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Related Experiment Video

Updated: Jun 30, 2026

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example
12:44

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example

Published on: December 3, 2014

Electrophoretic Mobility Shift Assay (EMSA) for Assessing RNA-Protein Binding and Complex Formation Using Recombinant

David W J McQuarrie1, Matthias Soller2

  • 1Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA.

Bio-Protocol
|June 29, 2026
PubMed
Summary

This study provides a detailed protocol for Electrophoretic Mobility Shift Assays (EMSAs) to analyze RNA-protein interactions. It covers RNA and protein preparation, binding reactions, and gel electrophoresis for gene regulation studies.

Keywords:
Band-shift assayEMSAIn vitro transcriptionKd determinationMultimerizationProtein complexRNA–protein complexRecombinant protein expression

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Related Experiment Videos

Last Updated: Jun 30, 2026

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example
12:44

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example

Published on: December 3, 2014

Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes
06:36

Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes

Published on: July 28, 2017

An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • RNA-protein interactions are crucial for post-transcriptional gene regulation.
  • Electrophoretic Mobility Shift Assays (EMSAs) are a standard method for studying these interactions, providing insights into binding affinity and complex formation.

Purpose of the Study:

  • To provide a comprehensive, step-by-step protocol for performing EMSAs.
  • To detail the generation and purification of radiolabeled RNA and recombinant proteins.
  • To demonstrate reproducible EMSA setup and analysis using ELAV protein as an example.

Main Methods:

  • In vitro transcription for 32P-radiolabeled RNA production and purification.
  • Recombinant protein expression and purification in E. coli.
  • Microtiter plate-based binding reactions with serial dilutions.
  • Native low-crosslinked acrylamide gel electrophoresis for complex separation.

Main Results:

  • Efficient production and purification of radiolabeled RNA probes.
  • Reproducible RNA-protein binding assays demonstrated with recombinant ELAV.
  • Quantitative binding curves obtained through serial dilution in microtiter plates.
  • High-resolution separation of RNA-protein complexes on native gels.

Conclusions:

  • The protocol enables robust and quantitative analysis of RNA-protein interactions.
  • This method is valuable for studying gene regulation at the post-transcriptional level.
  • The detailed instructions and troubleshooting guide facilitate successful EMSA execution.