Measured and calculated CD spectra of G‐quartets stacked with the same or opposite polarities

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. Chirality, 2008. © 2007 Wiley‐Liss, Inc.