ArticleGenes2017
A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle.
Article in Genes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 14 citations in OpenAlex.
- DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis.Nucleic acids research · 2026Article
- Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function.Nucleic acids research · 2024Article
- Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses.Nucleic acids research · 2024Article
- 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
- Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches.Acta crystallographica. Section D, Structural biology · 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
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
- Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank.International journal of molecular sciences · 2018Article
- A DNA structural alphabet provides new insight into DNA flexibility.Acta crystallographica. Section D, Structural biology · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and associations between ten CANA letters and sixteen dinucleotide sequences were investigated. The associations showed features discriminating between specific and non-specific binding of DNA to proteins. Important is the specific role of two DNA structural forms, A-DNA, and BII-DNA, represented by the CANA letters AAA and BB2: AAA structures are avoided in non-specific NCP complexes, where the wrapping of the DNA duplex is explained by the periodic occurrence of BB2 every 10.3 steps. In both regulatory and NCP complexes, the extent of bending of the DNA local helical axis does not influence proportional representation of the CANA alphabet letters, namely the relative incidences of AAA and BB2 remain constant in bent and straight duplexes.
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