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pcrman, on 08 February 2013 - 06:02 PM, said:
whole cell lysate can give you a lot of non-specific binding. I think you can try expressing your protein in bacteria and use the purified protein for EMSA or use nuclear extract from HeLa cells. For proteins to bind DNA, it must be nuclear so nuclear extract is typically used for EMSA.
I was wondering if the DNA-protein binding can be improved by using the whole cell lysate of my human cells instead of purified proteins. Of course, I will include a negative control mutant DNA that's not supposed to bind to my protein of interest.
