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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), pp. 128-140. (doi:10.1016/j.ymeth.2007.01.002).

Record type: Article

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.

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More information

Published date: 1 June 2007
Keywords: footprinting, DNase I, hydroxyl radicals, sequence selectivity, dna binding

Identifiers

Local EPrints ID: 56060
URI: http://eprints.soton.ac.uk/id/eprint/56060
ISSN: 1046-2023
PURE UUID: 12ec99ec-df07-4d3c-b334-64d89311e10d
ORCID for David A. Rusling: ORCID iD orcid.org/0000-0002-7442-686X
ORCID for Keith R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 08 Aug 2008
Last modified: 17 Jul 2017 14:31

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Contributors

Author: Andrew J. Hampshire
Author: Victoria J. Broughton-Head
Author: Keith R. Fox ORCID iD

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