Hi everyone, I'm working on a transcription factor which binds as a dimer its target DNA, composed by two palindromic half-sites (5'-TTGGCnnnnnGCCAA-3'). Talking about Electrophoretic Mobility Shift Assay, I was wondering if I should consider the concentration of the dimer or the one of the monomer. I'll explain myself better: I use the relative concentration with respect to the DNA probe (20nM) to express the concentrations of the protein serial dilutions, so that in my lanes I will have 1x (20nM of protein), 2x (40nM) and so on and so forth. Do you think it is more appropriate to consider the ratio between DNA concentration and monomer concentration or the one between DNA concentration and dimer concentration? Maybe it's a naive question but I wanted to know your opinion.
Thank you all,
Michele
The important thing is to be clear about it when you present the result. You can state the concentration "as monomer" or "as dimer," as you see fit. If the protein is normally found in solution as the dimer, I would express it "as dimer," whereas if it exists in solution as a monomer, I would express it "as monomer."
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