title: A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures.
abstract: G-quadruplex DNA (G4-DNA) structures are four-stranded helical DNA (or RNA) structures, comprising stacks of G-tetrads, which are the outcome of planar association of four guanines in a cyclic Hoogsteen hydrogen-bonding arrangement. In the last decade the number of publications where CD spectroscopy has been used to study G4-DNAs, is extremely high. However, with very few exceptions, these investigations use an empirical interpretation of CD spectra. In this interpretation two basic types of CD spectra have been associated to a single specific difference in the features of the strand folding, i.e. the relative orientation of the strands, "parallel" (all strands have the same 5' to 3' orientation) or "antiparallel". Different examples taken from the literature where the empirical interpretation is not followed or is meaningless are presented and discussed. Furthermore, the case of quadruplexes formed by monomeric guanosine derivatives, where there is no strand connecting the adjacent quartets and the definition parallel/antiparallel strands cannot apply, will be discussed. The different spectral features observed for different G-quadruplexes is rationalised in terms of chromophores responsible for the electronic transitions. A simplified exciton coupling approach or more refined QM calculations allow to interpret the different CD features in terms of different stacking orientation (head-to-tail, head-to-head, tail-to-tail) between adjacent G-quartets irrespectively of the relative orientation of the stands (parallel/antiparallel).
authors.affiliation: Alma Mater Studiorum-Università di Bologna, Dipartimento di Chimica Organica A. Mangini, via San Giacomo 11, I-40126, Bologna, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Masiero
authors.forename: Roberta
authors.initials: R
authors.lastname: Trotta
authors.forename: Silvia
authors.initials: S
authors.lastname: Pieraccini
authors.forename: Stefano
authors.initials: S
authors.lastname: De Tito
authors.forename: Rosaria
authors.initials: R
authors.lastname: Perone
authors.forename: Antonio
authors.initials: A
authors.lastname: Randazzo
authors.forename: Gian Piero
authors.initials: GP
authors.lastname: Spada
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA