Quintana J R, Grzeskowiak K, Yanagi K, Dickerson R E
Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.
J Mol Biol. 1992 May 20;225(2):379-95. doi: 10.1016/0022-2836(92)90928-d.
The X-ray crystal structure analysis of the decamer C-G-A-T-T-A-A-T-C-G has been carried out to a resolution of 1.5 A. The crystals are space group P2(1)2(1)2(1), cell dimensions a = 38.60 A, b = 39.10 A, c = 33.07 A. The structure was solved by molecular replacement and refined with X-PLOR and NUCLSQ. The final R factor for a model with 404 DNA atoms, 108 water molecules and one magnesium hexahydrate cation is 15.7%. The double helix is essentially isostructural with C-G-A-T-C-G-A-T-C-G, with closely similar local helix parameters. The structure of the T-T-A-A center differs from that found in C-G-C-G-T-T-A-A-C-G-C-G in that the minor groove in our decamer is wide at the central T-A step rather than narrow, and the twist angle of the T-A step is small (31.1 degrees) rather than large. Whereas the tetrad model provides a convenient framework for discussing local DNA helix structure, it cannot be the entire story. The articulated helix model of DNA structure proposes that certain sequence regions of DNA show preferential twisting or bending properties, whereas other regions are less capable of deformation, in a manner that may be useful in sequence recognition by drugs and protein. Further crystal structure analyses should help to delineate the precise nature of sequence-dependent articulation in the DNA double helix.
已对十聚体C-G-A-T-T-A-A-T-C-G进行了X射线晶体结构分析，分辨率达到1.5埃。晶体属于空间群P2(1)2(1)2(1)，晶胞参数a = 38.60埃，b = 39.10埃，c = 33.07埃。该结构通过分子置换法解析，并使用X-PLOR和NUCLSQ进行精修。对于一个包含404个DNA原子、108个水分子和一个六水合镁阳离子的模型，最终的R因子为15.7%。该双螺旋结构与C-G-A-T-C-G-A-T-C-G基本同构，局部螺旋参数非常相似。T-T-A-A中心的结构与C-G-C-G-T-T-A-A-C-G-C-G中的不同，在于我们的十聚体在中央T-A步处小沟较宽而非较窄，且T-A步的扭转角较小（31.1度）而非较大。虽然四重体模型为讨论局部DNA螺旋结构提供了一个方便的框架，但它不可能是全部情况。DNA结构的铰接螺旋模型提出，DNA的某些序列区域表现出优先扭转或弯曲的特性，而其他区域则较不易变形，这种方式可能有助于药物和蛋白质进行序列识别。进一步的晶体结构分析应有助于阐明DNA双螺旋中序列依赖性铰接的确切性质。
