A method for identification of a protein-binding site on a DNA molecule. For example, DNase I footprinting identifies those phosphodiester bonds which are covered by a specific DNA-binding protein and thus protected from cleavage by DNase I.

Technique for identifying protein-binding regions of DNA or RNA. A radiolabeled nucleic acid sample is digested with a nuclease in the presence and absence of a specific binding protein. Because regions of DNA or RNA with bound protein are protected from digestion, the patterns of fragment bands separated by gel electrophoresis obtained from protected and unprotected samples differ, permitting identification of the protein-binding regions. ( Figure 10-6)

Footprinting is the technique of gathering information about computer systems and the entities they belong to.