General Nearest Neighbor Preferences in G/C Oligomers Interrupted by A/T: Correlation with DNA Structure |
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| Authors: | Ruth Nussinov |
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| Affiliation: | 1. Laboratory of Mathematical Biology , National Cancer Institute, NIH , Bldg. 10, Rm. 4B-56, Bethesda , MD , 20892 , U.S.A.;2. Institute of Molecular Medicine, Faculty of Medicine Tel Aviv University , Ramat Aviv, Israel , 69978 |
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| Abstract: | ![]()
Abstract The frequencies of occurrence of the 5′ and 3′ nearest neighbor doublets of oligonucleotides containing (G/C) and (A/T) blocks show strong trends. Specifically, the following trends are observed. Given a (G/C)n (A/T)m oligomer (where G/C)n indicates a sequence of length n composed solely of Gs and/or Cs and (A/T)mis a sequence of length m composed solely of As and/or Ts, and n=3,2,1; m = 1,2,3) and a (G/C)2 doublet, (G/C)n (A/T)m (G/C)n > (G/C)n+2 (A/T)m- That is the (G/C)2 doublet is preferentially located 3′ of the oligomer, enclosing the (A/T)m stretch. The trends are strongest for n=3, m= 1 and gradually weaken as the size of the (G/C)n block decreases (with a concomitant increase of (A/T)m). (A/T)2 nearest neighbor flank preferentially encloses the (G/C)n block (to produce (A/T) 2(G/C) n (A/T)m). The (A/T)2 flank trends are weaker than the (G/C)2 flank ones. The (A/T)2 flank trends also decrease in strength as the size of the (G/C)n block decreases. The statistical significance of these trends in eukaryotes is very high. A possible correlation with DNA structural parameters, in particular groove geometry, is discussed. |
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