More specifically, if my protein (transcription factor: TF) is known, the binding site is also known. I have a couple of TF mutants and want to quantitatively measure the differences in binding between the wild-type TF and the mutants TF to the DNA sequence. I won't likely need high throughput methods that measure "hundreds and thousands of binding sites", but I need something sensitive enough to capture the differences between the wild-type and the mutants TF.
update: My TF comes from E. coli.
You have lots of choices. Are you going to use in vitro or in vivo? Do a literature search for your organism. You might even find a commercially available kit if it's a common transcription factor and/or a common organism.
Based on what you are planning, try a reporter assay in Vivo. You may need a fancy microplate reader.
Direct measurement of protein to DNA binding is doable but the problem is with DNA stability. The easiest way would be to run a DNA gel shift assay to estimate your affinity differences.
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