ArticleActa crystallographica. Section D, Structural biology2018
A DNA structural alphabet provides new insight into DNA flexibility.
Article in Acta crystallographica. Section D, Structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Reconstructing biological molecules with help from video gamers.Acta crystallographica. Section D, Structural biology · 2025Article
- Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation ofJournal of chemical theory and computation · 2025Article
- Conformation-based refinement of 18-mer DNA structures.Acta crystallographica. Section D, Structural biology · 2023Article
- Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.Acta crystallographica. Section D, Structural biology · 2022Article
- Developing Community Resources for Nucleic Acid Structures.Life (Basel, Switzerland) · 2022Review
- 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
- New restraints and validation approaches for nucleic acid structures in PDB-REDO.Acta crystallographica. Section D, Structural biology · 2021Article
- Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches.Acta crystallographica. Section D, Structural biology · 2020Article
- Slow motions in A·T rich DNA sequence.Scientific reports · 2020Article
- 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
- A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).F1000Research · 2020Article
- Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank.International journal of molecular sciences · 2018Article
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6 authors.
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Abstract
DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson-Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.
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