatively, use: 10x TBS (catalog #170-6435) 100 ml 10% Tween 20 (catalog #166-2404) 5 ml diH2O 895 ml

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Instruction Manual and Application Guide

Bulletin # Title

4006183 Criterion™ Cell Instruction Manual

4006197 Criterion™ Dodeca™ Cell Instruction Manual

10014472 Gel Doc™ EZ System Installation Guide

10019634 Stain-Free Sample Tray Instruction Manual

4006190 Criterion Blotter Instruction Manual

4006066 Trans-Blot® SD Semi-Dry Transfer Cell Quick Reference Guide

10020688 Trans-Blot® Turb o™ Blotting System Instruction Manual

1703940 Trans-Blot SD Semi-Dry Transfer Cell Instruction Manual

6007 Criterion™ TGX™ Precast Gels Product Information Sheet

5974 Criterion™ TGX Stain-Free™ Precast Gels Product Information Sheet

2911 Criterion™ XT Precast Gels Product Information Sheet

Related Literature

2895 Protein Blotting Guide

6039 Trans-Blot Turbo Transfer System Brochure

3133 Molecular Weight Determination by SDS-PAGE

3144 Using Precision Plus Protein™ Standards to Determine Molecular Weight

1939 Blotting Membrane Brochure

2032 Western Blotting Detection Reagents Brochure

2317 Ready-to-Run Buffers and Solutions Brochure

2414 The Little Book of Standards

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Page 52

Criterion Precast Gels

Criterion TGX™ Gels

7. 5% 5 67-1023 567-1024 5 67-1025 567-1021 567-102 2

10% 5 67-10 33 567-1034 5 67-10 35 5 67-1031 5 67-1032

12% 5 67-1043 5 67-10 44 567-104 5 567-10 41 567-1042

18% 5 67-107 3 567-1074 567-1075 567-1071 567-1072

4–15% 5 67-10 83 567-1084 5 67-10 85 5 67-1081 5 67-10 82

4–20% 5 67-1093 567-109 4 5 67-1095 567-1091 5 67-1092

8–16% 567-1103 567-110 4 567-110 5 5 67-110 1 5 6 7-1102

10–20% 567-1113 567-1114 5 67-1115 5 67-1111 5 67-1112

Any kD

Criterion

7. 5% 56 7- 8023 5 67-8 0 24 5 67- 8 0 25 567- 8 021 567- 8 022

10% 5 67-80 3 3 56 7-8034 567- 8035 56 7-803 1 56 7-8032

12% 567- 8 0 43 5 67-8 0 4 4 5 67-8 0 4 5 5 67-80 41 5 67-80 42

18% 5 67-8 073 5 67-8074 567- 8075 56 7-8071 56 7-8072

4–15% 567-8083 567-8084 567-8085 567-8081 567-8082

4–20% 5 67-8 0 9 3 5 67-80 9 4 5 67-80 9 5 5 67-8 0 91 567- 8 092

8–16% 567- 810 3 5 67-810 4 567- 8105 56 7-8101 567- 8102

10–20% 5 67-8113 56 7- 8114 567-8115 5 67-8111 56 7- 8112

Any kD 5 67-8 123 567- 8124 5 67-8 125 567- 8121 567- 8122

™

Ordering Information

12+2 Well

(45 µl/well)

567-1123 5 67-1124 5 67-112 5 5 67-112 1 56 7-1192

™

TGX Stain-Free™ Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

26-Well

(15 µl/well)

IPG+1 Well

(11 cm IPG Strip)

IPG+1 Well

(11 cm IPG Strip)

Prep+2 Well

(800 µl/well)

Prep+2 Well

(800 µl/well)

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Instruction Manual and Application Guide

™

Criterion

Tris-HCl Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

IPG+1 Well

(11 cm IPG Strip)

Prep+2 Well

(800 µl/well)

