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Methods Mol Biol. 2012;905:201-11. doi: 10.1007/978-1-61779-949-5_12.

Gel mobility shift assays to detect protein-RNA interactions.

Author information

1
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.

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.

PMID:
22736005
PMCID:
PMC4687016
DOI:
10.1007/978-1-61779-949-5_12
[Indexed for MEDLINE]
Free PMC Article

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