Kinetics of Sodium Ion Binding to DNA Quadruplexes

Abstract

The binding environments of sodium ions on oligomeric DNA quadruplex structures have been examined by 23Na NMR. Competitive ion binding experiments confirm that the selectivity of univalent cations for the strong sites on the G-quadruplex d(G 4T 4G 4) follows the order K +> Na +> Cs +. 23Na intensity measurements demonstrate a class of sodium ions that are not detectable by NMR, establishing that the sodium ions bind with loss of water of hydration. These measurements define the number of occupied, specific sodium ion binding sites per quadruplex as 2(±1). In contrast to the rapid exchange of specifically bound sodium ions from the tetrameric G-quadruplex structure d(T 2G 4T), exchange from the dimeric G-quadru plex structure of d(G 4T 4G 4) is slow on the timescale of the 23Na NMR relaxation. 23Na NMR relaxation measurements, performed as a function of temperature, allow the kinetics of sodium ion complexation to be determined. The lifetime of specifically bound sodium ions is estimated as 180 μs at 20°C. The temperature dependence of the exchange rates suggests a fully hydrated transition state.