Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: May 11, 2026

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Identifying and characterizing Hfq-RNA interactions.

M A Faner¹, A L Feig

¹Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, United States.

Methods (San Diego, Calif.)

|May 28, 2013

Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.

RNA (New York, N.Y.)·2001

Same author

The use of manganese as a probe for elucidating the role of magnesium ions in ribozymes.

Metal ions in biological systems·2000

Same author

Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy.

Chemistry & biology·1999

Same author

Cryoenzymology of the hammerhead ribozyme.

RNA (New York, N.Y.)·1998

Same author

Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb.

Science (New York, N.Y.)·1998

Same author

Mutagenicity of the nuclease activity of 1,10-phenanthroline-copper ion.

Biochemical and biophysical research communications·1988

Bacteria use small regulatory RNAs (sRNAs) to control stress and virulence. This review details methods for discovering Hfq-dependent RNAs, their interactions, and functions in bacterial gene regulation.

Area of Science:

Microbiology
Molecular Biology
Genetics

Background:

Bacteria utilize small regulatory RNAs (sRNAs) to modulate stress responses and virulence.
sRNAs regulate target messenger RNAs (mRNAs) by influencing ribosomal access and RNA decay.
Trans-encoded sRNAs require the RNA binding protein Hfq for base pairing with target mRNAs.

Purpose of the Study:

To review methodologies for identifying Hfq-binding RNAs.
To outline techniques for characterizing RNA-RNA interactions.
To elucidate the functional roles of Hfq-dependent sRNAs in bacteria.

Main Methods:

Literature review of discovery approaches for Hfq-binding RNAs.
Analysis of methods for characterizing RNA-RNA interactions.

Keywords:

(ARN)(x)2-methylnicotinic acid imidizolide 5′ phosphate dependent terminator endonuclease 5′ rapid amplification of cDNA ends 5′RACE CLIP CLR EMSA HTS Hfq ITC LC–MS MALDI-TOF MAST MEME N-methylisatoic anhydride NAI NMIA Protein–RNA interactions RNP RT SELEX SHAPE SPR TBE TEX Tris/Borate/EDTA co-IP coimmunoprecipitation context likelihood of relatedness cross-linking and immunoprecipitation electrophoretic mobility gel shift assay high through-put sequencing isothermal titration calorimetry liquid chromatography–mass spectrometry matrix-assisted laser desorption/ionization time-of-flight motif alignment and search tool multiple em for motif elicitation ncRNA qRT-PCR quantitative reverse transcription polymerase chain reaction reverse transcription ribonucleoprotein sRNA sRNAs selective 2′-hydroxyl acylation analyzed by primer extension small regulatory RNAs surface plasmon resonance systematic evolution of ligands by exponential enrichment where A is adenine, R is adenine or guanosine, and N is any nucleotide

Related Experiment Videos

Last Updated: May 11, 2026

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Synthesis of functional studies on bacterial sRNAs.

Main Results:

Established methods exist for discovering Hfq-binding RNAs.
Techniques for characterizing RNA-RNA interactions are available.
Functional roles of Hfq-dependent sRNAs are increasingly understood.

Conclusions:

Hfq-dependent sRNAs are crucial for bacterial gene regulation across diverse species.
Further research using presented methods will expand our understanding of sRNA networks.
This review consolidates knowledge on Hfq-dependent sRNA discovery and function.