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 ¹⁵[math] 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 ¹⁵[math]-ion-binding sites (O₁, I and O₂). Quantitative analysis utilizing ¹⁵[math] ions as a NMR probe clearly demonstrates that there is no unidirectional ¹⁵[math] ion movement through the central cavity of the G-quadruplex. ¹⁵[math] ions move...

d[G₄(T₄G₄)₃] has been folded into a unimolecular G-quadruplex in the presence of ¹⁵[math] 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 ¹⁵[math]-ion-binding sites (O₁, I and O₂). Quantitative analysis utilizing ¹⁵[math] ions as a NMR probe clearly demonstrates that there is no unidirectional ¹⁵[math] ion movement through the central cavity of the G-quadruplex. ¹⁵[math] ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. ¹⁵[math] ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for ¹⁵[math] ion passage and diagonal versus edge-type arrangement of the T₄ loops. The movement of ¹⁵[math] 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 ¹⁵[math] 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.