Hi everybody
I am doing EMSA (using pierce Lightshift kit 20148) to study activation of transcription factors (NF-kB and AP-1). Every time I see the shift but the bands are always near the well and I am unable to see the supershift with the addition of antibodies against transcription factor subunits. Firstly I thought that amount of protein is too much but decresing protein changed nothing. I am using BioRad Mini protein 3 Cell electrophoresis system. Could you please suggest something?
Thanks in advance.

If your problem is merely bands too near the well, the solution is simple - just decrease the gel percentage, and/or run the gel longer till the dye front and an appropriate size of a prestained marker has run out.
Also, rather than using something like the mini-Protean for supershift assays, you might want to try using a larger gel for supershift assays.