ArticleBiophysical journal2012
Individual basepair stability of DNA and RNA studied by NMR-detected solvent exchange.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 36 citations in OpenAlex.
- Contrasting effects of different molecular crowding environments on base-pair opening/closing dynamics of DNA triplex structures.The FEBS journal · 2026Article
- RNA•DNA:DNA triplex formation byRNA (New York, N.Y.) · 2026Article
- Dissecting the Chemical and Thermal Stabilities of Tetrads in G-Quadruplexes to Derive a Structure-Activity Relation for a Thrombin-Binding DNA G-Quadruplex Aptamer.Chembiochem : a European journal of chemical biology · 2026Article
- 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
- Relaxation Optimized Heteronuclear Experiments for Extending the Size Limit of RNA Nuclear Magnetic Resonance.Journal of the American Chemical Society · 2025Article
- Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2.Journal of the American Chemical Society · 2024Article
- The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA.Nucleic acids research · 2024Article
- A thermosensitive gel matrix for bioreactor-assisted in-cell NMR of nucleic acids and proteins.Journal of biomolecular NMR · 2023Article
- RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics.Nucleic acids research · 2022Article
- The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.Nucleic acids research · 2021Article
- Mechanisms that ensure speed and fidelity in eukaryotic translation termination.Science (New York, N.Y.) · 2021Article
- Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer.Biophysical journal · 2020Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.Nucleic acids research · 2020Article
- RNA Dynamics by NMR Spectroscopy.Chembiochem : a European journal of chemical biology · 2019Review
- Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function.Computational and structural biotechnology journal · 2019Review
- Three tRNAs on the ribosome slow translation elongation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Impact of spin label rigidity on extent and accuracy of distance information from PRE data.Journal of biomolecular NMR · 2017Article
- Structural Insights into Conformation Differences between DNA/TNA and RNA/TNA Chimeric Duplexes.Chembiochem : a European journal of chemical biology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, we have optimized NMR methodology to determine the thermodynamic parameters of basepair opening in DNA and RNA duplexes by characterizing the temperature dependence of imino proton exchange rates of individual basepairs. Contributions of the nuclear Overhauser effect to exchange rates measured with inversion recovery experiments are quantified, and the influence of intrinsic and external catalysis exchange mechanisms on the imino proton exchange rates is analyzed. Basepairs in DNA and RNA have an approximately equal stability, and the enthalpy and entropy values of their basepair dissociation are correlated linearly. Furthermore, the compensation temperature, T(c), which is derived from the slope of the correlation, coincides with the melting temperature, and duplex unfolding occurs at that temperature where all basepairs are equally thermodynamically stable. The impact of protium-deuterium exchange of the imino hydrogen on the free energy of RNA basepair opening is investigated, and it is found that two A·U basepairs show distinct fractionation factors.
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.