Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization.
Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization.
复制标题
通过 NMR 和能量最小化得出含有凸出鸟苷的寡核苷酸的结构模型。
DOI：
10.1021/bi00409a004
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发表时间：
1988
期刊：
影响因子：
2.9
通讯作者：
Crothers,DM
中科院分区：
文献类型：
--
作者：
Woodson,SA;Crothers,DM
耶鲁大学化学系，纽黑文，康涅狄格州 06511 收稿日期：1987 年 8 月 3 日；修订稿于 1987 年 12 月 1 日收到摘要：我们基于质子 NMR 数据和能量最小化计算，提出了含有凸出鸟苷的 DNA 寡聚物的三维结构模型。双链体 5'd (GATGGCAG)-d (CTGCGCCATC) 的不可交换质子共振通过核欧沃豪瑟效应光谱 (NOESY) 和相关光谱连通性进行分配，并将 NMR 光谱与相似序列的常规 8 聚体 5'd (GATGGCAG)-d (CTGCCATC) 的光谱进行比较。实验质子-质子距离是从混合时间为 100、150 和 200 ms 时获得的 NOESY 光谱中获得的。使用 AMBER 分子力学程序，从常规 B DNA 起始坐标计算出包含凸起的双链体的精细三维结构 [Weiner, S. J.、Kollman, P. A.、Case, D. A.、Singh, U. C.、Ohio, C.、Aragona, G.、Profeta, S. 和 Weiner, P.(1984) J. Am.。化学。苏克。 [106, 765-784]，我们将通过以三个和四个碱基对增量构建螺旋获得的结构与通过直接最小化整个九个碱基序列获得的结构进行比较，有或没有实验距离限制。所有计算结构的一般特征都非常相似。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，与包含凸出序列的凝胶迁移率数据一致 [Rice, J. A.(1987) Ph. D. Thesis, Yale University]，
Department of Chemistry, Yale University, New Haven, Connecticut 06511 Received August 3, 1987; Revised Manuscript Received December 1, 1987 abstract: 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 refinedthree-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., Ohio, 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, in agreement with gel mobility data for bulge-containing sequences [Rice, J. A.(1987) Ph. D. Thesis, Yale University],