ArticleBiophysical journal2006
Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 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
- Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy.The journal of physical chemistry. B · 2023Article
- 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
- Clusters of hairpins induce intrinsic transcription termination in bacteria.Scientific reports · 2021Article
- Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch.Nucleic acids research · 2021Article
- 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
- A Model for Viral Assembly around an Explicit RNA Sequence Generates an Implicit Fitness Landscape.Biophysical journal · 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
- De novo design of heat-repressible RNA thermosensors in E. coli.Nucleic acids research · 2015Article
- Design criteria for synthetic riboswitches acting on transcription.RNA biology · 2015Article
- The impact of a ligand binding on strand migration in the SAM-I riboswitch.PLoS computational biology · 2013Article
- 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
- 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
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Authors and funding
2 authors.
Funding
Abstract
Depending on the nucleotide sequence, the temperature, and other conditions, RNA hairpin-folding kinetics can be very complex. The complexity with a wide range of cooperative and noncooperative kinetic behaviors arises from the interplay between the formation of the loops, the disruption of the misfolded states, and the formation of the rate-limiting base stacks. With a rate constant model and a kinetic-cluster theory, we explore the broad landscape for RNA hairpin-folding kinetics. The model is validated through direct tests against several experimental measurements. The general kinetic folding mechanisms and the predicted great variety of folding kinetics are directly applicable and quantitatively testable in experiments. The results from this study suggest that 1), previous experimental findings based on the individual hairpins revealed only a small fraction of much broader and more complex RNA hairpin-folding landscapes; 2), even for structures as simple as hairpins, universal folding timescales and pathways do not exist; and 3), to treat the loop size as the sole factor to determine the hairpin-folding rate is an oversimplification.
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