Zhou N, Bianucci A M, Pattabiraman N, James T L
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143.
Biochemistry. 1987 Dec 1;26(24):7905-13. doi: 10.1021/bi00398a055.
Phase-sensitive two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 in aqueous deuterium oxide solution at four mixing times were quantified to give all nonoverlapping cross-peak intensities. A structural model for [d(GGTATACC)]2 was built in which the GG- and -CC moieties were in the B-DNA form, while the middle -TATA- moiety was in the wrinkled-D form (BDB model). This model was subjected to energy refinement by molecular mechanics calculations with the program AMBER. Counterions (Na+) were added to neutralize the charges, and water molecules were placed bridging across the minor groove. A complete relaxation matrix analysis was used to calculate two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 from the above models (before and after energy refinement) and from four other [d(GGTATACC)]2 structural models: regular A, crystalline A, regular B, and energy-minimized B. Among them, the energy-minimized BDB model yielded a set of theoretical spectra that gave the best fit to the experimental spectra. It was also the energetically most stable. Therefore, it is a good representation of the ensemble- and time-averaged structure of the octamer in solution. This model has backbone torsion angles similar to those of B-form DNA in the GG- and -CC moieties and torsion angles similar to those of wrinkled D form DNA in the -TATA- moiety. The base stacking and base pairing are not interrupted at the junctions between the two structural moieties. Its minor groove is narrower than that of B DNA, and the solvent-accessible surface of the minor groove forms a closed hydration tunnel in the middle -TATA- segment.
在重水氧化氘溶液中，对处于四个混合时间点的[d(GGTATACC)]₂进行相敏二维核Overhauser效应谱定量分析，以得到所有不重叠的交叉峰强度。构建了一个[d(GGTATACC)]₂的结构模型，其中GG和CC部分呈B-DNA形式，而中间的TATA部分呈皱缩D形式（BDB模型）。使用AMBER程序通过分子力学计算对该模型进行能量优化。添加抗衡离子（Na⁺）以中和电荷，并放置水分子跨越小沟桥接。采用完整的弛豫矩阵分析，从上述模型（能量优化前后）以及其他四个[d(GGTATACC)]₂结构模型：规则A、晶体A、规则B和能量最小化B计算[d(GGTATACC)]₂的二维核Overhauser效应谱。其中，能量最小化的BDB模型产生了一组与实验谱拟合最佳的理论谱。它也是能量上最稳定的。因此，它很好地代表了溶液中八聚体的系综平均和时间平均结构。该模型在GG和CC部分具有与B型DNA相似的主链扭转角，在TATA部分具有与皱缩D型DNA相似的扭转角。两个结构部分之间的连接处碱基堆积和碱基配对未被打断。其小沟比B-DNA的窄，小沟的溶剂可及表面在中间的TATA片段形成一个封闭的水合隧道。
