Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences

Qinqin Wu, Weiqiang Zhou, Jiajun Wang, Hong Yan

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Nucleosome formation and positioning, which play important roles in a number of biological processes, are thought to be related to the distinctive periodic dinucleotide patterns observed in the DNA sequence wrapped around the protein octamer. Previous research shows that flexibility is a key structural property of a nucleosomal DNA sequence. However, the relationship between the flexibility and the periodic dinucleotide patterns has received little attention in research in the past. In this study, we propose the use of three different models to measure the flexibility of yeast DNA sequences. Although the three models involve different parameters, they deliver consistent results showing that yeast nucleosomal DNA sequences are more flexible than non-nucleosomal ones. In contrast to random flexibility values along non-nucleosomal DNA sequences, the flexibility of nucleosomal DNA sequences shows a clear periodicity of 10.14 base pairs, which is consistent with the periodicity of dinucleotide distributions. We also demonstrate that there is a strong relationship between the peak positions of the flexibility and the dinucleotide frequencies. Correlation between the flexibility and the dinucleotide patterns of CA/TG, CG, GC, GG/CC, AG/CT, AC/GT and GA/TC are positive with an average value of 0.5946. The highest correlation is shown by CA/TG with a value of 0.7438 and the lowest correlation is shown by AA/TT with a value of -0.7424. The source codes and data sets are available for downloading on

Original languageEnglish (US)
Pages (from-to)92-98
Number of pages7
JournalJournal of Theoretical Biology
Issue number1
StatePublished - Sep 7 2011
Externally publishedYes


  • DNA sequence flexibility
  • Nucleosome positioning and formation
  • Nucleosomes
  • Periodic dinucleotides

ASJC Scopus subject areas

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


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