The relationship between geometric patterns of hydrogen bonds and periodic dinucleotides in nucleosome structures

Pearl P. Guan, Weiqiang Zhou, Hong Yan

Research output: Contribution to journalArticle

Abstract

Statistical analysis of hydrogen bonds between the DNA chain and histones in nucleosomes shows that there is a periodicity about 10 base pairs along the DNA sequence. This periodicity also exists in dinucleotides which are found to be highly correlated with these hydrogen bonds. By analyzing the components of these protein-DNA hydrogen bonds, we find that more than 86% of them are formed in periodic dinucleotides and one or more hydrogen bonds exist in the majority of periodic dinucleotides. We use the alpha shape model to study the geometric properties of hydrogen bonds in nucleosomes, and find that periodic dinucleotides have convex surface curvatures, which indicates that they have close contact with the histones. The results in this work show that hydrogen bonds in the periodic dinucleotides play a crucial role in the formation of a nucleosome.

Original languageEnglish (US)
Pages (from-to)136-141
Number of pages6
JournalJournal of Theoretical Biology
Volume313
DOIs
StatePublished - Nov 21 2012
Externally publishedYes

Keywords

  • Alpha shape model
  • Dinucleotide periodicity
  • Nucleosome structure
  • Solid angle

ASJC Scopus subject areas

  • Statistics and Probability
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

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