Summary: The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the cleavage pattern of DNA in the presence of a DNA binding protein. If the protein binds to the DNA fragment, the binding site is protected from enzymatic cleavage. This protection will result in a clear area on the gel which is referred to as a “footprint”. By varying the concentration of the DNA-binding protein, the binding affinity of the protein can be estimated according to the minimum concentration of protein at which a footprint is observed.
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