Eisenstein M, Shakked Z
Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
J Mol Biol. 1995 May 5;248(3):662-78. doi: 10.1006/jmbi.1995.0250.
Crystallographic studies of DNA fragments of the A and B conformations have shown that the structure and hydration of the DNA double helix depend both on the base sequence and the environment. Detailed analyses of solvent organization in DNA crystals and its role in intermolecular interactions have been reported mainly for B-DNA structures. We have determined the crystal structures of several isomorphous A-DNA octamers at resolutions from 1.8 to 2.5 A and refined them by the same procedure. Comparative analysis of five independently refined structures in terms of hydration and intermolecular interactions has been performed leading to the following findings. The A-DNA major groove is extensively hydrated and together with the hydration shells of the sugar-phosphate backbone can form an ordered network of fused polygons. The water structure of the phosphate backbone is less conserved than that of the grooves. Characteristic hydration patterns are associated with specific base sequences. The A-DNA minor groove provides sites for intermolecular contacts through hydrophobic and polar interactions. Well-ordered water molecules mediate interduplex interactions that involve either the grooves or the backbone, or both. The direct and water-mediated intermolecular interactions observed in the A-DNA crystal structures are relevant to various recognition motifs between DNA and other molecules. In particular, intermolecular interactions at the DNA minor groove are analogous to those observed in the recently reported crystal structures of complexes between the TATA-binding protein and the TATA-box.
对A构象和B构象的DNA片段进行的晶体学研究表明，DNA双螺旋的结构和水合作用既取决于碱基序列，也取决于环境。关于DNA晶体中溶剂组织及其在分子间相互作用中的作用的详细分析，主要是针对B-DNA结构进行报道的。我们已经确定了几种同晶型A-DNA八聚体的晶体结构，分辨率在1.8至2.5埃之间，并通过相同的程序对其进行了优化。对五个独立优化的结构在水合作用和分子间相互作用方面进行了比较分析，得出了以下发现。A-DNA的大沟被大量水合，并且与糖-磷酸骨架的水合壳一起可以形成一个有序的融合多边形网络。磷酸骨架的水结构不如沟的水结构保守。特征性的水合模式与特定的碱基序列相关。A-DNA的小沟通过疏水和极性相互作用提供了分子间接触的位点。排列有序的水分子介导了涉及沟或骨架或两者的双链间相互作用。在A-DNA晶体结构中观察到的直接和水介导的分子间相互作用与DNA和其他分子之间的各种识别基序相关。特别是，DNA小沟处的分子间相互作用类似于最近报道的TATA结合蛋白与TATA盒之间复合物的晶体结构中观察到的相互作用。
