Gel shifts: run them fast or slow?

[John Pawlowski]

Hi all,
I am interested in getting the best possible resolution in gel shift-
assays in which radiolabelled oligonucleotide probes are incubated with 
protein extracts from cells, and run under non-denaturing conditions. A 
particular question I have is whether or not the gels should be run fast 
(approx 2 hours for 15 cm gel) or slow (overnight). It seems to me that 
running the gels fast (applying a higher current) might "strip" away the 
probe from the bound protein due to charge differences between the probe 
and the protein. On the other hand, it seems to me that applying a lower 
current and running the gel slowly would give the oligonucleotide 
probe/protein complexes more time to disassociate in the gel, leading to 
poorer resolution. All thoughts on these questions are greatly 
appreciated, as well as any other advice on performing high-quality gel-
shift experiments. Thanks much.

John Pawlowski
johnp at qadas.com