Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences |
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Authors: | Ruth Nussinov |
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Institution: | (1) Laboratory of Mathematical Biology, NCI, NIH, Building 10, Room 4B-56, 20892 Bethesda, MD, USA;(2) Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel |
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Abstract: | 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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Keywords: | DNA sequence analysis Frequencies Sequence patterns DNA structure |
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