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Fujii, S., Kono, H., Takenaka, S., Go, N. and Sarai, A. (2007) Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Research, 35(18), 6063-6074.

has been cited by the following article:

• TITLE: Statistical analysis of conformational properties of periodic dinucleotide steps in nucleosomes

  AUTHORS: Xi Yang, Hong Ya

  KEYWORDS: Deformability of DNA; Nucleosome; Dinucleotides; 10.5-Base Periodicity; Deformation Preferences; Flexibility; DNA Bending

  JOURNAL NAME: Journal of Biomedical Science and Engineering, Vol.3 No.4, April 28, 2010

  ABSTRACT: Deformability of DNA is important for its superhelical folding in the nucleosome and has long been thought to be facilitated by periodic occurrences of certain dinucleotides along the sequences, with the period close to 10.5 bases. This study statistically examines the conformational properties of dinucleotides containing the 10.5 - base periodicity and those without that periodicity through scanning all nucleosome structures provided in PDB. By categorizing performances on the distribution of step parameter values, averaged net values, standard deviations and deformability based on step conformational energies, we give a detailed description as to the deformation preferences correlated with the periodicity for the 10 unique types of dinucleotides and summarize the possible roles of various steps in how they facilitate DNA bending. The results show that the structural properties of dinucleotide steps are influenced to various extents by the periodicity in nucleosomes and some periodic steps have shown a clear tendency to take specific bending or shearing patterns.