ArticleNucleic acids research2020
A unified dinucleotide alphabet describing both RNA and DNA structures.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 51 citations in OpenAlex.
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- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Deciphering Dickerson-Drew DNA Equilibrium beyond the BI/BII DNA Dichotomy by Interpretation ofJournal of chemical theory and computation · 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
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
- Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.Journal of chemical theory and computation · 2025Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function.Nucleic acids research · 2024Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants.Briefings in bioinformatics · 2024Article
- Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses.Nucleic acids research · 2024Article
- Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis.Analytical chemistry · 2024Article
- The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.Nucleic acids research · 2024Article
- The pseudotorsional space of RNA.RNA (New York, N.Y.) · 2023Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- Conformation-based refinement of 18-mer DNA structures.Acta crystallographica. Section D, Structural biology · 2023Article
- Machine learning shows torsion angle preferences in left-handed and right-handed quadruplex DNAs.Biophysical journal · 2022Article
- Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.Acta crystallographica. Section D, Structural biology · 2022Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
By analyzing almost 120 000 dinucleotides in over 2000 nonredundant nucleic acid crystal structures, we define 96+1 diNucleotide Conformers, NtCs, which describe the geometry of RNA and DNA dinucleotides. NtC classes are grouped into 15 codes of the structural alphabet CANA (Conformational Alphabet of Nucleic Acids) to simplify symbolic annotation of the prominent structural features of NAs and their intuitive graphical display. The search for nontrivial patterns of NtCs resulted in the identification of several types of RNA loops, some of them observed for the first time. Over 30% of the nearly six million dinucleotides in the PDB cannot be assigned to any NtC class but we demonstrate that up to a half of them can be re-refined with the help of proper refinement targets. A statistical analysis of the preferences of NtCs and CANA codes for the 16 dinucleotide sequences showed that neither the NtC class AA00, which forms the scaffold of RNA structures, nor BB00, the DNA most populated class, are sequence neutral but their distributions are significantly biased. The reported automated assignment of the NtC classes and CANA codes available at dnatco.org provides a powerful tool for unbiased analysis of nucleic acid structures by structural and molecular biologists.
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