Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands

Andrew J. Hampshire, David A. Rusling, Victoria J. Broughton-Head, Keith R. Fox

    Research output: Contribution to journalLiterature reviewpeer-review

    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.

    Original languageEnglish
    Pages (from-to)128-140
    Number of pages13
    JournalMethods
    Volume42
    Issue number2
    Early online date27 Apr 2007
    DOIs
    Publication statusPublished - 1 Jun 2007

    Keywords

    • Base Sequence
    • Binding Sites
    • DNA/chemistry
    • DNA Footprinting/methods
    • Deoxyribonuclease I/chemistry
    • Hydroxyl Radical/chemistry
    • Kinetics
    • Ligands
    • Sensitivity and Specificity
    • Substrate Specificity

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