Gray Donald M, Wen Jin-Der, Gray Carla W, Repges Rudolf, Repges Charlotte, Raabe Gerhard, Fleischhauer Jörg
Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA.
Chirality. 2008 Mar;20(3-4):431-40. doi: 10.1002/chir.20455.
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(G3T4G3), 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(G3T4G3). 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.
圆二色光谱（CD）被广泛用于表征DNA G-四链体的结构。200 - 300 nm处的CD谱带根据经验与具有平行或反平行糖磷酸骨架的G-四链体相关。我们提出，对CD谱带起源的一种更基本的解释在于相邻G-四重体的堆积相互作用，其氢键受体和供体可以具有相同或相反的极性。通过对d(G)5 G-四链体和凝血酶结合适体的CD光谱进行经验总结，它们分别具有相邻极性相同和相反的G-四重体，由Ff基因5蛋白（g5p）选择的适体光谱似乎源于两种相邻G-四重体极性的组合。适体CD光谱类似于d(G3T4G3)的光谱，其中两个相邻四重体具有相同极性，另外两个具有相反极性。基于与d(G3T4G3)中鸟嘌呤发色团取向相同的情况，使用矩阵方法进行了量子化学光谱计算。计算表明，两种类型的G-四重体堆叠具有的CD光谱特征类似于相应类型G-四链体的实验光谱。
