Footprinting analysis of sequence-specific DNA-drug interactions.

Footprinting is a technique widely used in the analysis of sequence-specificity of proteins and drugs which bind to DNA in an equilibrium manner. Footprinting studies combine the enzymatic or chemical cleavage of DNA with the analysis of the resulting products by sequencing gels, thus revealing the position and length of individual binding sites. This review compares the information that can be obtained by using different footprinting agents and the characteristics of DNA-drug interactions that can be inferred from footprinting results.