Criterion Tris-HCl

5% 345-0001 345-0002 345-0003 — —

7. 5% 345-0005 345-0006 345-0007 — 345-0008

10% 345-0009 345-0010 345-0011 345-0101 345-0012

12.5% 345-0014 345-0015 345-0016 3 45 -0102 345-0017

15% 345-0019 345-0020 345-0021 — 345-0022

18% 345-0023 345-0024 345-0025 — 345-0026

4–15% 345-0027 345-0028 345-0029 345-0103 345-0030

4–20% 345-0032 345-0033 345-0034 345- 0104 345-0035

8–16% 345-0037 345-0038 345-0039 345-0105 345-0040

10.5 –14% 345-9949 345-9950 345-9951 3 45-0106 —

10–20% 345-0042 345-0043 345-0044 345-0107 345-0045

Criterion Stain Free

™

10% 345-1012 3 4 5-1018 — — —

4–20% 345 -0412 345 - 0418 345-0426 — —

8–16% 345-816 2 — 345-816 6 345-8161 —

Criterion

™

XT Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

IPG+1 Well

(11 cm IPG Strip)

Prep Well

(800 µl/well)

Criterion XT Bis-Tris

10% 3 4 5 - 0111 3 4 5 - 0112 345-0113 3 4 5 - 0 115 —

12% 3 45-0117 345-0118 3 4 5 - 0119 345 -0121 34 5-0120

4–12% 3 45- 0123 3 45- 0124 345 -0125 3 45- 0127 345-0126

Criterion XT Tris-Acetate

7% 3 45 -0135 345-0136 345-0137 — —

3– 8% 345-0129 345-0130 345- 0131 345 -0133 —

Criterion Tris-Tricine Peptide Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

Prep+2 Well

(800 µl/well)

16.5% 345-0063 345-0064 345-0065 345-0066

10–20% 345-0067 345-0068 345-0069 —

Criterion IEF Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

pH 3–10 345-0071 345-0072 345-0073

pH 5–8 — 345-0076 —

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Page 54

Criterion Precast Gels

Criterion Zymogram Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

10% Zymogram, gelatin 345-0079 345-0080 345-0081

12.5% Zymogram, casein 345-0082 345-0083 345-0084

Criterion TBE Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

5% TBE 345-0047 345-0048 345-0049

10% 345-0051 345-0052 345-0053

15% 345-0055 345-0056 345-0057

4–20% 345-0059 345-0060 345-0061

Criterion TBE-Urea Gels

12+2 Well

(45 µl/well)

18-Well

(30 µl/well)

26-Well

(15 µl/well)

5% TBE-urea — 345-0086 —

10% 345-0088 345-0089 345-0090

15% 345-0091 345-0092 345-0093

Catalog # Description

Criterion Gel Accessories

345-9901 Criterion Empty Cassettes, 1.0 mm with 12+2 well comb, 10

345-9902 Criterion Empty Cassettes, 1.0 mm with 18-well comb, 10

345-9903 Criterion Empty Cassettes, 1.0 mm with 26-well comb, 10

345-9904 Criterion Empty Cassettes, 1.0 mm with prep+2 well comb, 10

345-9906 Criterion Empty Cassettes, 1.0 mm with IPG+1 well comb, 10

165-6006 Criterion Sample Loading Guide, 12+2 well, 1

165-6007 Criterion Sample Loading Guide, 18-well, 1

165-6008 Criterion Sample Loading Guide, 26-well, 1

Equipment

165-6001 Criterion Cell, includes tank, lid with power cables, three sample loading guides

165-4130 Criterion™ Dodeca™ Cell

170-4070 Criterion Blotter with Plate Electrodes

170-4071 Criterion Blotter with Wire Electrodes

170 -4155 Tran s-B lot® Turb o™ Transfer Starter System

170-3940 Trans-Blot® SD Semi-Dry Electrophoretic Transfer Cell

164-5050 PowerPac™ Basic Power Supply

164-5052 PowerPac HC High Current Power Supply

170-8270 Gel Doc™ EZ Imaging System

170-8274 Stain-Free™ Sample Tray

48 Technical Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com

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Instruction Manual and Application Guide

Catalog # Description

Protein Standards

161-0363 Precision Plus Protein™ Unstained Standards (10–250 kD), 1 ml, 100 applications

