TY - JOUR
T1 - Trends in the 5′ vs. 3′ flanks of oligonucleotides in eukaryotic and prokaryotic genomes
T2 - The asymmetric roles played by cytosine and guanine
AU - Nussinov, Ruth
AU - Smythers, Gary
N1 - Funding Information:
Research sponsored at least in part, by the National Cancer Institute, DHHS, Under contract NO1-CO-74102 with Program Resources, Incorporated/Dyncorp. The contents of this publication do not necessarily reflect the views or policies of the DHHS, nor does mention of trade names, commercial products, or organizations imply indorsement by the U.S. Government.
PY - 1991/11/7
Y1 - 1991/11/7
N2 - 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 > (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 > (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.
AB - 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 > (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 > (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.
UR - http://www.scopus.com/inward/record.url?scp=0025953674&partnerID=8YFLogxK
U2 - 10.1016/S0022-5193(05)80355-8
DO - 10.1016/S0022-5193(05)80355-8
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AN - SCOPUS:0025953674
SN - 0022-5193
VL - 153
SP - 111
EP - 135
JO - Journal of Theoretical Biology
JF - Journal of Theoretical Biology
IS - 1
ER -