Gel mobility shift assays to detect protein-RNA interactions

Alexander V. Yakhnin, Helen Yakhnin, Paul Babitzke

Research output: Chapter in Book/Report/Conference proceedingChapter

34 Scopus citations


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
Number of pages11
StatePublished - 2012

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics


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