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

Abstract 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 Tx S 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.