| In this Thesis we have shown for the first time that, contrary to the commonly accepted viewpoint, 23Na, 39K, and 87Rb NMR can be directly used as probes for studying alkali metal ion binding in G-quadruplex DNA (G = guanine). We have used solution 23Na NMR to examine Na+ binding in three G-rich DNA sequences, d(TG4T), d(G4T3G4), and d(G4T4G4) (T = Thymine). In these systems, we have detected, a distinct class of Na+ ions that are tightly bound to the G-quadruplex structure in solution. This class of Na+ ions resides between two adjacent G-quartet planes, denoted as channel ions in this Thesis. Interestingly, for d(G4T4G 4), a second class of tightly bound Na+ ions was shown to exist. This class of Na+ ions resides in the diagonal thymine loop region, denoted as loop ions in this Thesis. In d(G4T 4G4) these two classes of Na+ ions exhibit very different dynamics with the residence lifetime of the loop Na + ion considerably shorter than that of the channel Na+ ion. We have examined K+ ion binding in G-quadruplex structures formed by 5'-GMP. Using solution 39K NMR we showed that channel K+ ions can be directly detected. We have used both solid-state and solution 87Rb NMR to help probe the binding environment of Rb+ ions in G-quadruplex systems. Using solid-state NMR we were able to obtain accurate 87Rb NMR parameters and establish the NMR signature for channel Rb+ ions. With these insights we were able to directly detect the channel Rb+ ions in the G-quadruplex structures formed by 5'-GMP and d(TG4T) using solution 87Rb NMR. Finally we were then able to measure the thermodynamic parameters for the competitive binding for the channel site between Rb+ and Na+ in both these systems. |
