PFGE help - bands only running half way - (Apr/11/2007 )

Hi

I have been trying to do PFGE on Staphs and I have had numerous problems the latest being that my bands only seem to run halfway down the gel. There is nothing in the bottom half of my gel. Does anyone know why this is?

Thanks

i know it sounds trivial, and you have probably thought of that, but are you staining your gel with EtBr at the beginning or at the end of the run? since when you put in EtBR from the start and let gel run for extended periods of time, the EtBr in the lower half of the gel will deplete, and hence there will will no bands visible anymore....so when doing long PFGE runs, i usually stain the gel after the run, i know it's messier, but gives better results...

mike