PFGE - ?contamination - Contamination problem?! (Jun/19/2006 )

I hope someone can help me with this problem.
Our lab has been doing PFGE for quite some time now. It seems that:
(1) when we stop using the equipment for a period of time, it degrades the DNA when we use it again.
(2) sometimes when we take the photo after destaining, the DNA bands start disappearing if we take longer time to adjust/resize.

I don't have experience with PFGE, but I can tell you that when I was trying to take pictures of agarose gels, the bands were disappearing on my gels as well. I think it is because when you expose DNA to UV light, you are nicking the DNA.

Check the pH of your buffers. Long run times on pulse field gels can sometimes dramatically change the buffer pH.