I am planning to perform EMSA with a supposedly DNA binding protein and a 22-mer oligo DNA. But I was wondering what's the difference between using purified protein fraction and cell extract extracts + noncompetitve DNA such as dIdC? My protein is transiently transfected to human cells using lipofectamine 2000.
I already can have my protein of interest purified from 293T human cells using anti-FLAG beads, but I can only get this much (see attached picture) protein. It's also time consuming and costly. Is this much protein expression enough for whole cell EMSA?