ArticleNucleic acids research2008
Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Integrated NMR and MD structure and dynamics of the stem-loop-II motif (s2m) from the Omicron variant of SARS-CoV-2.RNA (New York, N.Y.) · 2025Article
- A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.Biochemistry · 2020Article
- Structural features of DNA that determine RNA polymerase II core promoter.BMC genomics · 2016Article
- An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.Chemical reviews · 2016Review
- The intrinsic mechanics of B-DNA in solution characterized by NMR.Nucleic acids research · 2016Article
- Role of microscopic flexibility in tightly curved DNA.The journal of physical chemistry. B · 2014Article
- Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.The journal of physical chemistry. B · 2014Article
- All-atom polarizable force field for DNA based on the classical Drude oscillator model.Journal of computational chemistry · 2014Article
- Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications.Transcription · 2014Review
- Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA.The journal of physical chemistry. A · 2013Article
- Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.Biochemistry · 2012Article
- Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.Journal of chemical theory and computation · 2012Article
- Sequence-specific B-DNA flexibility modulates Z-DNA formation.Journal of the American Chemical Society · 2011Article
- Sequence-specific ultrasonic cleavage of DNA.Biophysical journal · 2011Article
- RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis.Journal of biomolecular NMR · 2009Article
- Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR.Journal of biomolecular NMR · 2009Article
- Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.Nucleic acids research · 2009Article
- Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.Journal of the American Chemical Society · 2008Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using (13)C spin relaxation NMR in combination with molecular dynamic (MD) simulations, we characterized internal motions within double-stranded DNA on the pico- to nano-second time scale. We found that the C-H vectors in all cytosine ribose moieties within the Dickerson-Drew dodecamer (5'-CGCGAATTCGCG-3') are subject to high amplitude motions, while the other nucleotides are essentially rigid. MD simulations showed that repuckering is a likely motional model for the cytosine ribose moiety. Repuckering occurs with a time constant of around 100 ps. Knowledge of DNA dynamics will contribute to our understanding of the recognition specificity of DNA-binding proteins such as cytosine methyltransferase.
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