Dear Community, Sorry for this off topic question. I am dealing with a non specific DNA binding protein. In a non radio-labelled EMSA DNA:protein titration experiment when I EtBr stained the 5% native acrylamide gel, I could see the DNA control (101 bps) but as the amount of my protein increases I saw the free DNA band getting thinner and thinner but I could not see any band shift and probably all the complex stuck at wells. But, even if I assume the whole DNA length is occupied by my protein (I determined the ratio to be 1:15 ish) the molecular weight should not reach the molecular weight of the highest DNA marker band (20kbps = 13,200 kDa). Then why I could not see a retarded band in the gel? Or is it forming a EtBr resistant nucleoprotein filament? Could you guys please give me an idea/suggestions?
Many thanks in advance...!!! My best regards, Sudipta.
