Lewis Frederick D, Zhang Ligang, Liu Xiaoyang, Zuo Xiaobing, Tiede David M, Long Hai, Schatz George C
Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA.
J Am Chem Soc. 2005 Oct 19;127(41):14445-53. doi: 10.1021/ja0539387.
The structure and properties of oligonucleotide conjugates possessing stilbenedicarboxamide chromophores at both ends of a poly(dA):poly(dT) base-pair domain of variable length have been investigated using a combination of spectroscopic and computational methods. These conjugates form capped hairpin structures in which one stilbene serves as a hairpin linker and the other as a hydrophobic end-cap. The capping stilbene stabilizes the hairpin structures by ca. 2 kcal/mol, making possible the formation of a stable folded structure containing a single A:T base pair. Exciton coupling between the stilbene chromophores has little effect on the absorption bands of capped hairpins. However, exciton-coupled circular dichroism (EC-CD) can be observed for capped hairpins possessing as many as 11 base pairs. Both the sign and intensity of the EC-CD spectrum are sensitive to the number of base pairs separating the stilbene chromophores, as a consequence of the distance and angular dependence of exciton coupling. Calculated spectra obtained using a static vector model based on canonical B-DNA are in good agreement with the experimental spectra. Molecular dynamics simulations show that conformational fluctuations of the capped hairpins result in large deviations of the averaged spectra in both the positive and negative directions. These results demonstrate for the first time the ability of B-DNA to serve as a helical ruler for the study of electronic interactions between aligned chromophores. Furthermore, they provide important tests for atomistic theoretical models of DNA.
利用光谱学和计算方法相结合的方式，研究了在可变长度的聚（dA）：聚（dT）碱基对结构域两端带有二苯乙烯二甲酰胺发色团的寡核苷酸缀合物的结构和性质。这些缀合物形成封端发夹结构，其中一个二苯乙烯充当发夹连接体，另一个充当疏水封端。封端的二苯乙烯使发夹结构稳定约2千卡/摩尔，使得包含单个A：T碱基对的稳定折叠结构的形成成为可能。二苯乙烯发色团之间的激子耦合对封端发夹的吸收带影响很小。然而，对于拥有多达11个碱基对的封端发夹，可以观察到激子耦合圆二色性（EC-CD）。由于激子耦合的距离和角度依赖性，EC-CD光谱的符号和强度都对分隔二苯乙烯发色团的碱基对数量敏感。使用基于标准B-DNA的静态矢量模型获得的计算光谱与实验光谱吻合良好。分子动力学模拟表明，封端发夹的构象波动导致平均光谱在正负方向上都有很大偏差。这些结果首次证明了B-DNA作为螺旋尺用于研究排列发色团之间电子相互作用的能力。此外，它们为DNA的原子理论模型提供了重要检验。
