Sarma M H, Gupta G, Sarma R H
Institute of Biomolecular Stereodynamics State University of New York, Albany 12222.
J Biomol Struct Dyn. 1985 Dec;3(3):433-6. doi: 10.1080/07391102.1985.10508432.
The basic assumption of Dickerson and Kopka (J. Biomole. Str. Dyns. 2, 423, 1985) that the conformation of poly(dA).poly(dT) in solution is identical to the AT rich region of the single crystal structure of the Dickerson dodecamer is not supported by any experimental data. In poly(dA).poly(dT), NOE and Raman studies indicate that the dA and dT units are conformationally equivalent and display the (anti-S-type sugar)-conformation; incorporation of this nucleotide geometry into a double helix leads to a conventional regular B-helix in which the width of the minor groove is 8A. The derived structure is consistent with all available experimental data on poly(dA).poly(dT) obtained under solution conditions. In the crystal structure of the dodecamer, the dA and dT units have distinctly different conformations-dA residues adopt (anti, S-type sugar pucker), while dT residues belong to (low anti, N-type sugar pucker). These different conformations of the dA and dT units along with the large propeller twist can be accommodated in a double helix in which the minor groove is shrunk from 8A to less than 4A. In the conventional right handed B-form of poly(dA).poly(dT) with the 8A wide minor groove, netropsin has to bind asymmetrically along the dA strand to account for the NOE and chemical shift data and to generate a stereochemically sound structure (Sarma et al, J. Biomole. Str. Dyns. 2, 1085, 1985).
迪克森和科普卡（《生物分子结构与动力学杂志》2, 423, 1985）的基本假设是，溶液中聚（dA）·聚（dT）的构象与迪克森十二聚体单晶结构中富含AT的区域相同，但没有任何实验数据支持这一假设。在聚（dA）·聚（dT）中，核Overhauser效应（NOE）和拉曼研究表明，dA和dT单元在构象上是等效的，并呈现出（反式-S型糖）构象；将这种核苷酸几何结构纳入双螺旋会形成传统的规则B型螺旋，其中小沟宽度为8埃。推导得到的结构与在溶液条件下获得的关于聚（dA）·聚（dT）的所有现有实验数据一致。在十二聚体的晶体结构中，dA和dT单元具有明显不同的构象——dA残基采用（反式，S型糖环构象），而dT残基属于（低反式，N型糖环构象）。dA和dT单元的这些不同构象以及大的螺旋桨扭转可以容纳在一个双螺旋中，其中小沟从8埃缩小到小于4埃。在具有8埃宽小沟的传统右手B型聚（dA）·聚（dT）中，纺锤菌素必须沿着dA链不对称结合，以解释NOE和化学位移数据，并生成一个立体化学合理的结构（萨尔马等人，《生物分子结构与动力学杂志》2, 1085, 1985）。
