I have to do an EMSA assay with a protein of pI 6. Is it possible to carry out the assay at pH of 4, or such an acid buffer may alter DNA-DNA or DNA-protein interactions? Or may be could be better at pH7 although protein has negative charge at that pH
Perhaps you have a typo in your question- at pH>pI, your protein will be negatively charged, not positively charged. And since many proteins use electrostatic interactions to interact with DNA, a negative charge could be a disadvantage for protein-DNA binding. Nonetheless, total protein charge matters less than the local charge potential at the prospective DNA binding surface. Check what is known about the mechanism of DNA binding for your protein of interest. In general, you want your EMSA to reflect physiological conditions (ie. not pH 4).
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