ArticleJournal of the American Chemical Society2014
The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- Structural Basis for Nucleobase Activation by the Adenine DNA Glycosylase MutY.Chembiochem : a European journal of chemical biology · 2026Article
- Structural Basis for Nucleobase Activation by the Adenine DNA Glycosylase MutY.bioRxiv : the preprint server for biology · 2026Article
- The XNA alphabet.Nucleic acids research · 2025Review
- Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.Nucleic acids research · 2025Article
- Elucidating the solution structure of the monomolecularChemical science · 2025Article
- Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study.The FEBS journal · 2025Article
- Simulations predict preferred MgBiophysical journal · 2024Article
- Advances in RNA Labeling with Trifluoromethyl Groups.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Article
- Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.Angewandte Chemie (International ed. in English) · 2021Article
- 2'-Chemical science · 2020Article
- Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme.RNA (New York, N.Y.) · 2018Article
- A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.Journal of chemical theory and computation · 2017Article
- Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic acids research · 2017Article
- Structural insights into RNA duplexes with multiple 2΄-5΄-linkages.Nucleic acids research · 2017Article
- Enzymatic Synthesis of Nucleic Acids with Defined Regioisomeric 2'-5' Linkages.Angewandte Chemie (International ed. in English) · 2015Article
- Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization.Nucleic acids research · 2015Article
- Expanding the Scope of 2'-SCF3 Modified RNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2015Article
- Impact of template backbone heterogeneity on RNA polymerase II transcription.Nucleic acids research · 2015Article
- Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2'-endo and C3'-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2'-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3'-endo state. However, at a 2'-5' linkage, the minimum shifts to the C2'-endo conformation. The free energy of the C3'-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3'-endo to C2'-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2'-5' linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations.
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.