ArticleNucleic acids research2008
DNA conformations and their sequence preferences.
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 71 papers.
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Who cites it
71 citing papers in PubMed.
- Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation.The journal of physical chemistry. B · 2025Article
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.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
- Evidence that DNA polymerase δ proofreads errors made by DNA polymerase α across the Saccharomyces cerevisiae nuclear genome.DNA repair · 2024Article
- Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing.NAR genomics and bioinformatics · 2024Article
- Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments.Molecules (Basel, Switzerland) · 2024Article
- Xplor-NIH: Better parameters and protocols for NMR protein structure determination.Protein science : a publication of the Protein Society · 2024Article
- Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field.Journal of chemical theory and computation · 2023Article
- Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations.Journal of chemical theory and computation · 2023Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures.Bioinformatics (Oxford, England) · 2023Article
- Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- Dinuclear platinum(II) complexes as the pattern for phosphate backbone binding: a new perspective for recognition of binding modes to DNA.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2022Article
- Structural Characterization of the Interaction of Hypoxia Inducible Factor-1 with Its Hypoxia Responsive Element at the -964G > A Variation Site of theInternational journal of molecular sciences · 2021Article
- Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.Nucleic acids research · 2021Article
- Accurate prediction of B-form/A-form DNA conformation propensity from primary sequence: A machine learning and free energy handshake.Patterns (New York, N.Y.) · 2021Article
- Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org.Acta crystallographica. Section D, Structural biology · 2020Article
- A unified dinucleotide alphabet describing both RNA and DNA structures.Nucleic acids research · 2020Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, we have also identified combined A + B backbone-deformed conformers, e.g. with alpha/gamma switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail.
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