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DNA Isolation

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Related Experiment Video

Updated: Apr 3, 2026

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

In Vitro DNase I Footprinting.

Benoît P Leblanc¹, Tom Moss²

¹Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'université, Sherbrooke, QC, Canada, J1K 2R1. Benoit.Leblanc@usherbrooke.ca.

Methods in Molecular Biology (Clifton, N.J.)

|September 26, 2015

Summary

DNase I footprinting reveals DNA-protein interactions by comparing DNA digestion patterns with and without proteins. This method identifies protected DNA regions and protein binding affinities, aiding in understanding DNA-protein complex formation.

Keywords:

DNase I Footprinting Protection Sequencing

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Area of Science:

Molecular Biology
Biochemistry
Genetics

Background:

Proteins binding to DNA can block access for enzymes like nucleases.
Bulky nucleases, such as DNase I, are particularly affected by DNA-protein associations.

Purpose of the Study:

To detail the DNase I footprinting method for studying DNA-protein interactions.
To explain how this technique identifies DNA regions protected by bound proteins.

Main Methods:

Comparing DNA fragment patterns generated by partial DNase I digestion in the absence and presence of a specific protein.
Analyzing gel electrophoresis results to identify regions with fewer or no DNA fragments (protected sites) or increased cleavage.

Main Results:

The presence of DNA-binding proteins creates 'footprints'—blank regions on gels indicating protection from DNase I digestion.
Enhanced cleavage sites can also be observed, suggesting increased nuclease accessibility.
The method can detect multiple binding sites and compare their affinities.

Conclusions:

DNase I footprinting is a valuable technique for mapping DNA-protein interactions.
It provides insights into DNA binding sites, protein occupancy, and relative binding strengths.
This method aids in characterizing the functional role of DNA-binding proteins.