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Updated: Jul 15, 2026
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DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
Published on: October 8, 2019
Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands
Andrew J Hampshire1, David A Rusling, Victoria J Broughton-Head
1School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
Methods (San Diego, Calif.)
|May 3, 2007
Summary
DNA footprinting is a simple method to study how sequence-specific DNA-binding ligands interact with DNA. This review covers common probes and techniques for assessing ligand binding and kinetics.
Area of Science:
- Biochemistry
- Molecular Biology
- Genetics
Background:
- DNA-binding ligands are crucial in biological processes.
- Understanding ligand-DNA interactions is key to drug discovery and molecular biology.
- Assessing sequence selectivity and binding affinity is essential.
Purpose of the Study:
- To review the footprinting technique for DNA-ligand interaction studies.
- To detail the use of DNase I and hydroxyl radicals in footprinting.
- To guide the selection and design of DNA substrates for optimal results.
Main Methods:
- DNA footprinting using enzymatic (DNase I) or chemical (hydroxyl radicals) cleavage.
- Protection of DNA from cleavage at ligand binding sites.
- Quantitative footprinting for binding strength estimation.
Main Results:
- Footprinting effectively reveals DNA binding sites.
- The method allows for assessment of ligand sequence selectivity.
- It can be adapted for quantitative analysis of binding affinity and kinetics.
Conclusions:
- DNA footprinting is a versatile and accessible method for studying DNA-binding ligands.
- The technique provides insights into sequence selectivity, binding strength, and kinetics.
- Proper DNA substrate selection is critical for successful footprinting experiments.
