I'm looking for a good binding buffer to look at the binding potential of a repressor with a region of DNA. I am going to do a gel-shift assay to prove the binding. Any suggestions on an incubation time would be welcome also.
When we investigate protein-DNA interaction using MicroScale Thermophoresis, we have best experience with a buffer at pH 7-7.5 and 50-150 mM NaCl, maybe a little bit of MgCl2 (10mM).
Helix-Turn-helix motifs to my knowledge do not need anything special for correct folding, so you should be able to get a binding in a standard buffer condition.
In case you would like to determine binding affinities also free in solution without any gel (which can be very smeary and unclear), I would recommend MicroScale Thermophoresis. It's fast and easy, and works really nicely for protein-DNA interactions!
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