ArticleNucleic acids research2013
Study of E. coli Hfq's RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 18 citations in OpenAlex.
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- A Dual-Color Electrophoretic Mobility Shift Assay to Examine RNA-Binding and RNA Chaperone Activity Simultaneously.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation.Nucleic acids research · 2024Article
- c-di-GMP regulates activity of the PlzA RNA chaperone from the Lyme disease spirochete.Molecular microbiology · 2023Article
- Hfq chaperone brings speed dating to bacterial sRNA.Wiley interdisciplinary reviews. RNA · 2018Review
- Fluorescence reporters for Hfq oligomerization and RNA annealing.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor.Nucleic acids research · 2014Article
- Identifying and characterizing Hfq-RNA interactions.Methods (San Diego, Calif.) · 2013Review
- The nonstructural protein 2C of a Picorna-like virus displays nucleic acid helix destabilizing activity that can be functionally separated from its ATPase activity.Journal of virology · 2013Article
- Cycling of RNAs on Hfq.RNA biology · 2013Review
- Exploring sRNA-mediated gene silencing mechanisms using artificial small RNAs derived from a natural RNA scaffold in Escherichia coli.Nucleic acids research · 2013Article
- Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA.RNA biology · 2013Article
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Folding of RNA molecules into their functional three-dimensional structures is often supported by RNA chaperones, some of which can catalyse the two elementary reactions helix disruption and helix formation. Hfq is one such RNA chaperone, but its strand displacement activity is controversial. Whereas some groups found Hfq to destabilize secondary structures, others did not observe such an activity with their RNA substrates. We studied Hfq's activities using a set of short RNAs of different thermodynamic stabilities (GC-contents from 4.8% to 61.9%), but constant length. We show that Hfq's strand displacement as well as its annealing activity are strongly dependent on the substrate's GC-content. However, this is due to Hfq's preferred binding of AU-rich sequences and not to the substrate's thermodynamic stability. Importantly, Hfq catalyses both annealing and strand displacement with comparable rates for different substrates, hinting at RNA strand diffusion and annealing nucleation being rate-limiting for both reactions. Hfq's strand displacement activity is a result of the thermodynamic destabilization of the RNA through preferred single-strand binding whereas annealing acceleration is independent from Hfq's thermodynamic influence. Therefore, the two apparently disparate activities annealing acceleration and duplex destabilization are not in energetic conflict with each other.
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