Huang C Y, Bi G, Miller P S
Department of Biochemistry, School of Hygiene and Public Health, The Johns Hopkins University, Baltimore, MD 21205, USA.
Nucleic Acids Res. 1996 Jul 1;24(13):2606-13. doi: 10.1093/nar/24.13.2606.
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.
双链DNA的同嘌呤序列是形成三链的寡聚脱氧核糖嘧啶的结合位点。通过紫外熔解、圆二色光谱和硫酸二甲酯烷基化实验，研究了合成的双链DNA靶标与含有N4-(6-氨基-2-吡啶基)脱氧胞苷(1)的寡聚脱氧核糖嘧啶之间的相互作用，该核苷旨在与嘌呤靶序列中的单个C-G碱基对中断处相互作用。核苷1在pH 7.0时支持稳定的三链形成，形成1-Y-Z三联体，其中Y-Z是靶标同嘌呤序列中的一个碱基对。当Y-Z为C-G时观察到选择性相互作用，尽管A-T以及程度较小的T-A和G-C碱基对也能被识别。具有1-C-G三联体的三链的圆二色光谱与具有C(+)-G-C三联体的三链的圆二色光谱相似，表明这两种三链的整体结构非常相似。从1中去除6-氨基基本上消除了三链的形成。具有1-C-G三联体的三链与硫酸二甲酯反应导致该三联体中G残基的甲基化减少50%。相比之下，含有U-C-G三联体的类似三链中的G不能被硫酸二甲酯保护而不被甲基化。这些结果与一种结合模式一致，即1的6-氨基-2-吡啶基在1-C-G结合位点跨越靶标双链的大沟，并与G的O6形成氢键。1的亚氨基互变异构体的N4与C的N4氨基之间可能形成额外的稳定氢键。
