title: Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+.
abstract: Guanine quadruplex (G-quadruplex) structures are formed by guanine-rich oligonucleotides. Because of their in vivo and in vitro importance, numerous studies have been demonstrated that the structure and stability of the G-quadruplex are dependent on the sequence of oligonucleotide and environmental conditions such as existing cations. Previously, we quantitatively investigated the divalent cation effects on the antiparallel G-quadruplex of d(G4T4G4), and found that Ca2+ induces a structural transition from the antiparallel to parallel G-quadruplex, and finally G-wire formation. In the present study, we report in detail the kinetic and thermodynamic analyses of the structural transition induced by Ca2+ using stopped-flow apparatus, circular dichroism, size-exclusion chromatography (SEC) and atomic force microscopy. The quantitative parameters showed that at least two Ca2+ ions were required for the transition. The kinetic parameters also indicated that d(G4T4G4) underwent the transition through multiple steps involving the Ca2+ binding, isomerization and oligomerization of d(G4T4G4). The parallel-stranded G-wire structure of d(G4T4G4), which is a well controlled alignment of numerous DNA strands with G-quartets, as the final product induced by Ca2+, was observed using SEC and atomic force microscopy. These results provide insight into the mechanism of the structural transition and G-wire formation and are useful for constructing a nanomaterial regulated by Ca2+.
authors.affiliation: Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
authors.forename: Akihiro
authors.initials: A
authors.lastname: Nakao
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002118:Calcium / Q000494:pharmacology*; D002851:Chromatography, High Pressure Liquid; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D007700:Kinetics; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009841:Oligonucleotides / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides; D006147:Guanine; D004247:DNA; D002118:Calcium