Ohishi Hirofumi, Suzuki Kenji, Ohtsuchi Masahiro, Hakoshima Toshio, Rich Alexander
Osaka University of Pharmaceutical Sciences, Nasahara, Takatsuki, 569-l094, Osaka, Japan.
FEBS Lett. 2002 Jul 17;523(1-3):29-34. doi: 10.1016/s0014-5793(02)02922-8.
The crystal structure of a left-handed Z-DNA hexamer, d(CG)(3) in complex with a synthetic polyamine, N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine, NH(3)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(3)(+) [PA(222)], has been determined by the X-ray diffraction method at 1.0 A resolution. In an orthorhombic crystal, the d(CG)(3) duplex binds two PA(222) molecules, and this synthetic polyamine exhibits dual conformational properties. One of the two PA(222) molecules resides on the floor of the minor groove of a Z-DNA duplex and imino groups bridge the two phosphate chains across a double helix, while the terminal amino groups link the oxygen atoms O2 of four cytosine bases. This PA(222) molecule makes a U-turn like a fishhook at one of its ends to provide a micro-environmental network previously unseen in complexes of DNA with polyamines. The width of the minor groove does not become considerably greater with the looped end of the polyamine, indicating conformational rigidity of the Z-DNA backbone imposed by the high stacking energy of the GC base pairs. While polyamine binding to the minor groove has been postulated by theoretical studies for stabilizing the Z-DNA double helical conformation, the finding in the crystal of the looped polyamine chain binding the minor groove of Z-DNA is observed for the first time from the data collected at 10 degrees C (so-called room temperature data). Another PA(222) molecule binds on the convex outer surface of the major groove of the Z-DNA duplex and links three d(CG)(3) duplexes which are symmetrically related to each other. The structure of this PA(222) presents the previously reported zig-zag type conformation [Egli et al., Biochemistry 30 (1991) 11388-11402]. Comparison of this structure with other polyamine-DNA cocrystals reveals structural themes and differences that may relate to the length of the polyamine.
已通过X射线衍射法在1.0埃分辨率下测定了左手Z-DNA六聚体d（CG）（3）与合成多胺N（1）-[2-（2-氨基-乙氨基）-乙基]-乙烷-1,2-二胺（NH₃⁺-(CH₂)₂-NH₂⁺-(CH₂)₂-NH₂⁺-(CH₂)₂-NH₃⁺ [PA(222)]）形成的复合物的晶体结构。在正交晶系晶体中，d（CG）（3）双链体结合两个PA(222)分子，并且这种合成多胺表现出双重构象性质。两个PA(222)分子中的一个位于Z-DNA双链体小沟的底部，亚氨基跨双螺旋桥接两条磷酸链，而末端氨基连接四个胞嘧啶碱基的O2氧原子。这个PA(222)分子在其一端像鱼钩一样形成一个U形转弯，以提供一个在DNA与多胺复合物中前所未见的微环境网络。多胺的环状末端并没有使小沟的宽度显著增加，这表明GC碱基对的高堆积能对Z-DNA主链造成了构象刚性。虽然理论研究推测多胺与小沟结合可稳定Z-DNA双螺旋构象，但从10℃收集的数据（所谓的室温数据）中首次观察到晶体中环状多胺链与Z-DNA小沟结合的情况。另一个PA(222)分子结合在Z-DNA双链体大沟的凸外表面上，并连接三个彼此对称相关的d（CG）（3）双链体。这个PA(222)的结构呈现出先前报道的锯齿形构象[Egli等人，《生物化学》30（1991）11388-11402]。将该结构与其他多胺-DNA共晶体进行比较，揭示了可能与多胺长度相关的结构主题和差异。
