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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]

Footprinting: A method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. [In: Methods Related to DNA Sequence Recognition]
Footprinting: A method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. [In: Methods Related to DNA Sequence Recognition]
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.
footprinting, DNase I, hydroxyl radicals, sequence selectivity, dna binding
1046-2023
128-140
Hampshire, Andrew J.
68aac3b7-88b7-4417-8793-9c2a06b01abc
Rusling, David A.
d08f1f97-f8a9-4980-a025-ae41c23a938f
Broughton-Head, Victoria J.
d094aa77-c889-4747-84d2-55542805c67c
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f
Hampshire, Andrew J.
68aac3b7-88b7-4417-8793-9c2a06b01abc
Rusling, David A.
d08f1f97-f8a9-4980-a025-ae41c23a938f
Broughton-Head, Victoria J.
d094aa77-c889-4747-84d2-55542805c67c
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f

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).

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: 16 Mar 2024 02:36

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Contributors

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

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