DNA‐Based Peroxidation Catalyst—What Is the Exact Role of Topology on Catalysis and Is There a Special Binding Site for Catalysis?

Abstract

In the last decade, there has been growing interests in studies aimed at delineating the strategies used by various nucleic acid enzymes to facilitate catalysis. Insights gained from such studies would enable the design of better DNA/RNA catalysts for various applications such as biosensing. DNA and RNA catalysts have been shown to be able to catalyze myriads of reactions, including peroxidation reactions, which are catalyzed by G-quadruplexes. In this report, we provide data that clarifies how G-quadruplex peroxidases achieve catalysis. Firstly, we show that by covalently linking a hemin cofactor to DNAzymes, anti-parallel G-quadruplexes, which have been previously shown to be catalytically inefficient, can be "resurrected" to become good peroxidation catalysts. We also reveal that the relative rates of peroxidation by DNAzyme peroxidases depend on the nature of the organic reductant, arguing for a special binding site in the peroxidase-mimicking DNAzymes for catalysis.

Harnessing Nature’s Insights: Synthetic Small Molecules with Peroxidase‐Mimicking DNAzyme Properties

“…We selected this quadruplex primarily because of its biological relevance, [2] even if its K + -promoted "antiparallel" quadruplex structure (Figure 1 A) makes it a more modest DNAzyme catalyst [10b, 16] than "parallel" quadruplexes, like c-myc. [17] We focused on the 22AG-quadruplex also because we initially aimed at using DNAzyme for telomerase activity assays, as pioneered by Willner and co-workers.…”

A Polymeric Liquid Membrane Electrode Responsive to 3,3′,5,5′-Tetramethylbenzidine Oxidation for Sensitive Peroxidase/Peroxidase Mimetic-Based Potentiometric Biosensing

“…24 Considering the wide utility of G-quadruplex/hemin DNAzymes in bioanalysis, the feasibility of the TMB oxidation-sensitive electrode in sensing G-quadruplex/hemin DNAzymes and DNAzyme-involved biorecognition events has been examined. As shown in Figure 4, in the presence of the model G-quadruplex/hemin DNAzyme, 25 a large potential response can be obtained toward the H 2 O 2 -mediated TMB oxidation, while hemin (with limited peroxidase-like activity) or G-rich sequence (with no catalytic activity) as the catalyst could only induce small or negligible potential responses. Based on the superior peroxidatic activity of the G-quadruplex/hemin DNAzyme, a label-free potentiometric DNA hybridization assay protocol has been developed.…”

Tetra(p‐tolyl)borate‐Functionalized Solvent Polymeric Membrane: A Facile and Sensitive Sensing Platform for Peroxidase and Peroxidase Mimetics

“…For DNAzyme measurements, HEPES buffer of pH 7.5 (20 mm N-2-hydroxyethylpiperazine-N'-ethane sulfonic acid Figure 5. Potential responses of the H 2 O 2 -mediated oxidation of o-PD catalyzed by the G-quadruplex (5'-GGGTAGGGCGGGTTGGGT-3')/ hemin complex, [46] hemin, and G-quadruplex. Experimental conditions: HEPES buffer (20 mm), pH 7.5, G-rich DNA (0.5 mm), hemin (0.5 mm), o-PD (1 mm), H 2 O 2 (1 mm).…”