Vojtechovsky J, Eaton M D, Gaffney B, Jones R, Berman H M
Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855-0939, USA.
Biochemistry. 1995 Dec 26;34(51):16632-40. doi: 10.1021/bi00051a011.
The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been determined to a resolution of 2.25 A and refined to a final R factor of 16.7%. The volume of the unit cell is significantly smaller by 16% than the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is in a different position in the unit cell, rotated by -85.9 degrees, and translated by 9.9 A around the helical axis with respect to the parent structure. The intermolecular arrangement of helices, characterized by double hydrogen bonded guanine-guanine minor groove interactions, remains conserved. The molecular geometry exhibits several significant changes that are related to the changed position of the helix and the presence of two mismatched base pairs with O6-methylguanine. Both mispairs are found in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups are in proximal orientation. The hydration pattern of the structure is different and can be related to changes in the minor groove geometry. An incorrect model that was isomorphous to the parent dodecamer could be refined to a low R factor. Characteristics of the refinement and of the geometry that are indicative of incorrect structures have been analyzed.
已确定合成十二聚体（d[CGTGAATTC(O6Me)GCG]）2的结构，分辨率为2.25埃，最终精修后的R因子为16.7%。晶胞体积比原始的德鲁和迪克森亲本十二聚体[德鲁，H.R.，温，R.M.，高野，T.，布罗卡，C.，田中，S.，板仓，K.，&迪克森，R.E.（1981年）美国国家科学院院刊78，7318 - 7322]显著小16%。双螺旋在晶胞中的位置不同，相对于亲本结构绕螺旋轴旋转了 - 85.9度，并平移了9.9埃。以双氢键鸟嘌呤 - 鸟嘌呤小沟相互作用为特征的螺旋分子间排列保持不变。分子几何结构呈现出一些显著变化，这些变化与螺旋位置的改变以及两个与O6 - 甲基鸟嘌呤错配的碱基对的存在有关。两个错配碱基对均处于对称的T（反式）.(O6Me)G（反式）构象，且甲基处于近端取向。该结构的水合模式不同，并且可能与小沟几何结构的变化有关。一个与亲本十二聚体同晶型的错误模型可以精修到较低的R因子。已分析了精修特征和表明结构错误的几何特征。
