ArticleJournal of biomolecular NMR2003
Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy.
Article in Journal of biomolecular NMR, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed, 151 citations in OpenAlex.
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- Blunt-force assembly of programmable DNA architectures using π-π stacking.Nature communications · 2026Article
- Hyperpolarized NMR Reveals Low-Populated Folding Intermediates in DNA.Journal of the American Chemical Society · 2025Article
- Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation ofJournal of chemical theory and computation · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Determination of silver(I)-binding sites in canonical B-DNA by NMR spectroscopy.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2025Article
- Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.Journal of chemical information and modeling · 2025Article
- Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.Journal of chemical theory and computation · 2025Article
- modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.Journal of chemical theory and computation · 2024Article
- Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications.Journal of applied crystallography · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field.Journal of chemical theory and computation · 2023Article
- Experimental detection of conformational transitions between forms of DNA: problems and prospects.Biophysical reviews · 2023Review
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
- Insights into DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.The journal of physical chemistry. B · 2022Article
- Identification of Effective Anticancer G-Quadruplex-Targeting Chemotypes through the Exploration of a High Diversity Library of Natural Compounds.Pharmaceutics · 2021Article
- Double-stranded RNA bending by AU-tract sequences.Nucleic acids research · 2020Article
- Exploring potentially alternative non-canonical DNA duplex structures through simulation.Journal of biomolecular structure & dynamics · 2019Article
- Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.Journal of biomolecular NMR · 2019Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
The solution structure of d(CGCGAATTCGCG)(2) has been determined on the basis of an exceptionally large set of residual dipolar couplings. In addition to the heteronuclear (13)C-(1)H and (15)N-(1)H and qualitative homonuclear (1)H-(1)H dipolar couplings, previously measured in bicelle medium, more than 300 quantitative (1)H-(1)H and 22 (31)P-(1)H dipolar restraints were obtained in liquid crystalline Pf1 medium, and 22 (31)P chemical shift anisotropy restraints. High quality DNA structures can be obtained solely on the basis of these new restraints, and these structures are in close agreement with those calculated previously on the basis of (13)C-(1)H and (15)N-(1)H dipolar couplings. In the newly calculated structures, (31)P-(1)H dipolar and (3)JsubH3(')Psub couplings and (31)P CSA data restrain the phosphodiester backbone torsion angles. The final structure represents a quite regular B-form helix with a modest bending of approximately 10 degrees, which is essentially independent of whether or not electrostatic terms are used in the calculation. Combined, the number of homo- and heteronuclear dipolar couplings significantly exceeds the number of degrees of freedom in the system. Results indicate that the dipolar coupling data cannot be fit by a single structure, but are compatible with the presence of rapid equilibria between C2(')-endo and C3(')-endo deoxyribose puckers (sugar switching). The C2(')-H2(')/H2(") dipolar couplings in B-form DNA are particularly sensitive to sugar pucker and yield the largest discrepancies when fit to a single structure. To resolve these discrepancies, we suggest a simplified dipolar coupling analysis that yields N/S equilibria for the ribose sugar puckers, which are in good agreement with previous analyses of NMR J(HH) couplings, with a population of the minor C3(')-endo form higher for pyrimidines than for purines.
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