Ban C, Ramakrishnan B, Sundaralingam M
Department of Chemistry, Ohio State University, Columbus 43210, USA.
Biophys J. 1996 Sep;71(3):1215-21. doi: 10.1016/S0006-3495(96)79350-5.
Alternating self-complementary oligonucleotides starting with a 5'-pyrimidine usually form left-handed Z-DNA; however, with a 5'-purine start sequence they form the right-handed A-DNA. Here we report the crystal structure of the decamer d(GCGCGCGCGC) with a 5'-purine start in the Z-DNA form. The decamer crystallizes in the hexagonal space group P6(5)22, unit cell dimensions a = b = 18.08 and c = 43.10 A, with one of the following four dinucleotide diphosphates in the asymmetric unit: d(pGpC)/d(GpCp)/d(pCpG)/d(CpGp). The molecular replacement method, starting with d(pGpC) of the isomorphous Z-DNA hexamer d(araC-dG)3 without the 2'-OH group of arabinose, was used in the structure analysis. The method gave the solution only after the sugar-phosphate conformation of the GpC step was manipulated. The refinement converged to a final R value of 18.6% for 340 unique reflections in the resolution range 8.0-1.9 A. A result of the sequence alternation is the alternation in the nucleotide conformation; guanosine is C3'-endo, syn, and cytidine is C2'-endo, anti. The CpG step phosphodiester conformation is the same as ZI or ZII, whereas that of the GpC step phosphodiester is "intermediate" in the sense that zeta (O3'-P bond) is the same as ZII but alpha (P-O5' bond) is the same as ZI. The duplexes generated from the dinucleotide asymmetric unit are stacked one on top of the other in the crystal to form an infinite pseudocontinuous helix. This renders it a quasi-polymerlike structure that has assumed the Z-DNA conformation further strengthened by the long inner Z-forming stretch d(CG)4. An interesting feature of the structure is the presence of water strings in both the major and the minor grooves. In the minor groove the cytosine carbonyl oxygen atoms of the GpC and CpG steps are cross-bridged by water molecules that are not themselves hydrogen bonded but are enclosed by the water rings in the mouth of the minor groove. In the major groove three independent water molecules form a zigzagging continuous water string that runs throughout the duplex.
以5'-嘧啶开头的交替自互补寡核苷酸通常形成左手Z-DNA；然而，以5'-嘌呤起始序列时，它们会形成右手A-DNA。在此我们报道了以5'-嘌呤起始的十聚体d(GCGCGCGCGC)呈Z-DNA形式的晶体结构。该十聚体在六方空间群P6(5)22中结晶，晶胞参数a = b = 18.08 Å，c = 43.10 Å，不对称单元中有以下四种二核苷酸二磷酸之一：d(pGpC)/d(GpCp)/d(pCpG)/d(CpGp)。结构分析采用分子置换法，起始模型为同晶型Z-DNA六聚体d(araC-dG)3的d(pGpC)，其中阿拉伯糖没有2'-OH基团。该方法仅在对GpC步的糖-磷酸构象进行处理后才得到结果。对于分辨率范围为8.0 - 1.9 Å的340个独立反射，精修收敛至最终R值为18.6%。序列交替的一个结果是核苷酸构象的交替；鸟苷为C3'-内型、反式，胞苷为C2'-内型、顺式。CpG步的磷酸二酯构象与ZI或ZII相同，而GpC步磷酸二酯的构象是“中间型”，即ζ（O3'-P键）与ZII相同，但α（P-O5'键）与ZI相同。由二核苷酸不对称单元产生的双链体在晶体中一个堆叠在另一个之上，形成一个无限的伪连续螺旋。这使其成为一种类似准聚合物的结构，其呈现出的Z-DNA构象因长的内部形成Z型的d(CG)4延伸而进一步得到加强。该结构的一个有趣特征是在大沟和小沟中都存在水链。在小沟中，GpC和CpG步的胞嘧啶羰基氧原子由水分子跨桥连接，这些水分子本身没有氢键，但被小沟口处的水环包围。在大沟中，三个独立的水分子形成一条曲折的连续水链，贯穿双链体。
