EMSA probe running weird - (Mar/09/2007 )

Hi all, new to the forum...

I'm having some problems with my EMSA... mainly, when I add my extract, the free probe at the bottom runs faster than the free probe without any extract. I am just wondering if there is anything that I should be looking at specifically that could cause this... gel, running buffer, binding buffer?

Thanks.

well, what do you do for controls? for neg controls, if you are having wierd stuff like that, you can narrow it down by running controls like: no binding buffer / no extract / etc; substitute PBS or diltuted binding buffer or whatever for each reagent and you can figure out what's making it run faster

how much of the volume comes from the extract? could it be the buffer that the extract is in?