title: Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities.
abstract: 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.
authors.affiliation: Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA. dongray@utdallas.edu
authors.forename: Donald M
authors.initials: DM
authors.lastname: Gray
authors.forename: Jin-Der
authors.initials: JD
authors.lastname: Wen
authors.forename: Carla W
authors.initials: CW
authors.lastname: Gray
authors.forename: Rudolf
authors.initials: R
authors.lastname: Repges
authors.forename: Charlotte
authors.initials: C
authors.lastname: Repges
authors.forename: Gerhard
authors.initials: G
authors.lastname: Raabe
authors.forename: Jörg
authors.initials: J
authors.lastname: Fleischhauer
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D013237:Stereoisomerism; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D004268:DNA-Binding Proteins; D014764:Viral Proteins; C057816:gene 5 protein, Enterobacteria phage M13; D004247:DNA