EMSA for non-DNA binding protein - (Jan/23/2008 )

im trying to perform an EMSA for a protein that is part of a transcriptional complex but does not bind DNA directly. is this possible/difficult? any experience anyone?

well, when you do an EMSA you probe with an oligo corresponding to the DNA binding sequence recognized by your TF.

I'm thinking you could do an EMSA - then add a second antibody against your POI and probe for it separately. add controls - one band means your POI is part of the complex, two means it's not

I suppose it all depends on which question you'd like to answer?