Triplex formation by oligonucleotides containing novel deoxycytidine derivatives

Homopurine sequences of duplex DNA are binding sites for triplex-forming oligodeoxyribopyrimidines. The interactions of synthetic duplex DNA targets with an oligodeoxyribopyrimidine containing N⁴-(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 triplex 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 triplex having a 1·C·G triad were similar to those of a triplex 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 triplex formation. Reaction of a triplex 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 triplex 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.