title: Triplex formation by oligonucleotides containing novel deoxycytidine derivatives.
abstract: 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.
authors.affiliation: Department of Biochemistry, School of Hygiene and Public Health, The Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: C Y
authors.initials: CY
authors.lastname: Huang
authors.forename: G
authors.initials: G
authors.lastname: Bi
authors.forename: P S
authors.initials: PS
authors.lastname: Miller
mesh_terms: D000478:Alkylation; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D003841:Deoxycytidine / Q000031:analogs & derivatives*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013463:Sulfuric Acid Esters
chemical_list: D009838:Oligodeoxyribonucleotides; D013463:Sulfuric Acid Esters; C051802:triplex DNA; D003841:Deoxycytidine; D004247:DNA; C007482:dimethyl sulfate