I've performed this assay on eukaryotic protein extracts in the presence of the poly dI/dC in order to remove all the aspecific interactions of the proteins with the DNA probe. I observe a shift of the alleged protein-DNA complex, a disappearing of that shift when I incubate the extract with the antibody specific for the protein I'm studying (the antibody recognizes the whole sequence of the protein), but nothing changes when I incubate the extracts both with 100x and 500x of cold competitor. Do you have any suggestions/explanations? Thanks in advance.
Antonio
