title: NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution.
abstract: d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15NH4+ ions. NMR spectroscopy confirmed that its topology is the same as the solution state structure determined earlier by Wang and Patel (J. Mol. Biol., 1995; 251: 76-94) in the presence of Na+ ions. The d[G4(T4G4)3] G-quadruplex exhibits four G-quartets with three 15NH4+-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15NH4+ ions as a NMR probe clearly demonstrates that there is no unidirectional 15NH4+ ion movement through the central cavity of the G-quadruplex. 15NH4+ ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15NH4+ ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15NH4+ ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15NH4+ ions from the interior of the G-quadruplex to bulk solution is faster than exchange within the G-quadruplex. The structural details of the G-quadruplex define stiffness of individual G-quartets that intimately affects 15NH4+ ion movement. The stiffness of G-quartets and steric hindrance imposed by thymine residues in the loops contribute to the 5-fold difference in the exchange rate constants through the outer G-quartets.
authors.affiliation: Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
authors.forename: Peter
authors.initials: P
authors.lastname: Podbevsek
authors.forename: Nicholas V
authors.initials: NV
authors.lastname: Hud
authors.forename: Janez
authors.initials: J
authors.lastname: Plavec
mesh_terms: D001665:Binding Sites; D002412:Cations / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D008958:Models, Molecular; D009038:Motion; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D000644:Quaternary Ammonium Compounds / Q000737:chemistry*; D012996:Solutions; D013696:Temperature
chemical_list: D002412:Cations; D000644:Quaternary Ammonium Compounds; D012996:Solutions; C520334:d(G4(T4G4)3); D006147:Guanine; D004247:DNA