Insights into How NH<sub>4</sub><sup>+</sup> Ions Enhance the Activity of Dimeric G-Quadruplex/Hemin DNAzyme
Wenqin Zhou, Rui Lai, Yu Cheng, Yu Bao, Wenhui Miao, Xupeng Cao, Guoqing Jia, Guohui Li, Can Li
Abstract
Dimeric G-quadruplex (G4)/Hemin has been employed to expand the catalytic repertoire of nucleic acid. Herein, we aim to understand the effect of NH 4 + ions on the catalytic behavior of the dimeric G4/Hemin DNAzyme. Through EPR and UV–vis spectroscopy, we found that NH 4 + ions resulted in more accumulation of compound I (Cpd I, Fe (IV)═O •+ ) in the dimeric DNAzyme process. Furthermore, molecular dynamics simulations showed that NH 4 + 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 NH 4 + ion and H 2 O 2 contributes to a better stability of intermediate and transition-state species involved in the catalytic formation of Cpd I. Specifically, NH 4 + ions facilitate the O–O bond breaking of iron–porphyrin-bound H 2 O 2 (the rate-limiting step). With four available hydrogen atoms, a NH 4 + 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.