ArticleBiophysical journal2010
Predicting secondary structural folding kinetics for nucleic acids.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.Biophysical journal · 2019Article
- Effects of flanking regions on HDV cotranscriptional folding kinetics.RNA (New York, N.Y.) · 2018Article
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA.Frontiers in microbiology · 2018Article
- Computational Methods for Modeling Aptamers and Designing Riboswitches.International journal of molecular sciences · 2017Review
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
- RNA folding pathways and kinetics using 2D energy landscapes.Journal of mathematical biology · 2015Article
- The impact of a ligand binding on strand migration in the SAM-I riboswitch.PLoS computational biology · 2013Article
- Abstract folding space analysis based on helices.RNA (New York, N.Y.) · 2012Article
- Kinetic mechanism of conformational switch between bistable RNA hairpins.Journal of the American Chemical Society · 2012Article
- Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods.Nucleic acids research · 2012Article
- Predicting folding pathways between RNA conformational structures guided by RNA stacks.BMC bioinformatics · 2012Article
- Sequence-structure relationships in yeast mRNAs.Nucleic acids research · 2012Article
- Cotranscriptional folding kinetics of ribonucleic acid secondary structures.The Journal of chemical physics · 2011Article
- Folding kinetics for the conformational switch between alternative RNA structures.The journal of physical chemistry. B · 2010Article
- Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design.Wiley interdisciplinary reviews. RNAReview
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3 authors.
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Abstract
We report a new computational approach to the prediction of RNA secondary structure folding kinetics. In this approach, each elementary kinetic step is represented as the transformation between two secondary structures that differ by a helix. Based on the free energy landscape analysis, we identify three types of dominant pathways and the rate constants for the kinetic steps: 1), formation; 2), disruption of a helix stem; and 3), helix formation with concomitant partial melting of a competing (incompatible) helix. The third pathway, termed the tunneling pathway, is the low-barrier dominant pathway for the conversion between two incompatible helices. Comparisons with experimental data indicate that this new method is quite reliable in predicting the kinetics for RNA secondary structural folding and structural rearrangements. The approach presented here may provide a robust first step for further systematic development of a predictive theory for the folding kinetics for large RNAs.
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