ArticleProceedings of the National Academy of Sciences of the United States of America2002
RNA hairpin-folding kinetics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed.
- RNA and proteins joined up at the Origins of Life: Persistence is the point.bioRxiv : the preprint server for biology · 2026Article
- Revealing hidden protonated conformational states in RNA dynamic ensembles.Nucleic acids research · 2025Article
- Kinetic Dissection of Proton-Coupled Conformational Transitions in Nucleic Acids by Integrating pH-Dependent NMR and Chemical Modifications.Journal of the American Chemical Society · 2025Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- RNA four-way junction (4WJ) for spontaneous cancer-targeting, effective tumor-regression, metastasis suppression, fast renal excretion and undetectable toxicity.Biomaterials · 2024Article
- Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Characterizing the Conformational Free-Energy Landscape of RNA Stem-Loops Using Single-Molecule Field-Effect Transistors.Journal of the American Chemical Society · 2023Article
- High-temperature adaptation of anScience advances · 2022Article
- Measuring RNA UNCG Tetraloop Refolding Dynamics Using Temperature-Jump/Drop Infrared Spectroscopy.The journal of physical chemistry letters · 2022Article
- RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform.PLoS computational biology · 2022Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- 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
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- RNA folding kinetics using Monte Carlo and Gillespie algorithms.Journal of mathematical biology · 2018Article
- Nanopore electric snapshots of an RNA tertiary folding pathway.Nature communications · 2017Article
- Tractable RNA-ligand interaction kinetics.BMC bioinformatics · 2017Article
1 more citing papers are in PubMed but not listed here.
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Abstract
Based on the complete ensemble of hairpin conformations, a statistical mechanical model that combines the eigenvalue solutions of the rate matrix and the free-energy landscapes has been able to predict the temperature-dependent folding rate, kinetic intermediates, and folding pathways for hairpin-forming RNA sequences. At temperatures higher than a "glass transition" temperature, T(g), the eigenvalues show a distinct time separation, and the rate-limiting step is a two-state single exponential process determined by the slowest eigenmode. At temperatures lower than T(g), no distinct time separation exists for the eigenvalues, hence multiple (slow) eigenmodes contribute to the rate-determining processes, and the folding involves the trapping and detrapping of kinetic intermediates. For a 21-nt sequence we studied, T(g) is lower than the transition temperature, T(m), for thermodynamic equilibrium folding. For T > T(m), starting from the native state, the chain undergoes a biphasic unfolding transition: a preequilibrated quasi-equilibrium macrostate is formed followed by a rate-limiting two-state transition from the macrostate to the unfolded state. For T(g) < T < T(m), the chain undergoes a two-state on-pathway folding transition, at which a nucleus is formed by the base stacks close to the loop region before a rapid assembly of the whole hairpin structure. For T < T(g), the multistate kinetics involve kinetic trapping, causing the roll-over behavior in the rate-temperature Arrhenius plot. The complex kinetic behaviors of RNA hairpins may be a paradigm for the folding kinetics of large RNAs.
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