| | Re: Emsa
In my experience, a 6% polyacrylamide (PA) gel resolves bands above 100 bp, 8% might resolve a little further. I have only gone to a 12% PA gel, which resolved me bands from 70 to 40 bp quite well, the latter showing a bit faint, though.
EMSA technique allows you to see if a protein of interest binds to DNA, this is done by using a probe (radio/fluorescent-labeled DNA) containing the putative binding sequence for the protein. After hybridize probes with proteins, inhibitors or whatever your essay requires; you run the probes in PAGE. Free (unbound) probes will show an electrophoretic pattern while protein-bound probes will be "delayed", this is, they will migrate less across the gel than unbound probes.
The above paragraph is to show you that in EMSA you run DNA so it requires a DNA PAGE not a protein PAGE (SDS-PAGE). DNA does not need to "stack" as it is done for proteins, so PA gels are done in one piece and they run smoothly, just look at the picture.
Hope this helps you.
By the way, the pic I post is a PA gel with silver staining showing a BSA (protein) band (upper), DNA fragments (below) and DNA ladder (right).