Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA

Ruth Nussinov, Akinori Sarai, Gary W. Smythers, Robert L. Jernigan

Research output: Contribution to journalArticlepeer-review

Abstract

The distributions of the junction sequences of homooligomer tracts of various lengths have been examined in prokaryotic DNA sequences and compared with those of eukaryotes. The general trends in the nearest and next to nearest neighbors to the tracts are similar for both groups. In both prokaryotes and eukaryotes A/T runs are preferentially flanked on either the 5′ or the 3′ ends by A and/or T.G/C runs are preferentially flanked by G and/or C. There is discrimination against A/T runs flanked by G or C and G/C runs flanked by A or T. However, whereas the distribution of prokaryotic homooligomer tract junction sequences was quite homogeneous, large variations were observed in the 5-fold larger eukaryotic database, increasing in magnitude from tracts of length 2 to 3 to 4 base pairs long. Possible DNA conformational implications and in particular DNA curvature and packaging aspects of prokaryotes and eukaryotes are discussed.

Original languageEnglish
Pages (from-to)329-338
Number of pages10
JournalBBA - Gene Structure and Expression
Volume1008
Issue number3
DOIs
StatePublished - 14 Aug 1989

Keywords

  • DNA conformation
  • DNA sequence
  • Sequence pattern

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