Shui X, McFail-Isom L, Hu G G, Williams L D
School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta 30332-0400, USA.
Biochemistry. 1998 Jun 9;37(23):8341-55. doi: 10.1021/bi973073c.
We describe a very accurate addition (called structure X here) to the B-DNA dodecamer family of X-ray structures. Our results confirm the observation of Drew and Dickerson [(1981) J. Mol. Biol. 151, 535-556] that the spine of hydration in AT tract DNA is two layers deep. However, our results suggest that the primary spine is partially occupied by sodium ions. We suggest that many sequence-dependent features of DNA conformation are mediated by site specific binding of cations. For example, preferential localization of cations, as described here within the minor groove of structure X, is probably the structural origin of AT tract bending and groove narrowing. The secondary spine, which does not interact directly with the DNA, is as geometrically regular as the primary spine, providing a model for transmission of sequence information into solvent regions. A fully hydrated magnesium ion located in the major groove of structure X appears to pull cytosine bases partially out from the helical stack, exposing pi-systems to partial positive charges of the magnesium ion and its outer sphere. A partially ordered spermine molecule is located within the major groove of structure X. Dodecamer structures are derived from crystals of [d(CGCGAATTCGCG)]2 in space group P212121 (a = 25 A, b = 40 A, and c = 66 A). On average, those crystals diffracted to around 2.5 A resolution with 2500 unique reflections. Structure X, with the same space group, DNA sequence, and crystal form as the "Dickerson dodecamer", is refined against a complete, low-temperature, 1.4 A resolution data set, with over 11000 reflections. Structure X appears to be conformationally more ordered than previous structures, suggesting that at least a portion of the conformational heterogeneity previously attributed to DNA sequence in fact arises from experimental error.
我们描述了一种对B-DNA十二聚体X射线结构家族非常精确的补充结构（此处称为结构X）。我们的结果证实了德鲁和迪克森（[(1981) J. Mol. Biol. 151, 535 - 556]）的观察结果，即AT序列DNA中的水合脊柱有两层深。然而，我们的结果表明主脊柱部分被钠离子占据。我们认为DNA构象的许多序列依赖性特征是由阳离子的位点特异性结合介导的。例如，此处所述阳离子在结构X小沟内的优先定位可能是AT序列弯曲和沟变窄的结构起源。不直接与DNA相互作用的副脊柱在几何形状上与主脊柱一样规则，为序列信息传递到溶剂区域提供了一个模型。位于结构X大沟中的一个完全水合的镁离子似乎将胞嘧啶碱基部分地从螺旋堆积中拉出，使π电子体系暴露于镁离子及其外层球壳的部分正电荷中。一个部分有序的精胺分子位于结构X的大沟内。十二聚体结构源自空间群为P212121（a = 25 Å，b = 40 Å，c = 66 Å）的[d(CGCGAATTCGCG)]2晶体。这些晶体平均衍射到约2.5 Å分辨率，有2500个独立反射。结构X与“迪克森十二聚体”具有相同的空间群、DNA序列和晶体形式，针对一个完整的、低温的、1.4 Å分辨率数据集进行了精修，该数据集有超过11000个反射。结构X在构象上似乎比以前的结构更有序，这表明先前归因于DNA序列的构象异质性至少有一部分实际上是由实验误差引起的。
