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DNA Agarose Gel Electrophoresis

DNA Agarose Gel Electrophoresis

Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify DNA fragments using a gel extraction protocol.
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Electrophoresis is a powerful analytical separation technique that relies on the differential migration of charged species when subjected to an electric field. The core strength of electrophoresis lies in its ability to separate high-molecular-weight species in complex mixtures. It has found widespread use in biochemistry, molecular biology, and analytical chemistry, allowing the separation of compounds like amino acids, nucleotides, carbohydrates, and proteins with excellent resolution.
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Updated: May 28, 2026

An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides

An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides

Published on: November 29, 2016

Mobility shift DNA-binding assay using gel electrophoresis.

S Buratowski¹, L A Chodosh

¹Harvard Medical School, Boston, Massachusetts, USA.

Current Protocols in Pharmacology

|October 1, 2011

Summary

This summary is machine-generated.

This study details a sensitive gel electrophoresis method for identifying DNA-binding proteins. The technique, nondenaturing polyacrylamide gel electrophoresis (PAGE), allows for precise characterization of protein-DNA interactions.

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Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes

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Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes

Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes

Published on: July 28, 2017

Area of Science:

Molecular Biology
Biochemistry
Genetics

Background:

Identifying sequence-specific DNA-binding proteins is crucial for understanding gene regulation.
Traditional methods can be time-consuming and lack sensitivity.
A need exists for rapid, sensitive, and quantitative assays for DNA-binding proteins.

Purpose of the Study:

To present a simple, rapid, and sensitive gel electrophoresis assay for detecting sequence-specific DNA-binding proteins.
To demonstrate the utility of the assay for both purified proteins and crude extracts.
To illustrate the quantitative capabilities of the assay for characterizing protein-DNA interactions.

Main Methods:

Nondenaturing polyacrylamide gel electrophoresis (PAGE) of end-labeled DNA fragments incubated with proteins.
Analysis of retarded DNA fragment mobility to detect protein-DNA complex formation.
Application of competition assays, antibody supershift assays, and multicomponent gel shift assays for further characterization.

Main Results:

The nondenaturing PAGE assay effectively detects sequence-specific DNA-binding proteins.
The assay allows for the visualization of discrete protein-DNA complexes.
Quantitative analysis of binding affinity, kinetics, and specificity is achievable.

Conclusions:

Nondenaturing PAGE is a powerful and versatile tool for studying DNA-binding proteins.
The assay facilitates the characterization of uncharacterized DNA-binding factors.
This method provides a comprehensive approach to analyzing protein-DNA interactions.