Mooers B H, Schroth G P, Baxter W W, Ho P S
Department of Biochemistry and Biophysics, Oregon State University Corvallis 97331, USA.
J Mol Biol. 1995 Jun 16;249(4):772-84. doi: 10.1006/jmbi.1995.0336.
We have solved the single-crystal X-ray structures of two different hexanucleotides: the alternating sequence d(Gm5CGm5CGC), and the non-alternating sequence d(Gm5CCGGC). Both of these hexamers crystallize readily as A-DNA in the orthorhombic space group C222(1). Although hexanucleotides have been previously crystallized as Z-DNA, and in one case as B-DNA, this is the first time hexanucleotides have been crystallized as A-DNA. Both hexamers adopt a typical A-conformation, which is surprisingly more similar to the structure of A-DNA fibers than to other A-DNA single crystals. The structure of d(Gm5CGm5CGC) was solved to a resolution of 2.1 A (R-factor = 19.6%). This structure has all of the features characteristic of canonical A-DNA, including it's helical repeat (11.2 bp/turn), helical rise (2.6 A/bp), base-pair displacement (-4.7 A), base inclination angle (16.9 degrees), and sugar puckers that are predominantly 3'-endo. The lower resolution, non-alternating structure has similar overall average values for these parameters. We observed several sequence-dependent correlations in these parameters, especially in the d(CG) base step. These steps have lower twist and rise values, coupled with high roll angles as compared to d(GC) steps. The molecular interactions involved in crystal packing and the detailed structure of the bound water in the crystals, however, are similar to those of longer 8 and 10 bp A-DNA crystal structures. Although the structural effect of cytosine methylation on A-DNA appears to be minimal, this modification significantly affects the ability of these sequences to crystallize as A-DNA. In conclusion, we present the A-DNA forming class of hexanucleotides, a new crystallographic system for studying DNA structure at near atomic resolution.
我们解析了两种不同六核苷酸的单晶X射线结构：交替序列d(Gm5CGm5CGC)和非交替序列d(Gm5CCGGC)。这两种六聚体均易于以正交空间群C222(1)中的A-DNA形式结晶。尽管六核苷酸此前已以Z-DNA形式结晶，还有一次是以B-DNA形式结晶，但这是六核苷酸首次以A-DNA形式结晶。两种六聚体均采用典型的A构象，令人惊讶的是，其与A-DNA纤维的结构比与其他A-DNA单晶的结构更为相似。d(Gm5CGm5CGC)的结构解析分辨率为2.1 Å（R因子 = 19.6%）。该结构具有标准A-DNA的所有特征，包括其螺旋重复（11.2 bp/圈）、螺旋上升（2.6 Å/bp）、碱基对位移（-4.7 Å）、碱基倾斜角（16.9度）以及主要为3'-内型的糖环构象。分辨率较低的非交替结构在这些参数上具有相似的总体平均值。我们在这些参数中观察到了几种序列依赖性相关性，特别是在d(CG)碱基步。与d(GC)步相比，这些步具有更低的扭转和上升值，以及高滚转角。然而，晶体堆积中涉及的分子相互作用以及晶体中结合水的详细结构与更长的8和10 bp A-DNA晶体结构的相似。尽管胞嘧啶甲基化对A-DNA的结构影响似乎最小，但这种修饰显著影响了这些序列以A-DNA形式结晶的能力。总之，我们展示了形成A-DNA的六核苷酸类别，这是一种用于在近原子分辨率下研究DNA结构的新晶体学系统。
