Footprinting analysis has been used to identify the binding sites of drugs and other ligands bound to DNA molecules (see Chapter 1) (1–3). It is particularly useful for equilibrium binding drugs or ligands that leave no record of their residence position on DNA In the footprinting procedure, the ligand-DNA complex is exposed to an agent or probe that can cleave DNA, and the oligonucleotide products from the cleavage reaction are separated using, for example, electrophoresis in a polyacrylamide gel. If the ligand, when bound, inhibits cleavage by the probe, the oligonucleotides that terminate at the ligand binding site will be underrepresented among the products analyzed using the sequencing gel. This appears as omissions or “footprints” in the spots on the sequencing autoradiogram