Pan B, Ban C, Wahl M C, Sundaralingam M
Biological Macromolecular Structure Center, Department of Chemistry, The Ohio State University, Columbus 43210-1002, USA.
Biophys J. 1997 Sep;73(3):1553-61. doi: 10.1016/S0006-3495(97)78187-6.
The crystal structure of the DNA heptamer d(GCGCGCG) has been solved at 1.65 A resolution by the molecular replacement method and refined to an R-value of 0.184 for 3598 reflections. The heptamer forms a Z-DNA d(CGCGCG)2 with 5'-overhang G residues instead of an A-DNA d(GCGCGC)2 with 3'-overhang G residues. The overhang G residues from parallel strands of two adjacent duplexes form a trans reverse Hoogsteen G x G basepair that stacks on the six Z-DNA basepairs to produce a pseudocontinuous helix. The reverse Hoogsteen G x G basepair is unusual in that the displacement of one G base relative to the other allows them to participate in a bifurcated (G1)N2 . . . N7(G8) and an enhanced (G8)C8-H . . . O6(G1) hydrogen bond, in addition to the two usual hydrogen bonds. The 5'-overhang G residues are anti and C2'-endo while the 3'-terminal G residues are syn and C2'-endo. The conformations of both G residues are different from the syn/C3'-endo for the guanosine in a standard Z-DNA. The two cobalt hexammine ions bind to the phosphate groups in both GpC and CpG steps in Z(I) and Z(II) conformations. The water structure motif is similar to the other Z-DNA structures.
通过分子置换法，已在1.65埃分辨率下解析了DNA七聚体d(GCGCGCG)的晶体结构，并针对3598个反射将其精修至R值为0.184。该七聚体形成了带有5'-突出端G残基的Z-DNA d(CGCGCG)2，而非带有3'-突出端G残基的A-DNA d(GCGCGC)2。来自两个相邻双链体平行链的突出端G残基形成了一个反式反向Hoogsteen G×G碱基对，该碱基对堆积在六个Z-DNA碱基对上，形成一个假连续螺旋。反向Hoogsteen G×G碱基对不同寻常之处在于，一个G碱基相对于另一个的位移使它们能够参与一个分叉的(G1)N2...N7(G8)和一个增强的(G8)C8-H...O6(G1)氢键，此外还有两个常见的氢键。5'-突出端G残基为反式且C2'-内型，而3'-末端G残基为顺式且C2'-内型。两个G残基的构象均不同于标准Z-DNA中鸟苷的顺式/C3'-内型。两个六氨合钴离子在Z(I)和Z(II)构象中与GpC和CpG步中的磷酸基团结合。水结构基序与其他Z-DNA结构相似。
