Insights into How NH4+ Ions Enhance the Activity of Dimeric G-Quadruplex/Hemin DNAzyme

Dimeric G-quadruplex (G4)/Hemin has been employed to expand the catalytic repertoire of nucleic acid. Herein, we aim to understand the effect of NH4+ ions on the catalytic behavior of the dimeric G4/Hemin DNAzyme. Through EPR and UV–vis spectroscopy, we found that NH4+ ions resulted in more accumulation of compound I (Cpd I, Fe (IV)═O•+) in the dimeric DNAzyme process. Furthermore, molecular dynamics simulations showed that NH4+ ions could be present in the catalytic chamber to stabilize the dimeric G4 while interacting with the substrate hydrogen peroxide by hydrogen bonds. The interaction between the NH4+ ion and H2O2 contributes to a better stability of intermediate and transition-state species involved in the catalytic formation of Cpd I. Specifically, NH4+ ions facilitate the O–O bond breaking of iron–porphyrin-bound H2O2 (the rate-limiting step). With four available hydrogen atoms, a NH4+ ion can be an effective “additive” to promote the activity of the dimeric DNAzyme. The results provide the strategy for adjusting the DNAzyme by transition-state stabilization by hydrogen bonding networks. Our data shed light on the mechanistic clues on the design and application of G4-based catalysts.