Not all G-quadruplexes exhibit ion-channel-like properties:: NMR study of ammonium ion (non)movement within the d(G3T4G4)2 quadruplex

A solution-state NMR study on (NH4+)-N-15 ion movement within d(G(3)T(4)G(4))(2,) a dimeric G-quadruplex consisting of three G-quartets and two T-4 loops, rather unexpectedly demonstrated the absence of (NH4+)-N-15 ion movement between the binding sites U and L along the central axis of the G-quadruplex. Distinct temperature dependences of autocorrelation signals for U and L binding sites have been observed in N-15-H-1 NzExHSQC spectra which correlate with the local stiffness of the G-quadruplex. The volumes of the cross-peaks, which are the result of (NH4+)-N-15 ion movement, have been interpreted in terms of rate constants, T-1 relaxation, and proton exchange. (NH4+)-N-15 ion movements from the binding sites U and L into the bulk solution are characterized by lifetimes of 139 ms and 1.7 s at 298 K, respectively. The 12 times faster movement from the binding site U demonstrates that (NH4+)-N-15 ion movement is controlled by the structure of T-4 loop residues, which through diagonal- vs edge-type orientations impose distinct steric restraints for cations to leave or enter the G-quadruplex. Arrhenius-type analysis has afforded an activation energy of 66 kJ mol(-1) for the UB process, while it could not be determined for the LB process due to slow rates at temperatures below 298 K. We further the use of the (NH4+)-N-15 ion as an NMR probe to gain insight into the occupancy of binding sites by cations and kinetics of ion movement which are intrinsically correlated with the structural details, dynamic fluctuations, and local flexibility of the DNA structure.