ArticleBiophysical journal2006
Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states.
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 14 papers.
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Who cites it
14 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
- Inverted Molecular Beacons as Reaction-Based Hybridization Probes for Small-Molecule Activation by Nucleic Acid Inputs.ACS chemical biology · 2025Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch.Nucleic acids research · 2021Article
- Modulation and Visualization of EF-G Power Stroke During Ribosomal Translocation.Chembiochem : a European journal of chemical biology · 2019Article
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Design criteria for synthetic riboswitches acting on transcription.RNA biology · 2015Article
- Importance of diffuse metal ion binding to RNA.Metal ions in life sciences · 2011Review
- Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.PLoS computational biology · 2009Article
- Salt dependence of nucleic acid hairpin stability.Biophysical journal · 2008Article
- Loop dependence of the stability and dynamics of nucleic acid hairpins.Nucleic acids research · 2008Article
- RNA folding: conformational statistics, folding kinetics, and ion electrostatics.Annual review of biophysics · 2008Review
- RNA helix stability in mixed Na+/Mg2+ solution.Biophysical journal · 2007Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The complexity of RNA hairpin folding arises from the interplay between the loop formation, the disruption of the slow-breaking misfolded states, and the formation of the slow-forming native base stacks. We investigate the general physical mechanism for the dependence of the RNA hairpin folding kinetics on the sequence and the length of the hairpin loop and the helix stem. For example, 1), the folding would slow down when a stable GC basepair moves to the middle of the stem; 2), hairpin with GC basepair near the loop would fold/unfold faster than the one with GC near the tail of the stem; 3), within a certain range of the stem length, a longer stem can cause faster folding; and 4), certain misfolded states can assist folding through the formation of scaffold structures to lower the entropic barrier for the folding. All our findings are directly applicable and quantitatively testable in experiments. In addition, our results can be useful for molecular design to achieve desirable fast/slow-folding hairpins, hairpins with/without specific misfolded intermediates, and hairpins that fold along designed pathways.
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