Gel mobility shift assays to detect protein-RNA interactions

Research output: Chapter in Book/Report/Conference proceedingChapter

15 Citations (Scopus)

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

Electrophoretic Mobility Shift Assay
Gels
RNA
Proteins
Calorimetry
RNA-Binding Proteins
Glycine

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
Yakhnin, Alexander Victor ; Yakhnina, Elena Borisovna ; Babitzke, Paul Lee. / Gel mobility shift assays to detect protein-RNA interactions. Bacterial Regulatory RNA: Methods and Protocols. editor / Kenneth C. Keiler. 2012. pp. 201-211 (Methods in Molecular Biology).
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Yakhnin, AV, Yakhnina, EB & Babitzke, PL 2012, Gel mobility shift assays to detect protein-RNA interactions. in KC Keiler (ed.), Bacterial Regulatory RNA: Methods and Protocols. Methods in Molecular Biology, vol. 905, pp. 201-211. https://doi.org/10.1007/978-1-61779-949-5_12

Gel mobility shift assays to detect protein-RNA interactions. / Yakhnin, Alexander Victor; Yakhnina, Elena Borisovna; Babitzke, Paul Lee.

Bacterial Regulatory RNA: Methods and Protocols. ed. / Kenneth C. Keiler. 2012. p. 201-211 (Methods in Molecular Biology; Vol. 905).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Yakhnin AV, Yakhnina EB, Babitzke PL. Gel mobility shift assays to detect protein-RNA interactions. In Keiler KC, editor, Bacterial Regulatory RNA: Methods and Protocols. 2012. p. 201-211. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-949-5_12