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 language | English |
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Pages (from-to) | 128-140 |
Number of pages | 13 |
Journal | Methods |
Volume | 42 |
Issue number | 2 |
Early online date | 27 Apr 2007 |
DOIs | |
Publication status | Published - 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