Summary
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.
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Nussinov, R. Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences. J Mol Evol 33, 259–266 (1991). https://doi.org/10.1007/BF02100677
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DOI: https://doi.org/10.1007/BF02100677