ArticleNucleic acids research2003
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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.
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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.
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Who cites it
25 citing papers in PubMed, 68 citations in OpenAlex.
- Enzyme therapy as a promising strategy to overcome multi-drug resistance in pathogens: current advances, key challenges, and future directions.RSC advances · 2026Review
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- The Effects of Flexibility on dsDNA-dsDNA Interactions.Life (Basel, Switzerland) · 2022Article
- Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A.Nature communications · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).Biochimica et biophysica acta · 2015Article
- CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.Biochimica et biophysica acta · 2015Review
- Mesoscopic model parametrization of hydrogen bonds and stacking interactions of RNA from melting temperatures.Nucleic acids research · 2013Article
- Structure of yeast Argonaute with guide RNA.Nature · 2012Article
- Recent Developments and Applications of the CHARMM force fields.Wiley interdisciplinary reviews. Computational molecular science · 2012Article
- A molecular dynamics study of a miRNA:mRNA interaction.Journal of molecular modeling · 2011Article
- Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.Journal of computational chemistry · 2011Article
- Thermophoretic melting curves quantify the conformation and stability of RNA and DNA.Nucleic acids research · 2011Article
- Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Methods (San Diego, Calif.) · 2009Review
- Analyzing the flexibility of RNA structures by constraint counting.Biophysical journal · 2008Article
- Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study.The journal of physical chemistry. B · 2008Article
- Review
- Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.Biophysical journal · 2006Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DNA and RNA are known to have different structural properties. In the present study, molecular dynamics (MD) simulations on a series of RNA and DNA duplexes indicate differential structural flexibility for the two classes of oligonucleotides. In duplex RNA, multiple base pairs experienced local opening events into the major groove on the nanosecond time scale, while such events were not observed in the DNA simulations. Three factors are indicated to be responsible for the base opening events in RNA: solvent-base interactions, 2'OH(n)-O4'(n+1) intra-strand hydrogen bonding, and enhanced rigid body motion of RNA at the nucleoside level. Water molecules in the major groove of RNA contribute to initiation of base pair opening. Stabilization of the base pair open state is due to a 'conformational switch' comprised of 2'OH(n)-O4'(n+1) hydrogen bonding and a rigid body motion of the nucleoside moiety in RNA. This rigid body motion is associated with decreased flexibility of the glycosyl linkage and sugar moieties in A-form structures. The observed opening rates in RNA are consistent with the imino proton exchange experiments for AU base pairs, although not for GC base pairs, while structural and flexibility changes associated with the proposed conformational switch are consistent with survey data of RNA and DNA crystal structures. The possible relevance of base pair opening events in RNA to its many biological functions is discussed.
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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.