Jain S, Zon G, Sundaralingam M
Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706.
Biochemistry. 1991 Apr 9;30(14):3567-76. doi: 10.1021/bi00228a030.
The alternating DNA octamer d(GTGTACAC) has been grown in a novel hexagonal crystal form. The structure has been determined and refined to a 2-A resolution, with 51 water molecules. The A-DNA conformation is a variant of that observed for the tetragonal form of the same sequence (Jain et al., 1989) containing a bound spermine. The crystals belong to the space group P6(1)22, a = b = 32.40 A and c = 79.25 A, with one strand in the asymmetric unit. The new hexagonal structure was solved by rotation and translation searches in direct space and refined to a final R value of 12.7% by using 1561 unique reflections greater than 1.5 sigma (I). The electron density clearly shows that the penultimate A7 sugar had flipped into the alternative C2'-endo pucker. This dent in the molecule can be attributed to close intermolecular contacts. In contrast, in the tetragonal structure, the DNA is distorted in the central TA step, where the A5 backbone bonds C4'-C5' and O5'-P assume trans conformations. The hexagonal double helix more closely resembles the fiber diffraction A-DNA, compared to the tetragonal form. For instance, the tilt angle is higher (16 degrees vs 10 degrees), which is correlated with a larger displacement from the helix axis (3.5 vs 3.3), a lower rise per residue (2.9 vs 3.2), and a smaller major-groove width (6.1 vs 8.7), thus indicating that the variations in these global helical parameters are correlated. The propeller twist angles in both forms are higher for the G-C base pairs (15.3 degrees, 12.14 degrees) than for the A-T base pairs (10.8 degrees, 9.1 degrees), which is the reverse of the expected order. Unlike the tetragonal structure, the hexagonal crystal structure interestingly does not contain a bound spermine molecule. Our analysis reveals that the conformational differences between the tetragonal and hexagonal forms are not entirely due to the spermine binding, and crystal packing seems to play an important role.
交替的DNA八聚体d(GTGTACAC)以一种新型的六方晶体形式生长。该结构已被确定并精修至2埃分辨率，包含51个水分子。A-DNA构象是同一序列四方晶体形式（Jain等人，1989年）所观察到的构象的变体，其中包含一个结合的精胺。晶体属于空间群P6(1)22，a = b = 32.40埃，c = 79.25埃，不对称单元中有一条链。通过在直接空间中的旋转和平移搜索解析了新的六方结构，并使用1561个大于1.5σ(I)的独特反射将其精修至最终R值为12.7%。电子密度清楚地表明，倒数第二个A7糖翻转到了另一种C2'-内型构象。分子中的这个凹陷可归因于紧密的分子间接触。相比之下，在四方结构中，DNA在中心TA步处发生扭曲，其中A5主链键C4'-C5'和O5'-P呈反式构象。与四方形式相比，六方双螺旋更类似于纤维衍射A-DNA。例如，倾斜角更高（16度对10度），这与从螺旋轴的更大位移（3.5对3.3）、每个残基的更低上升（2.9对3.2）以及更小的大沟宽度（6.1对8.7）相关，因此表明这些全局螺旋参数的变化是相关的。两种形式中G-C碱基对的螺旋桨扭转角（15.3度，12.14度）高于A-T碱基对（10.8度，9.1度），这与预期顺序相反。与四方结构不同，有趣的是六方晶体结构中不包含结合的精胺分子。我们的分析表明，四方和六方形式之间的构象差异并不完全归因于精胺结合，晶体堆积似乎起着重要作用。
