Frederick C A, Quigley G J, Teng M K, Coll M, Van der Marel G A, Van Boom J H, Rich A, Wang A H
Department of Biology, Massachusetts Institute of Technology, Cambridge.
Eur J Biochem. 1989 May 1;181(2):295-307. doi: 10.1111/j.1432-1033.1989.tb14724.x.
The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dimensions of a = b = 3.923 nm and c = 7.80 nm in the space group P6(1)22. The overall conformation of this A-DNA decamer is very similar to that of the fiber model for A-DNA which has a large average base-pair tilt and hence a wide and shallow minor groove. This structure is in contrast to that of several A-DNA octamers in which the molecules all have low base-pair-tilt angles (8-12 degrees) resulting in an appearance intermediate between B-DNA and A-DNA. The average helical parameters of this decamer are typical of A-DNA with 10.9 base pairs/turn of helix, an average helical twist angle of 33.1 degrees, and a base-pair-tilt angle of 18.2 degrees. However, the CpG step in this molecule has a low local-twist angle of 24.5 degrees, similar to that seen in other A-DNA oligomers, and therefore appears to be an intrinsic stacking pattern for this step. The molecules pack in the crystal using a recurring binding motif, namely, the terminal base pair of one helix abuts the surface of the shallow minor groove of another helix. In addition, the GC base pairs have large propeller-twist angles, unlike those found most other A-DNA structures.
通过在0.20纳米分辨率下的单晶X射线衍射分析，已解析并精修了DNA十聚体d(ACCGGCCGGT)的分子结构，最终R因子为18.0%。该十聚体结晶为A-DNA双螺旋片段，在空间群P6(1)22中，晶胞尺寸为a = b = 3.923纳米，c = 7.80纳米。这种A-DNA十聚体的整体构象与A-DNA纤维模型非常相似，后者具有较大的平均碱基对倾斜度，因此小沟宽而浅。这种结构与几种A-DNA八聚体的结构形成对比，在这些八聚体中，分子的碱基对倾斜角都很低（8-12度），导致其外观介于B-DNA和A-DNA之间。该十聚体的平均螺旋参数是A-DNA的典型参数，每螺旋圈有10.9个碱基对，平均螺旋扭转角为33.1度，碱基对倾斜角为18.2度。然而，该分子中的CpG步具有低至24.5度的局部扭转角，与其他A-DNA寡聚物中的情况相似，因此似乎是该步的一种固有堆积模式。分子在晶体中通过一种重复的结合基序堆积，即一个螺旋的末端碱基对邻接另一个螺旋浅小沟的表面。此外，与大多数其他A-DNA结构不同，GC碱基对具有较大的螺旋桨扭转角。
