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

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. © 2012 Elsevier Ltd.