DNA/protein mobility shift assay

[Mark Schoenbeck]

I am preparing to look at protein binding to regions of promoter DNA.  I
would appreciate hearing from anyone who can suggest a systematic method
for optimizing protein binding conditions for a gel mobility shift
assay.  A previous lab member here used nuclear and whole-cell extracts
and allowed 10 minutes for binding before running the labeled DNA
through a 12% acrylamide 0.5 x TBE buffered gel.  Can anyone tell me if
this is even a suitable buffer for retaining protein-DNA interactions?

Thanks in advance for any assistance you can offer,

Mark Schoenbeck
Agronomy
University of Kentucky