Assignment of hydrogen-bond structure in a ligand-nucleobase complex inside duplex DNA: combined use of quantum chemical calculations and 15N NMR experiments.
Assignment of hydrogen-bond structure in a ligand-nucleobase complex inside duplex DNA: combined use of quantum chemical calculations and 15N NMR experiments.
复制标题
双链 DNA 内配体-核碱基复合物中氢键结构的分配：量子化学计算和 15N NMR 实验的结合使用。
DOI：
10.1093/nass/49.1.255
复制
发表时间：
2005
期刊：
影响因子：
--
通讯作者：
M. Maeda
中科院分区：
文献类型：
--
作者：
Keitaro Yoshimoto;S. Nishizawa;H. Koshino;Yusuke Sato;N. Teramae;M. Maeda
我们提出了一种实验和理论相结合的方法，通过比较计算和实验的15N核磁共振化学位移，可以阐明双链DNA中配体-核酸基复合体的氢键结构。在这项工作中，我们重点研究了2-氨基-7-甲基-1，8-萘啶(ANND)与胞嘧啶(C)碱基的高选择性相互作用，尽管中性的氢键阵列与鸟氨酸(G)完全互补，但胞嘧啶(C)与DNA双链中的碱性位置相对。对结合常数的盐依赖关系的研究表明，配体上的有效电荷数为+1.0，表明质子化的AND确实与C结合，这显然得到了15N核磁共振测量的支持，其中观察到配体与C结合时，配体上的芳香族氮发生了剧烈的化学位移。此外，从15N1(前场83.1ppm)、15N8(14.1ppm前场)和15NH2(18.3ppm下场)的络合引起的化学位移的变化来看，配体是通过三点氢键与C结合的。用与规范无关的原子轨道密度泛函方法计算的AMND-C络合物的化学位移与实验值吻合较好。这些结果清楚地解释了在含有碱性位点的双链DNA中，ANND与C而不是G选择性结合。
We present a combined experimental and theoretical approach, whereby a comparison of calculated and experimental 15N NMR chemical shifts allows the elucidation of hydrogen-bond structure in a ligand-nucleobase complex inside duplex DNA. In this work, we focus on the highly selective interaction of 2-amino-7-methyl-1,8-naphthyridine (AMND) to cytosine (C) base opposite the abasic site in DNA duplexes, despite the hydrogen-bond array of neutral AMND being fully complementary to guanine (G). Examination of the salt dependence of the binding constants reveals that the effective number of charges on the ligand is +1.0, indicating protonated AMND does bind to C. This is clearly supported by 15N NMR measurements, where the drastic changes in chemical shift are observed for the aromatic nitrogens on the ligand when binding to C. Furthermore, from the complexation-induced changes in chemical shift at 15N1 (83.1 ppm upfield), 15N8 (14.1 ppm upfield), and 15NH2 (18.3 ppm downfield) on AMND, the ligand is found to bind to C via three point hydrogen-bonds. The chemical shifts of the AMND-C complex, calculated by gauge-independent atomic orbital-DFT method, are in fair agreement with the experimental values. These results clearly explain the selective binding of AMND to C over G in abasic site-containing duplex DNA.