Suddenly my Coomassie staining has produced strange results (see photo attached). The past 8 gels all share the same trends: the bottom half of the gel fades out and is absent of any bands. I have tried troubleshooting by re-making all of my buffers and using fresh protein extraction, but none of it changes the results. It is so strange, as I've been doing things the same way for over a year now and have never had this problem. I make hand cast Tris-glycine gels. The stacking gel is 4.5% and the separation gel is 10%. I run it first on 80V until the protein drops down into the separation gel, whereby I increase to 120V. Total run time is around 2 hours. Has anyone ever had this happen before?
So I'm still not sure what the problem is....but I think the pH of the gel was changing half way through the run. This is in spite of making sure all buffers were at the correct pH. I changed to bis-tris and the problem has been resolved.
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