I am new to PFGE... So at first I had a problem with my bands not separating but optimized by increasing the running time from 21 to 24 hours which allowed my bands to separate. Now I am kind of having a problem with my gel constantly breaking at the 'feet' (holes) where I put agarose in to hold my gel on one place but that doesn't seem to keep the gel intact and that results in my bands being skew. The % of my gel is 1%... should I try 2% for my gel to be stronger? I'm a little hesitant because I'm not sure if it will be too dense then to separate my DNA. Does anyone know anything about this? Or have had similar problems?
Will really appreciate the help!!! :-)