161-0373 Precision Plus Protein All Blue Prestained Standards (10–250 kD), 500 μl, 50 applications

161-0374 Precision Plus Protein Dual Color Standards (10–250 kD), 500 μl, 50 applications

161-0375 Precision Plus Protein™ Kaleidoscope™ Standards (10–250 kD), 500 μl, 50 applications

161-0376 Precision Plus Protein™ WesternC™ Standards (10–250 kD), 250 μl, 50 applications

161-0377 Precision Plus Protein Dual Xtra Standards (2.5–250 kD), 500 μl, 50 applications

161-0385 Precision Plus Protein WesternC Pack (10–250 kD), 50 applications each of standard and StrepTactin-HRP

161-0317 SDS-PAGE Standards, broad range, 200 μl

Premixed Running Buffers

161-0732 10x Tris/Glycine/SDS, 1 L

161-0772 10x Tris/Glycine/SDS, 5 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 XT MOPS Buffer Kit, includes 500 ml 20x XT MOPS 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 20 x 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

161-0733 10x Tris/Boric Acid/EDTA, 1 L

161-0770 10x Tris/Boric Acid/EDTA, 5 L

161-0765 Zymogram Renaturation Buffer, 125 ml

161-0766 Zymogram Development Buffer, 125 ml

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Criterion Precast Gels

Catalog # Description

Premixed Sample Buffers

161-0737 Laemmli Sample Buffer, 30 ml

161-0738 Native Sample Buffer, 30 ml

161-0791 XT Sample Buffer, 4x, 10 ml

161-0792 XT Reducing Agent, 20x, 1 ml

161-0739 Tricine Sample Buffer, 30 ml

161-0763 IEF Sample Buffer, 30 ml

161-0764 Zymogram Sample Buffer, 30 ml

161-0767 Nucleic Acid Sample Buffer, 5x, 10 ml

161-0768 TBE-Urea Sample Buffer, 30 ml

Component Reagents

161-0719 Tris, 1 kg

161-0718 Glycine, 1 kg

161-0301 SDS, 100 g

161-0416 SDS Solution, 10% (w/v), 250 ml

166-2404 10% Tween 20, 5 ml

170-6404 Blotting-Grade Blocker, 300 g

161-0710 2-Mercaptoethanol, 25 ml

161-0611 Dithiothreitol (DTT), 5 g

161-0404 Bromophenol Blue, 10 g

Total Protein Gel and Blot Stains

161-0786 Bio-Safe™ Coomassie Stain, 1 L

161-0400 Coomassie Brilliant Blue R-250, 10 g

161-0436 Coomassie Blue R-250 Stain Solution, 1 L

161-0438 Coomassie Blue R-250 Destain Solution, 1 L

161-0443 Silver Stain Kit

161-0449 Silver Stain Plus™ Kit

170-6527 Colloidal Gold Total Protein Stain, 500 ml

161-0440 Zinc Stain and Destain Kit

170-3127 SYPRO Ruby Protein Blot Stain, 200 ml

161-0491 Flamingo™ Fluorescent Gel Stain (10x), 100 ml

161-0496 Oriole™ Fluorescent Protein Gel Stain (1x), 1 L

May require addition of 2-mercaptoethanol or DTT

50 Technical Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com

Page 57

Instruction Manual and Application Guide

Catalog # Description

Immunoblot Detection Reagents

161-0385 Precision Plus Protein™ WesternC™ Pack

170-5070 Immun-Star™ WesternC™ Chemiluminescent Kit, 100 ml

170-6431 HRP Conjugate Substrate Kit, 4CN

170-6535 HRP Color Development Reagent, DAB, 5 g

170-8238 Ampliﬁed Opti-4CN™ Substrate Kit

170-8235 Opti-4CN Substrate Kit

170-6432 AP Conjugate Substrate Kit

170-5012 Immun-Star™ Substrate Pack

Blotting Membranes

162-0232 0.2 μm Nitrocellulose/Filter Paper Sandwich, 8.5 x 13.5 cm, 20 pack

162-0233 0.2 μm Nitrocellulose/Filter Paper Sandwich, 8.5 x 13.5 cm, 50 pack

