ArticleBiophysical journal2009
Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Perspective - RNA Dynamics Today and Tomorrow.Journal of molecular biology · 2026Review
- 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
- Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.Journal of chemical theory and computation · 2022Article
- Urea-aromatic interactions in biology.Biophysical reviews · 2020Review
- Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure.RNA (New York, N.Y.) · 2018Article
- 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
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels.Advanced healthcare materials · 2016Article
- Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.Journal of chemical theory and computation · 2016Article
- RNA folding pathways in stop motion.Nucleic acids research · 2016Article
- Free-energy landscape of a hyperstable RNA tetraloop.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape.Journal of the American Chemical Society · 2015Article
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We investigate the microsecond-timescale kinetics of the RNA hairpin ga*cUUCGguc. The fluorescent nucleotide 2-aminopurine (a*) reports mainly on base stacking. Ten kinetic traces and the temperature denaturation curve are globally fitted to four-state models of the free-energy surface. In the best-fitting sequential model, the hairpin unfolds over successively larger barriers in at least three stages: stem fraying and increased base-stacking fluctuations; concerted loss of hydrogen bonding and partial unstacking; and additional unstacking of single strands at the highest temperatures. Parallel and trap models also provide adequate fits: such pathways probably also play a role in the complete free-energy surface of the hairpin. To interpret the model states structurally, 200 ns of molecular dynamics, including six temperature-jump simulations, were run. Although the sampling is by no means comprehensive, five different states were identified using hydrogen bonding and base stacking as reaction coordinates. The four to five states required to explain the experiments or simulations set a lower limit on the complexity of this small RNA hairpin's energy landscape.
Indexed as
Identifiers
What OpenQuestion holds
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.