problems with DNase1 footprinting - DNA won't enter a denaturing urea polyacrylamide gel (May/21/2009 )

Does anyone know why DNA would not enter a 5% acrylamide, 7.5M urea gel? I'm doing a DNase 1 footprint and I can't get the DNA to enter the gel. I did a phenol/chloroform, ethanol precip of the DNA and it should be relatively free of salt, but still it won't enter. Also, the dye markers migrate funny with the bromophenol blue marker disappearing during the run, about half way down. Not normal. Any ideas/suggestions?

thanks,

dusty

Check the buffer pH.

You might still have etOH in the sample. try warming the tube with the lid open for 5-10 minutes and repeating the gel.

No idea, though, about the disappearing dye.