NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution

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.