162-0234 0.45 μm Nitrocellulose/Filter Paper Sandwich, 8.5 x 13.5 cm, 20 pack

162-0235 0.45 μm Nitrocellulose/Filter Paper Sandwich, 8.5 x 13.5 cm, 50 pack

162-0236 Sequi-Blot™ PVDF/Filter Paper Sandwich, 8.5 x 13.5 cm, 20 pack

162-0237 Sequi-Blot PVDF/Filter Paper Sandwich, 8.5 x 13.5 cm, 50 pack

170-4157 Trans-Blot Turbo Midi PVDF Transfer Packs

170-4159 Trans-Blot Turbo Midi Nitrocellulose Transfer Packs

For additional product sizes, please refer to the Bio-Rad catalog or website.

Technical Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 51

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Criterion Precast Gels

52 Technical Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com

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Instruction Manual and Application Guide

Technical Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 53

Page 60

Life Science Group

Bio-Rad Laboratories, Inc.

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4110001 Rev F US/EG 1011 Sig 0211

Bio-Rad Criterion TBE-Urea Precast Gels User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

1.1 Introduction

1.2 Gel Formulations

1.3 Comb Configurations

1.4 Specifications

1.5 Storage Conditions

1.6 Important Notes

2.1 Workflow Overview

2.2 Required Materials

2.3 Setting Up and Running Criterion Gels in the Criterion Cell

2.4 Removing the Gel

3.1 Introduction

3.2 Criterion Gel Selection Guide for SDS-PAGE

3.2.1 Criterion TGX and Criterion TGX Stain-Free Gels

3.2.2 Criterion Tris-HCl and Criterion Stain Free Gels

3.2.3 Criterion XT Bis-Tris Gels

3.2.4 Criterion XT Tris-Acetate Gels

3.3 SDS-PAGE Buffers

3.3.1 Running Buffers

3.3.2 Sample Buffers

3.4 Sample Preparation

3.5 Running Conditions

4.1 Introduction

4.2.1 Criterion TGX and Criterion TGX Stain-Free Gels

4.2.2 Criterion Tris-HCl and Criterion Stain Free Gels

4.2.3 Criterion XT Tris-Acetate Gels

4.3 Native PAGE Buffers

4.4 Sample Preparation

4.5 Running Conditions

5.1 Introduction

5.2 Criterion Stain Free Workflow

5.3 Electrophoresis with Criterion TGX Stain-Free Gels

5.4 Using the Gel Doc EZ Imager

6.1 Introduction

6.2 Criterion Tris-Tricine/Peptide Gels

6.2.1 Gel Composition

6.2.2 Gel Selection Guide

6.3 Tris-Tricine/Peptide Buffers

6.4 Sample Preparation

6.5 Running Conditions

7.1 Introduction

7.2 Criterion IEF Gels

7.2.1 Gel Composition

7.2.2 Gel Selection Guide

7.3 IEF Buffers

7.4 Sample Preparation

7.5 Running Conditions

8.1 Introduction

8.2 Criterion Zymogram Gels

8.2.1 Gel Composition

8.2.2 Gel Selection Guide

8.3 Zymogram Buffers

8.4 Sample Preparation

8.5 Running Conditions

9.1 Introduction

9.2 Criterion TBE Gels

9.2.1 Gel Composition

9.2.2 Gel Selection Guide

9.3 Nondenaturing Nucleic Acid PAGE Buffers

9.4 Sample Preparation

9.5 Running Conditions

10.1 Introduction

10.2 Criterion TBE-Urea Gels

10.2.1 Gel Composition

10.2.2 Gel Selection Guide

10.3 TBE-Urea Buffers

10.4 Sample Preparation

10.5 Running Conditions

11.1 Introduction

11.2 Equilibration

11.3 Agarose Overlay

11.4 Second-Dimension Electrophoresis

12.1 SDS-PAGE and Native PAGE Detection

12.2 Peptide Gel Staining

12.3 IEF Gel Staining

12.4 Zymogram Gel Staining

12.5 TBE Gel Staining