ArticleRNA (New York, N.Y.)2010
Loop and stem dynamics during RNA hairpin folding and unfolding.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.ACS omega · 2025Article
- RNA adapts its flexibility to efficiently fold and resist unfolding.Nucleic acids research · 2025Article
- Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy.The journal of physical chemistry. B · 2023Article
- Characterizing the Conformational Free-Energy Landscape of RNA Stem-Loops Using Single-Molecule Field-Effect Transistors.Journal of the American Chemical Society · 2023Article
- Measuring RNA UNCG Tetraloop Refolding Dynamics Using Temperature-Jump/Drop Infrared Spectroscopy.The journal of physical chemistry letters · 2022Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- The effect of mutation in the stem of the MicroROSE thermometer on its thermosensing ability: insights from molecular dynamics simulation studies.RSC advances · 2022Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 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
- Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine.RNA (New York, N.Y.) · 2015Article
- Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.Methods in enzymology · 2015Article
- Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity.Nucleic acids research · 2014Article
- Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase.Nucleic acids research · 2014Article
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle.The journal of physical chemistry letters · 2014Article
- Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods.Nucleic acids research · 2012Article
- G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots.Nucleic acids research · 2012Article
- A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics.Biophysical journal · 2012Article
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Corrections and comments
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
2-Aminopurine (2AP) is a fluorescent adenine analog that probes mainly base stacking in nucleic acids. We labeled the loop or the stem of the RNA hairpin gacUACGguc with 2AP to study folding thermodynamics and kinetics at both loci. Thermal melts and fast laser temperature jumps detected by 2AP fluorescence monitored the stability and folding/unfolding kinetics. The observed thermodynamic and kinetic traces of the stem and loop mutants, though strikingly different at a first glance, can be fitted to the same free-energy landscape. The differences between the two probe locations arise because base stacking decreases upon unfolding in the stem, whereas it increases in the loop. We conclude that 2AP is a conservative adenine substitution for mapping out the contributions of different RNA structural elements to the overall folding process. Molecular dynamics (MD) totaling 0.6 μsec were performed to look at the conformations populated by the RNA at different temperatures. The combined experimental data, and MD simulations lead us to propose a minimal four-state free-energy landscape for the RNA hairpin. Analysis of this landscape shows that a sequential folding model is a good approximation for the full folding dynamics. The frayed state formed initially from the native state is a heterogeneous ensemble of structures whose stem is frayed either from the end or from the loop.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.