General nearest neighbor preferences in G/C oligomers interrupted by A/T: correlation with DNA structure

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)m is a sequence of length m composed solely of As and/or Ts, and n = 3,2,1; m = 1,2,3) and a (G/mC)2 doublet, (G/C)n (A/T)m (G/C)2 greater than (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 (mG/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.