Home Biochemistry Western Blotting
Steps
  1. 1 Prepare gel and equilibrate in buffer 00:20
  2. 2 Assemble the blotting sandwich 01:07
  3. 3 Set up electrophoresis chamber for transfer 03:36
  4. 4 Run protein transfer at constant voltage 04:30
  5. 5 Disassemble sandwich and recover membrane 05:04
  6. 6 Block and incubate with antibodies 06:09
  7. 7 Apply secondary antibody and wash 07:52
  8. 8 Develop, visualize, and store membrane 09:11
Biochemistry Bio-Rad Laboratories

Western Blotting

Protocol
Difficulty
intermediate

Steps

1
Prepare gel and equilibrate in buffer

Fill a tray with blotting buffer, remove the gel from the cassette using the opening key, trim the top and bottom of the gel, and equilibrate the gel in the buffer for 15 minutes on a rocking platform.

▶ 00:20
2
Assemble the blotting sandwich

Pre-soak fiber pads in blotting buffer. Place the gel holder in a container with buffer, then layer one fiber pad, blotting paper, the gel, the nitrocellulose membrane, another blotting paper, and a second fiber pad, removing air bubbles between each layer.

▶ 01:07
3
Set up electrophoresis chamber for transfer

Fold the clear plastic side of the gel holder and clamp it with the white clip, insert the gel holder into the inner module with black sides aligned, place the module in the electrophoresis chamber with a frozen cooling unit, and fill with blotting buffer.

▶ 03:36
4
Run protein transfer at constant voltage

Place the lid on the chamber, connect the electrical leads to the power supply (red to red, black to black), and run the blot at 20 volts for approximately 2.5 hours.

▶ 04:30
5
Disassemble sandwich and recover membrane

Turn off the power supply, disassemble the chamber, and remove the inner module. Open the module in a buffer-filled container and carefully remove each layer until the nitrocellulose membrane is exposed.

▶ 05:04
6
Block and incubate with antibodies

Immerse the membrane in 25 mL of blocking solution for 15 minutes on a rocking platform. Add 10 mL of primary antibody and incubate for 10-20 minutes, then perform a quick rinse and a 3-minute wash in wash buffer.

▶ 06:09
7
Apply secondary antibody and wash

Add 10 mL of secondary antibody and incubate for 5-15 minutes on the rocking platform at fast speed. Perform a quick rinse in wash buffer, followed by a 3-minute wash in fresh wash buffer.

▶ 07:52
8
Develop, visualize, and store membrane

Add 10 mL of substrate and incubate the membrane for 10-30 minutes while watching for color development. Rinse twice with distilled water, blot dry with paper towel, air dry for 3-60 minutes, and cover in plastic wrap for storage.

▶ 09:11

🚨 Failure Case Library (10) + Submit your own case

severe
White Bands or Ghost Bands with ECL Detection
Target protein bands appear white or light-colored instead of dark on film or imager. The bands are present but show inverted contrast, appearing as 'ghost bands' where signal should be strongest.
💡 5 · ✓ 6
moderate
Bands Appear Lower Than Expected Molecular Weight
All protein bands or the target band migrate further down the membrane than expected based on the predicted molecular weight. Coomassie blue staining of the membrane confirms abnormally low band positions before immunostaining.
💡 4 · ✓ 4
moderate
Low Acrylamide Percentage for Target Protein Size
Lower molecular weight proteins migrate excessively fast through the gel, resulting in poor resolution and bands appearing at the bottom of the membrane or running off entirely.
💡 3 · ✓ 4
moderate
Electrophoresis Time Not Optimized for Target Protein
Protein bands do not align with expected molecular weight markers, with systematic upward or downward shifts affecting all bands uniformly. Pre-staining reveals migration issues before antibody detection.
💡 4 · ✓ 5
moderate
Black Dots or Speckled Background on Western Blot
Non-specific dark dots or speckled pattern appear across the membrane background, not localized to protein bands. The signal appears as discrete spots rather than uniform background.
💡 5 · ✓ 5
moderate
Bands Appear Higher Than Expected Molecular Weight
All protein bands or the target band remain near the top of the membrane, migrating less than expected based on the predicted molecular weight. Coomassie blue staining confirms abnormally high band positions before immunostaining.
💡 4 · ✓ 4
moderate
High Acrylamide Percentage for Target Protein Size
Higher molecular weight proteins remain near the loading wells with minimal migration, resulting in poor resolution and bands clustered at the top of the membrane.
💡 4 · ✓ 4
moderate
Streaking and Uneven Migration from Buffer Issues
Bands show streaking, smearing, or uneven migration patterns. Multiple bands may merge or appear poorly resolved with inconsistent migration across the gel.
💡 5 · ✓ 5
minor
Non-parallel Bands
Protein bands appear curved, wavy, or not parallel to each other
💡 1 · ✓ 2
minor
Blue Background on Gel or Blot After Electrophoresis
After completing electrophoresis, the gel or blot membrane displays a diffuse blue background coloration instead of a clear background. The blue tint is distributed across the gel surface or transferred to the membrane.
💡 4 · ✓ 4
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