ArticleJournal of the American Chemical Society2012
Kinetic mechanism of conformational switch between bistable RNA hairpins.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Mechanistic Insights of miRNA Hybridization with ssDNA Self Assembled Monolayers on Gold Electrodes: An Electrochemical and Computational Study.Sensors and actuators. B, Chemical · 2026Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- Kinetic pathway of HIV-1 TAR cotranscriptional folding.Nucleic acids research · 2024Article
- Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA.Nucleic acids research · 2024Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.Nucleic acids research · 2021Article
- Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis.Biophysical journal · 2019Article
- A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.Biophysical journal · 2019Article
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.The journal of physical chemistry. B · 2018Article
- CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment.Scientific reports · 2017Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A Method to Predict the Structure and Stability of RNA/RNA Complexes.Methods in molecular biology (Clifton, N.J.) · 2016Article
- Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel.Journal of the American Chemical Society · 2015Article
- Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.Biophysical journal · 2015Article
- A Method to Predict the 3D Structure of an RNA Scaffold.Methods in molecular biology (Clifton, N.J.) · 2015Article
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- Physics-based RNA structure prediction.Biophysics reportsArticle
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Authors and funding
2 authors.
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Abstract
Transitions between the different conformational states play a critical role in many RNA catalytic and regulatory functions. In this study, we use the Kinetic Monte Carlo method to investigate the kinetic mechanism for the conformational switches between bistable RNA hairpins. We find three types of conformational switch pathways for RNA hairpins: refolding after complete unfolding, folding through basepair-exchange pathways and through pseudoknot-assisted pathways, respectively. The result of the competition between the three types of pathways depends mainly on the location of the rate-limiting base stacks (such as the GC base stacks) in the structures. Depending on the structural relationships between the two bistable hairpins, the conformational switch can follow single or multiple dominant pathways. The predicted folding pathways are supported by the activation energy results derived from the Arrhenius plot as well as the NMR spectroscopy data.
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