Biochemical Methods for the Study of the FinO Family of Bacterial RNA Chaperones

Hyeong Jin Kim; Steven Chaulk; David Arthur; Ross A Edwards; J N Mark Glover

doi:10.1007/978-1-0716-0231-7_1

Biochemical Methods for the Study of the FinO Family of Bacterial RNA Chaperones

Methods Mol Biol. 2020:2106:1-18. doi: 10.1007/978-1-0716-0231-7_1.

Authors

Hyeong Jin Kim¹, Steven Chaulk¹, David Arthur¹, Ross A Edwards¹, J N Mark Glover²

Affiliations

¹ Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
² Department of Biochemistry, University of Alberta, Edmonton, AB, Canada. mark.glover@ualberta.ca.

PMID: 31889248
DOI: 10.1007/978-1-0716-0231-7_1

Abstract

The FinO family of proteins constitutes a group of RNA chaperones that interacts with small RNAs (sRNAs) to regulate gene expression in many bacterial species. Here we describe detailed protocols for the biochemical analysis of the RNA chaperone activity of these proteins. Methods are described for preparation of RNA, RNA 5' end labeling with radioisotope and modified EMSA protocols to test the ability of these proteins to catalyze RNA strand exchange and RNA duplex formation.

Keywords: Annealing assay; Chaperone activity; Duplexing assay; FinO; ProQ; RNA chaperone; RocC; Strand displacement assay; Strand exchange assay.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Electrophoretic Mobility Shift Assay / methods*
Escherichia coli Proteins / chemistry*
Escherichia coli Proteins / metabolism
Molecular Chaperones / chemistry*
Molecular Chaperones / metabolism
Molecular Probe Techniques*
RNA Stability
RNA, Small Untranslated / chemistry*
RNA, Small Untranslated / metabolism
RNA-Binding Proteins / chemistry*
RNA-Binding Proteins / metabolism
Repressor Proteins / chemistry*
Repressor Proteins / metabolism

Substances

Escherichia coli Proteins
Molecular Chaperones
ProQ protein, E coli
RNA, Small Untranslated
RNA-Binding Proteins
Repressor Proteins
FinO protein, E coli