EMSA supershift problem - (Aug/30/2012 )

I got weird result from EMSA supershift assay. My shift band was still there with same intensity, but my free probe band shifted to a higher position. Does this mean my antibody binds free probe nonspecifically? Or maybe my shift is not caused by the transcription factor of interest? Any of you have experienced similar problems? Thanks

Hi Emmalee,

It looks like if your antibody its binding to another protein that its binding to your probe instead to your protein of interest. When I was doing my super-shifts I always was using a negative control antibody to show that the shift was specific to my antibody-protein of interest-probe complex.