Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities
Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities
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DOI：
10.1002/chir.20455
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发表时间：
2008-03-01
期刊：
影响因子：
2
通讯作者：
Fleischhauer, Joerg
中科院分区：
文献类型：
--
作者：
Gray, Donald M.;Wen, Jin-Der;Fleischhauer, Joerg
圆二色性（CD）光谱被广泛用于表征DNA G-四链体的结构。在200-300 nm处的CD谱带已经经验性地与具有平行或反平行糖-磷酸骨架的G-四链体相关。我们建议，CD带的起源的一个更根本的解释是在相邻的G-四重态，它可以有相同或相反的极性的氢键受体和供体的堆叠相互作用。根据d（G）（5）G-四链体和凝血酶结合适体的CD光谱的经验求和，所述适体具有分别具有相同和相反极性的相邻G-四联体，由Ff基因5蛋白（g5 p）选择的适体的光谱似乎是由相邻G-四联体的两种类型的极性的组合产生的。适体的CD谱类似于d（G（3）T（4）G（3））的谱，其中两个相邻的四联体具有相同的极性，两个具有相反的极性。量子化学光谱计算使用矩阵方法进行，基于鸟嘌呤发色团取向为d（G（3）T（4）G（3））。计算结果表明，这两类G-四重体的CD谱与相应类型G-四重体的实验谱相似。
Circular dichroism (CD) spectroscopy is widely used to characterize the structures of DNA G-quadruplexes. CD bands at 200-300 nm have been empirically related to G-quadruplexes having parallel or antiparallel sugar-phosphate backbones. We propose that a more fundamental interpretation of the origin of the CD bands is in the stacking interactions of neighboring G-quartets, which can have the same or opposing polarities of hydrogen bond acceptors and donors. From an empirical summation of CD spectra of the d(G)(5) G-quadruplex and of the thrombin binding aptamer that have neighboring G-quartets with the same and opposite polarities, respectively, the spectra of aptamers selected by the Ff gene 5 protein (g5p) appear to arise from a combination of the two types of polarities of neighboring G-quartets. The aptamer CD spectra resemble the spectrum of d(G(3)T(4)G(3)), in which two adjacent quartets have the same and two have opposite polarities. Quantum-chemical spectral calculations were performed using a matrix method, based on guanine chromophores oriented as in d(G(3)T(4)G(3)). The calculations show that the two types of G-quartet stacks have CD spectra with features resembling experimental spectra of the corresponding types of G-quadruplexes.