Triplex formation by oligonucleotides containing novel deoxycytidine derivatives

Homopurine sequences of duplex DNA are binding sites for tripler-forming oligodeoxyribopyrimidines. The interactions of synthetic duplex DNA targets with an oligodeoxyribopyrimidine containing N-4-(6-amino-2-pyridinyl)deoxycytidine (1), a nucleoside designed to interact with a single C.G base pair interruption of the purine target tract, was studied by UV melting, circular dichroism spectroscopy and dimethylsulfate alkylation experiments, Nucleoside 1 supports stable tripler formation at pH 7.0 with formation of a 1.Y.Z triad, where Y.Z is a base pair in the homopurine tract of the target, Selective interaction was observed when Y.Z was C.G, although A.T and, to a lesser extent, T.A and G.C base pairs were also recognized, The circular dichroism spectra of the tripler having a 1.C.G triad were similar to those of a tripler having a C+.G.C triad, suggesting that the overall structures of the two triplexes are quite similar, Removal of the 6-amino group from 1 essentially eliminated tripler formation. Reaction of a tripler having the 1.C.G triad with dimethylsulfate resulted in a 50% reduction of methylation of the G residue of this triad, In contrast, the G of a similar tripler containing a U.C.G triad was not protected from methylation by dimethylsulfate. These results are consistent with a binding mode in which the 6-amino-2-pyridinyl group of 1 spans the major groove of the target duplex at the 1.C.G binding site and forms a hydrogen bond with the O6 of G, An additional stabilizing hydrogen bond could form between the N4 of the imino tautomer of 1 and the N4 amino group of C.