I made a standard SDS-PAGE gel (5% stacking, 10% resolving) using the same recipe I have used successfully for years. I wrapped the gel in wet paper town and stored it at 4C for about 18 hours before running the gel. Nothing appears to be visually wrong with the gel prior to running. When I run the gel, the sides of the gel fail to run (not a smile though) and when I take the gel out of the casting, it has become all wrinkled. The sample buffer also separates and leaves behind yellow dye in the gel. This especially happens in the lanes that I've just loaded buffer into, but it spreads into my sample lanes.
What is happening to my gel?
Hello Katherine, check the pH of your loading dye as well as the running buffer. Also make sure the buffer covers the gel completely evenly. Another thing to check is your power supply, sometimes improper supply of power may result in one side separation of samples.
Hi Catherine,
To store the gel for next day use, I wrap the gel with paper towel and seal in a plastic bag containing running buffer. What buffer you use to wet your paper towel?
Thanks for the help so far!
For my gel: I have not tried running with a fresh gel. I cast the gel and wet the paper towel with diH20 and store in a plastic bag at 4C. I use the gel within 1 week of casting.
For my running buffer: I use a standard running buffer recipe. My buffer pH is 8.3/8.4 which seems to be within range.
For my loading dye: I'm not able to pH with the test strips our lab has, but I will make some fresh next time I run a western.
It really seems like the gel "melting" at the corners - should I be concerned about how long the gel runs for? I run at 100V until the dye reaches the bottom of the gel, which can take up to 2 hours.
Hi Catherine,
The running condition you used is absolutely fine. I also run at 100V until the dye diffuses into the running buffer. Sometimes I run up to 3 hours (with 12% gel) to get better separation.
It might be the buffering capacity affected instead of the pH. My lab once had problem with running (picture attached) due to the glycine. The glycine is sensitive to moisture. So, we order smaller package size afterwards to avoid prolonged storage after opening.
The wrinkle in the gel is due to shrinking of the gel. May be your gel is not wet enough to be stored at 4° C. And its obvious that your gel is not running b'cause the molecular pores are already closed. Don't store ur gel longer than 10-12hrs and wrap your casted gel in tissue papers and sprinkle miliQ water as much as enough to wet it (don't drench it with water just wet enough).
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