Ohishi H, Terasoma N, Nakanishi I, van der Marel G, van Boom J H, Rich A, Wang A H, Hakoshima T, Tomita K
Osaka University of Pharmaceutical Sciences, Takatsuki, Japan.
FEBS Lett. 1996 Dec 2;398(2-3):291-6. doi: 10.1016/s0014-5793(96)01225-2.
The DNA fragment, d(CG)3, was co-crystallized with N-(3-amino-propyl)-N-(5-aminopropyl)-l,4 -diaminobutane (thermospermine; PA(334)), a polyamine metabolized from the nucleic acid. By using a good crystal with dimensions of 0.5 x 0.5 x 0.5 mm3, X-ray intensity data were collected up to 1.0 A resolution. Two thermospermine molecules and a magnesium cation were bound to the left-handed double-helical d(CG)3 molecule. The d(CG)3 molecule adopted the left-handed Z-conformation and two thermospermine molecules and a magnesium cation neutralized the negative charges of the phosphate groups of the d(CG)3 molecule. Furthermore, the binding modes between d(CG)3 and thermospermine were different from those of d(CG)3 complexes with PA(24), spermidine and spermine. This is the first case in which it was determined by X-ray crystallographic analysis that one of two thermospermine molecules bound three d(CG)3 duplexes which were symmetrically related to each other, and the other formed two hydrogen bonds at the N(5) and N(9) atoms with two adjacent nucleotide phosphate groups of a single d(CG)3 strand at the minor groove. Furthermore, no direct coordination bond was found between the d(CG)3 molecule and the magnesium cation.
DNA片段d(CG)3与N-(3-氨基丙基)-N-(5-氨基丙基)-1,4-二氨基丁烷（热精胺；PA(334)）共结晶，热精胺是一种由核酸代谢产生的多胺。使用尺寸为0.5×0.5×0.5 mm3的良好晶体，收集了分辨率高达1.0 Å的X射线强度数据。两个热精胺分子和一个镁阳离子与左手双螺旋d(CG)3分子结合。d(CG)3分子呈左手Z构象，两个热精胺分子和一个镁阳离子中和了d(CG)3分子磷酸基团的负电荷。此外，d(CG)3与热精胺之间的结合模式不同于d(CG)3与PA(24)、亚精胺和精胺形成的复合物。这是首次通过X射线晶体学分析确定两个热精胺分子中的一个与三个彼此对称相关的d(CG)3双链体结合，另一个在小沟处与单链d(CG)3的两个相邻核苷酸磷酸基团的N(5)和N(9)原子形成两个氢键。此外，在d(CG)3分子与镁阳离子之间未发现直接配位键。
