When doing nuclear extraction for EMSA one would get a portion of letís say transcription factors that is bound to DNA and another portion that is not bound, (right?). So my question is: those proteins that are already bound to DNA would one detect them in EMSA?
Basically what I am getting at is that if condition-1 facilitates DNA binding then you would get a high amount nuclear extract that is pre-bound to DNA and when running those proteins on EMSA, you would interpret that as low binding ability since the pre-bound portion is higher than the portion that will bind during EMSA.
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Theoretical question about EMSA
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