Collision-induced transfer enhances ligand-binding kinetics in guanine quadruplex DNA

Guanine quadruplexes (G4s) are non-canonical DNA secondary structures thought to play critical regulatory roles in cells. Notably, G4s are implicated in oncogenesis, making them attractive therapeutic targets. Thus, understanding G4/ligand interactions is of great interest. Here, we introduce an experimental technique for characterizing G4/ligand interactions: relaxation dispersion nuclear magnetic resonance (RD-NMR) has many advantages over conventional techniques, including the ability to measure rapid (millisecond-timescale) binding and to focus exclusively on the most functionally relevant highest-affinity interactions. We used RD-NMR to study the binding mechanism of the ligand TMPyP4 with a G4 from the cMYC promoter. Consistent with previous reports, we found that ligand dissociation at dilute G4 concentrations was slow. Surprisingly, we saw this dissociation increase proportionally with the concentration of free G4, suggesting that collisions between bound and free G4s facilitated ligand transfer. Similar behavior was observed for ligand transfer between G4s and double-stranded DNA and confirmed by surface plasmon resonance. To our knowledge, this is the first observation of collision-induced ligand transfer involving a G4. This phenomenon could potentially be important in G4 therapeutics as it could help ligands escape from kinetic traps, akin to the mechanisms employed by DNA-binding proteins to efficiently locate their genomic targets.