help with agarose gel problem - (Apr/11/2007 )
We have recently started to have a problem with our agarose gels. After running the gel in 1X TAE we regularly have either a wavy line (similiar to looking through warped glass) or in more extreme cases, a wavy etching through the gel (similiar to a fault line, where an amount of agarose has been eroded from the gel leaving a groove, sometimes nearly through the full thickness of the gel). The wave is usually at the level of our DNA. We are running 1% gels, and I have tried using new buffer, lower voltage, different buffer rigs, and we still get the same result. Any ideas on how to prevent this? It is getting frustrating as each gel will sometimes have to be run two or three times.
It looks like it could be the only thing you haven't changed: the sample buffer. I don't know why it would be, but if the defect occurs at the DNA, and if you've changed everything else, the sample buffer might just be the culprit.
that may actually be the problem. We recently started using a new Taq with a new buffer. The only reason I would doubt that being the culprit, is because it doesn't happen every time, probably just 50%.
Unless you have some people who distrust the rest of the lab, and have their own aliquot of loading buffer... perhaps their paranoia was justified??