Koshlap K M, Schultze P, Brunar H, Dervan P B, Feigon J
Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
Biochemistry. 1997 Mar 4;36(9):2659-68. doi: 10.1021/bi962438a.
The three-dimensional structure of a pyrimidine-purine-pyrimidine DNA triplex containing an N7-glycosylated guanine (7G) in the third strand has been determined by NMR spectroscopy, restrained molecular dynamics calculations, and complete relaxation matrix refinement. Glycosylation of the guanine at the N7 position permits it to adopt a conformation such that the Hoogsteen face of the base mimics the arrangement of hydrogen bond donors seen in protonated cytosine. The NMR data confirm the previously proposed hydrogen bonding scheme of the 7G x G x C triplet. The three-dimensional structure of the triplex accommodates the 7G with less distortion of the phosphodiester backbone than would be required for an N9-glycosylated guanine in the same sequence position, but some changes in the positions of the phosphodiester backbone are present compared to a C+ x G x C triplet. The structure provides a rationale for the observations that 7G binds to Watson-Crick G x C base pairs with higher specificity and affinity than guanine, but with a lower stability at pH 5.2 than would be provided by a canonical C+ x G x C triplet.
通过核磁共振光谱、受限分子动力学计算和完全弛豫矩阵精修，已确定了在第三条链中含有N7-糖基化鸟嘌呤（7G）的嘧啶-嘌呤-嘧啶DNA三链体的三维结构。鸟嘌呤在N7位置的糖基化使其能够采取一种构象，使得该碱基的Hoogsteen面模拟了质子化胞嘧啶中氢键供体的排列。核磁共振数据证实了先前提出的7G x G x C三联体的氢键模式。与相同序列位置的N9-糖基化鸟嘌呤相比，三链体的三维结构容纳7G时磷酸二酯主链的扭曲较小，但与C+ x G x C三联体相比，磷酸二酯主链的位置存在一些变化。该结构为以下观察结果提供了一个理论依据：7G与沃森-克里克G x C碱基对结合时具有比鸟嘌呤更高的特异性和亲和力，但在pH 5.2时稳定性低于典型的C+ x G x C三联体。
