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The Mechanism of Cleavage of RNA Phosphodiesters by a Gold Nanoparticle Nanozyme.

ABSTRACT: The cleavage of uridine 3'-phosphodiesters bearing alcohols with pK_a ranging from 7.14 to 14.5 catalyzed by AuNPs functionalized with 1,4,7-triazacyclononane-Zn(II) complexes has been studied to unravel the source of catalysis by these nanosystems (nanozymes). The results have been compared with those obtained with two Zn(II) dinuclear catalysts for which the mechanism is fairly understood. Binding to the Zn(II) ions by the substrate and the uracil of uridine was observed. The latter leads to inhibition of the process and formation of less productive binding complexes than in the absence of the nucleobase. The nanozyme operates with these substrates mostly via a nucleophilic mechanism with little stabilization of the pentacoordinated phosphorane and moderate assistance in leaving group departure. This is attributed to a decrease of binding strength of the substrate to the catalytic site in reaching the transition state due to an unfavorable binding mode with the uracil. The nanozyme favors substrates with better leaving groups than the less acidic ones.

SUBMITTER: Czescik J

PROVIDER: S-EPMC8251847 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Covalently functionalized gold nanoparticles influence capillary electrophoresis separations of neurotransmitters in a concentration- and surface-chemistry-dependent manner. Gold nanoparticles with either primarily covalently functionalized carboxylic acid (Au@COOH) or amine (Au@NH(2)) surface groups are characterized using extinction spectroscopy, transmission electron microscopy, and zeta potential measurements. The impact of the presence of nanoparticles and their surface chemistry is investigated, and at least three nanoparticle-specific mechanisms are found to effect separations. First, the degree of nanoparticle-nanoparticle interactions is quantified using a new parameter termed the critical nanoparticle concentration (CNC). CNC is defined as the lowest concentration of nanoparticles that induces predominant nanoparticle aggregation under specific buffer conditions and is determined using dual-wavelength photodiode array detection. Once the CNC has been exceeded, reproducible separations are no longer observed. Second, nanoparticle-analyte interactions are dictated by electrostatic interactions which depend on the pK(a) of the analyte and surface charge of the nanoparticle. Finally, nanoparticle-capillary interactions occur in a surface-chemistry-dependent manner. Run buffer viscosity is influenced by the formation of a nanoparticle steady-state pseudostationary phase along the capillary wall. Despite differences in buffer viscosity leading to changes in neurotransmitter mobilities, no significant changes in electroosmotic flow were observed. As a result of these three nanoparticle-specific interactions, Au@NH(2) nanoparticles increase the mobility of the neurotransmitters while a smaller opposite effect is observed for Au@COOH nanoparticles. Understanding nanoparticle behavior in the presence of an electric field will have significant impacts in separation science where nanoparticles can serve to improve either the mobility or detection sensitivity of target molecules.

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The Mechanism of Cleavage of RNA Phosphodiesters by a Gold Nanoparticle Nanozyme.

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