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makes cuts in DNA is used to cleave the DNA randomly into subfragments, which are then denatured and separated by gel electrophoresis. The positions of the subfragments are visualized with autoradiography. This procedure is carried out both in the presence and in the absence of a particular DNA-binding protein. When the protein is absent, cleavage is random along the DNA, producing a continuous "ladder" of bands on the autoradiograph (I Figure 18.20). When the protein is present, it binds to specific nucleotides and protects their phosphodiester bonds from cleavage. Therefore, there is no cleavage in the area protected by the protein, and no labeled fragments terminating in the binding site appear on the autoradiograph. Their omission leaves a gap, or "footprint", on the ladder of bands (see Figure 18.20), and the position of the footprint identifies those nucleotides bound tightly by the protein.

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