Design of artificial nucleobases for the recognition of the AT inversion by triple-helix forming oligonucleotides: A structure stability relationship study and neighbour bases effect

We report herein on the synthesis, the incorporation into triplex forming oligonucleotides (TFO) and the recognition properties of a series of synthetic nucleosides designed for the specific recognition of an inverted A.T base pair in a pyrimidine triple helix motif. These analogues were designed on the basis of the results obtained with our previously reported compounds S and B-t, in order to define a structure-stability relationship. We report also on the chemical nature effect of the bases flanking S in the case of S-containing TFOs, in order to get further informations about the recognition process within the A.TxS triplet. This study establishes guidelines for the conception of more potent analogues for the recognition of both A.T and G.C inverted base pairs. (C) 2003 Elsevier Science Ltd. All rights reserved.