Trends in the 5′ vs. 3′ flanks of oligonucleotides in eukaryotic and prokaryotic genomes: The asymmetric roles played by cytosine and guanine

Abstract

Studies of sequence context preferences of oligonucleotides composed of (G/C)n and (A/T)m blocks (n + m = 3,4,5) unravel strong patterns. Comparisons of the 5' and 3' nearest neighbor doublets flanking these oligomers reveal the preference of (G/C)2 to be positioned immediately next to the (A/T)m block, enclosing it by (G/C) nucleotides rather than extending the (G/C)n block. That is, for a (G/C)n(A/T)m oligomer and a (G/C)2 doublet, (G/C)n(A/T)m(G/C)2 greater than (G/C)n + 2 (A/T)m. Similarly for an (A/T)m(G/C)n oligomer, (G/C)2(A/T)m(G/C)n greater than (A/T)m(G/C)n + 2. In an analogous manner, (A/T)2 flanking doublets prefer enclosing the (G/C)n blocks, although these patterns are weaker. Here we show a strong, direct relationship between the magnitude of the trends and the presence of Cs in the (G/C)n block in the (G/C)n(A/T)m oligomer, and the presence of Gs in the complementary (A/T)m(G/C)n oligomers. The trends are stronger in eukaryotic than in prokaryotic sequences. They are stronger for longer (G/C)n and shorter (A/T)m blocks. We suggest that the preference for (A/T)m to be enclosed by (G/C) rather than be flanked by them on only one side is related to DNA structure and DNA-protein interaction. Sequences of the (G/C)(A/T)(G/C) type may have more homogeneous minor groove geometry. In particular, the strong G vs. C asymmetry in the trends may be related to pyrimidine-purine junctions, possibly to CG sequences.