Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences

Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The eukaryotic and prokaryotic databases are scanned for potential nearest-neighbor doublet preferences at the 5′ and 3′ flanks of some oligomers. Here we focus on oligomers containing alternating nucleotides, i.e., UV, UVUV, and UUVV where U≠V. Strong, consistent trends are observed in eukaryotic sequences. A/T alternation oligomers are preferentially flanked by A/T. G/C flanks are disfavored. G/C alternation oligomers are preferentially flanked by G/C. A/T flanks are disfavored. These trends are consistent with those observed previously for homooligomer tracts (Nussinov et al. 1989a,b). G/C tracts are preferentially flanked by G/C. A/T nearest neighbors are disfavored. The reverse holds for A/T tracts. Additional patterns are described here as well. The possible origin of these DNA composition and sequence trends is discussed. These trends are suggested to stem from protein-DNA interaction constraints.

Original languageEnglish
Pages (from-to)259-266
Number of pages8
JournalJournal of Molecular Evolution
Volume33
Issue number3
DOIs
StatePublished - Sep 1991

Keywords

  • DNA sequence analysis
  • DNA structure
  • Frequencies
  • Sequence patterns

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