Face-to-face and edge-to-face π-π interactions in a synthetic DNA hairpin with a stilbenediether linker
Face-to-face and edge-to-face π-π interactions in a synthetic DNA hairpin with a stilbenediether linker
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DOI：
10.1021/ja0355527
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发表时间：
2003-09-10
影响因子：
15
通讯作者：
Lewis, FD
中科院分区：
文献类型：
--
作者：
Egli, M;Tereshko, V;Lewis, FD
具有双（2-羟乙基）二苯乙烯-4，4 '-二醚接头（Sd 2）的合成缀合物形成迄今报道的最稳定的DNA发夹。影响稳定性的因素是连接体的长度和柔性以及相邻碱基对上芪部分的π-堆叠。在1.5埃分辨率下测定发夹d（GT（4）G）-Sd 2-d（CA（4）C）的晶体结构。在不对称单元中的两个分子的构象在连接体和茎部分中均不同。其中一个显示了堆叠在相邻G：C碱基对上的平面芪。另一个显示了苯环之间的相当大的旋转和前所未有的二苯乙烯和碱基对的边到面取向。在晶体结构中的Sd部分的构象的观察相当大的变化，使我们能够排除限制运动的原因没有Sd光异构化的发夹。两个发夹分子的茎部分的构象差异与不同的Mg 2+结合模式一起沿着。其中最显着的是在狭窄的A道小沟中的金属离子的序列特异性协调。晶体结构提供了明确的证据表明，完全水合的Mg 2+离子可以穿透狭窄的A道小沟，导致沟进一步收缩。总的来说，结构数据提供了更好的理解发夹稳定性的起源和它们在溶液中的光化学行为。
Synthetic conjugates possessing bis(2-hydroxyethyl)stilbene-4,4'-diether linkers (Sd2) form the most stable DNA hairpins reported to date. Factors that affect stability are length and flexibility of the linkers and pi-stacking of the stilbene moiety on the adjacent base pair. The crystal structure of the hairpin d(GT(4)G)-Sd2-d(CA(4)C) was determined at 1.5 Angstrom resolution. The conformations of the two molecules in the asymmetric unit differ both in the linker and the stem portions. One of them shows a planar stilbene that is stacked on the adjacent G:C base pair. The other displays considerable rotation between the phenyl rings and an unprecedented edge-to-face orientation of stilbene and base pair. The observation of considerable variations in the conformation of the Sd moiety in the crystal structure allows us to exclude restriction of motion as the reason for the absence of Sd photoisomerization in the hairpins. Conformational differences in the stem portion of the two hairpin molecules go along with different Mg2+ binding modes. Most remarkable among them is the sequence-specific coordination of a metal ion in the narrow A-tract minor groove. The crystal structure provides unequivocal evidence that a fully hydrated Mg2+ ion can penetrate the narrow A-tract minor groove, causing the groove to further contract. Overall, the structural data provide a better understanding of the origins of hairpin stability and their photochemical behavior in solution.