Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands.
Footprinting is a simple method for assessing the sequence selectivity of DNA-binding ligands. The method is based on the ability of the ligand to protect DNA from cleavage at its binding site. This review describes the use of DNase I and hydroxyl radicals, the most commonly used footprinting probes, in footprinting experiments. The success of a footprinting experiment depends on using an appropriate DNA substrate and we describe how these can best be chosen or designed. Although footprinting was originally developed for assessing a ligand's sequence selectivity, it can also be employed to estimate the binding strength (quantitative footprinting) and to assess the association and dissociation rate constants for slow binding reactions.
Hampshire
Andrew J
AJ
School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
Rusling
David A
DA
Broughton-Head
Victoria J
VJ
Fox
Keith R
KR
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D018983:DNA Footprinting / Q000379:methods*; D003850:Deoxyribonuclease I / Q000737:chemistry / Q000378:metabolism; D017665:Hydroxyl Radical / Q000737:chemistry; D007700:Kinetics; D008024:Ligands; D012680:Sensitivity and Specificity; D013379:Substrate Specificity
D008024:Ligands; D017665:Hydroxyl Radical; D004247:DNA; D003850:Deoxyribonuclease I