Woodson S A, Crothers D M
Department of Chemistry, Yale University, New Haven, Connecticut 06511.
Biochemistry. 1988 May 3;27(9):3130-41. doi: 10.1021/bi00409a004.
We present three-dimensional structural models for a DNA oligomer containing a bulged guanosine based on proton NMR data and energy minimization computations. The nonexchangeable proton resonances of the duplex 5'd(GATGGGCAG).d(CTGCGCCATC) are assigned by nuclear Overhauser effect spectroscopy (NOESY) and correlated spectroscopy connectivities, and the NMR spectrum is compared with that of a regular 8-mer of similar sequence, 5'd(GATGGCAG).d(CTGCCATC). Experimental proton-proton distances are obtained from NOESY spectra acquired with mixing times of 100, 150, and 200 ms. A refined three-dimensional structure for the bulge-containing duplex is calculated from regular B DNA starting coordinates by using the AMBER molecular mechanics program [Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. (1984) J. Am. Chem. Soc. 106, 765-784]. We compare structures obtained by building the helix in three and four base pair increments with structures obtained by direct minimization of the entire nine base sequence, with and without experimental distance constraints. The general features of all the calculated structures are very similar. The helix is of the B family, with the extra guanine stacked into the helix, and the helix axis is bent by 18-23 degrees, in agreement with gel mobility data for bulge-containing sequences [Rice, J. A. (1987) Ph.D. Thesis, Yale University].
我们基于质子核磁共振（NMR）数据和能量最小化计算，提出了一种含有突出鸟苷的DNA寡聚物的三维结构模型。双链体5'd(GATGGGCAG).d(CTGCGCCATC)的非交换质子共振通过核Overhauser效应光谱（NOESY）和相关光谱连接性进行归属，并将该核磁共振谱与类似序列的常规8聚体5'd(GATGGCAG).d(CTGCCATC)的谱进行比较。实验性的质子-质子距离是从混合时间为100、150和200毫秒时采集的NOESY谱中获得的。使用AMBER分子力学程序[Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. (1984) J. Am. Chem. Soc. 106, 765 - 784]，从常规B型DNA起始坐标计算出含突出结构双链体的精细三维结构。我们将以三个和四个碱基对增量构建螺旋得到的结构与通过直接最小化整个九个碱基序列得到的结构进行比较，分别考虑有无实验距离约束的情况。所有计算结构的总体特征非常相似。该螺旋属于B家族，额外的鸟嘌呤堆积在螺旋中，螺旋轴弯曲18 - 23度，这与含突出结构序列的凝胶迁移率数据一致[Rice, J. A. (1987) 博士论文，耶鲁大学]。
