Hi,
I know that EMSA is used to study protein:DNA or protein:RNA binding where as western blot is used to detect protein. What I really don't get is why you cant use each of these techniques for both purposes. For instance why can't you just run an EMSA and try to find the protein you are looking for. Lets say you wanted to see the level of phosphorylated protein X, why is it that western blot would be used to determine it rather than EMSA.
Let me elaborate, lets say the protein of interest gets phosphorylated (PROTEIN A) and binds to another protein (PROTEIN B) and together they bind to DNA. If you want to find the phosphorylated levels of Protein A and B alone you do Western blot where as if you wanted to study ProteinA:ProteinB- DNA complex you use EMSA, can anyone help me get out of this tangled thought.
Cheers,
Nescafe.