Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

Sergey V. Buldyrev, Nikolay V. Dokholyan, Shlomo Havlin, H. Eugene Stanley, Rachel H.R. Stanley

Research output: Contribution to journalConference articlepeer-review

6 Scopus citations

Abstract

We review recent studies of distribution of dimeric tandem repeats and short oligomer clustering in DNA sequences. We find that distribution of dimeric tandem repeats in coding DNA is exponential, while in noncoding DNA it often has long power-law tails. We explain this phenomenon using mutation models based on random multiplicative processes. We also develop a clustering measure based on percolation theory that quantifies the degree of clustering of short oligomers. We find that mono-, di-, and tetramers cluster more in noncoding DNA than in coding DNA. However trimers have some degree of clustering in coding DNA and noncoding DNA. We relate this phenomena to modes of tandem repeat expansion.

Original languageEnglish
Pages (from-to)19-32
Number of pages14
JournalPhysica A: Statistical Mechanics and its Applications
Volume273
Issue number1-2
DOIs
StatePublished - 1 Nov 1999
EventProceedings of the 1999 13th Max Born Symposium on 'Statistical Physics in Biology: Perspectives in DNA Analysis, Population Dynamics and Ageing' - Wroclaw, Poland
Duration: 26 May 199930 May 1999

Bibliographical note

Funding Information:
We would like to thank N. Broude, C. Cantor, R.S. Dokholyan, M. Frank-Kamenetskii, A. Goldberger, M. Goodman, A.Yu. Grosberg, I. Grosse, I Labat, R.N. Mantegna, C.-K. Peng, E.I. Shakhmonvich, A. Shehter, M. Simons, C. Smith, F. Starr, E.N. Trifonov, G.M. Viswanathan, G.H. Weiss, and R. Wells for fruitful discussions. This work is supported by NIH-HGP. N.V.D. is supported by NIH NRSA molecular biophysics predoctoral traineeship (GM08291-09).

Keywords

  • DNA
  • Evolution
  • Oligomer clustering
  • Percolation theory

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