Footprinting: A method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. [In: Methods Related to DNA Sequence Recognition]


Hampshire, Andrew J., Rusling, David A., Broughton-Head, Victoria J. and Fox, Keith R. (2007) Footprinting: A method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. [In: Methods Related to DNA Sequence Recognition]. Methods, 42, (2), 128-140. (doi:10.1016/j.ymeth.2007.01.002).

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Description/Abstract

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.

Item Type: Article
ISSNs: 1046-2023 (print)
Related URLs:
Keywords: footprinting, DNase I, hydroxyl radicals, sequence selectivity, dna binding
Subjects: Q Science > QH Natural history > QH301 Biology
Divisions: University Structure - Pre August 2011 > School of Biological Sciences
ePrint ID: 56060
Date Deposited: 08 Aug 2008
Last Modified: 27 Mar 2014 18:38
URI: http://eprints.soton.ac.uk/id/eprint/56060

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