ArticleNucleic acids research2002
A pH-jump approach for investigating secondary structure refolding kinetics in RNA.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed, 23 citations in OpenAlex.
- Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis.Biophysical journal · 2019Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Kinetic mechanism of conformational switch between bistable RNA hairpins.Journal of the American Chemical Society · 2012Article
- TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.PLoS computational biology · 2010Article
- A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA.RNA (New York, N.Y.) · 2009Article
- Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism.RNA (New York, N.Y.) · 2007Article
- Structural parameters affecting the kinetics of RNA hairpin formation.Nucleic acids research · 2006Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has been shown that premature translation of the plasmid-mediated toxin in hok/sok of plasmid R1 and pnd/pndB of plasmid R483 is prevented during transcription of the hok and pnd mRNAs by the formation of metastable hairpins at the 5'-end of the mRNA. Here, an experimental approach is presented, which allows the accurate measurement of the refolding kinetics of the 5'-end RNA fragments in vitro without chemically modifying the RNA. The method is based on acid denaturation followed by a pH-jump to neutral pH as a novel way to trap kinetically favoured RNA secondary structures, allowing the measurement of a wide range of biologically relevant refolding rates, with or without the use of standard stopped-flow equipment. The refolding rates from the metastable to the stable conformation in both the hok74 and pnd58 5'-end RNA fragments were determined by using UV absorbance changes corresponding to the structural rearrangements. The measured energy barriers showed that the refolding path does not need complete unfolding of the metastable structures before the formation of the final structures. Two alternative models of such a pathway are discussed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.