## 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) 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/C)_{2} doublet, (G/C) (A/T)_{m}(G/C)_{2} > (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)). (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) 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.

Original language | English |
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Pages (from-to) | 399-411 |

Number of pages | 13 |

Journal | Journal of Biomolecular Structure and Dynamics |

Volume | 8 |

Issue number | 2 |

DOIs | |

State | Published - Oct 1990 |