title: Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences.
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 not equal to 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.
authors.affiliation: Laboratory of Mathematical Biology, NCI, NIH, Bethesda, MD 20892.
authors.forename: R
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics; D016208:Databases, Factual; D005057:Eukaryotic Cells; D006801:Humans; D008969:Molecular Sequence Data
chemical_list: D004247:DNA