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Related Concept Videos

Overview of DNA Repair02:25

Overview of DNA Repair

In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
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Related Experiment Video

Updated: Jul 4, 2026

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins
09:59

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

Published on: June 4, 2021

Footprinting protein-DNA complexes using the hydroxyl radical.

Swapan S Jain1, Thomas D Tullius

  • 1Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.

Nature Protocols
|June 13, 2008
PubMed
Summary

Hydroxyl radical footprinting offers high-resolution structural details of DNA-protein complexes. This accessible method provides superior insights compared to DNase I footprinting.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Hydroxyl radical footprinting is a key technique for analyzing DNA structure and DNA-protein interactions.
  • The hydroxyl radical's reactivity and lack of base specificity enable high-resolution mapping of protein-binding sites.
  • Existing methods may not achieve the same level of structural detail as hydroxyl radical footprinting.

Purpose of the Study:

  • To present a detailed protocol for hydroxyl radical footprinting of DNA-protein complexes.
  • To provide a troubleshooting guide for optimizing DNA cleavage in footprinting experiments.
  • To enable researchers to efficiently study DNA-protein interactions.

Main Methods:

  • Utilizing hydroxyl radicals to induce cleavage in DNA molecules bound by proteins.

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In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans
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  • Employing denaturing electrophoresis to separate cleavage products.
  • Identifying protein-binding sites on nucleic acid molecules based on cleavage patterns.

    • Main Results:

    • The described protocol allows for efficient DNA cleavage in both the presence and absence of proteins.
    • The method is cost-effective, using readily available reagents and equipment.
    • The entire footprinting protocol can be completed within two days.

    Conclusions:

    • Hydroxyl radical footprinting is a powerful and accessible technique for high-resolution structural studies of DNA-protein complexes.
    • The provided protocol facilitates efficient and reliable footprinting experiments.
    • This method offers advantages over traditional techniques like DNase I footprinting for detailed structural analysis.