Gel mobility shift assays to detect protein-RNA interactions

Alexander Victor Yakhnin, Elena Borisovna Yakhnina, Paul Lee Babitzke

Research output: Chapter in Book/Report/Conference proceedingChapter

20 Scopus citations

Abstract

The gel mobility shift assay is a powerful technique for detecting and quantifying protein-RNA interactions. While other techniques such as filter binding and isothermal titration calorimetry (ITC) are available for quantifying protein-RNA interactions, gel shift analysis provides the added advantage that you can visualize the protein-RNA complexes. In the gel shift assay, protein-RNA complexes are typically separated from the unbound RNA using native polyacrylamide gels in Tris/borate/EDTA buffer, although an alternative Tris-glycine buffering system is superior in many situations. Here, we describe both gel shift methods, along with strategies to improve separation of protein-RNA complexes from free RNA, which can be a particular challenge for small RNA binding proteins.

Original languageEnglish (US)
Title of host publicationBacterial Regulatory RNA
Subtitle of host publicationMethods and Protocols
EditorsKenneth C. Keiler
Pages201-211
Number of pages11
DOIs
StatePublished - Jul 27 2012

Publication series

NameMethods in Molecular Biology
Volume905
ISSN (Print)1064-3745

    Fingerprint

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Yakhnin, A. V., Yakhnina, E. B., & Babitzke, P. L. (2012). Gel mobility shift assays to detect protein-RNA interactions. In K. C. Keiler (Ed.), Bacterial Regulatory RNA: Methods and Protocols (pp. 201-211). (Methods in Molecular Biology; Vol. 905). https://doi.org/10.1007/978-1-61779-949-5_12