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

Overview

Journal Chemistry

Specialty Chemistry

Date 2021 Mar 29

PMID 33780067

Citations 3

Authors

Joanna Czescik

Fabrizio Mancin

Roger Stromberg

Paolo Scrimin

Affiliations

Soon will be listed here.

Abstract

The cleavage of uridine 3'-phosphodiesters bearing alcohols with pK 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.

Citing Articles

Short peptide-based cross-β amyloids exploit dual residues for phosphoesterase like activity.

Mahato C, Menon S, Singh A, Afrose S, Mondal J, Das D Chem Sci. 2022; 13(32):9225-9231.

PMID: 36092997 PMC: 9384705. DOI: 10.1039/d2sc03205h.

Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy.

Anjomshoa M, Amirheidari B Coord Chem Rev. 2022; 458:214417.

PMID: 35153301 PMC: 8816526. DOI: 10.1016/j.ccr.2022.214417.

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

Czescik J, Mancin F, Stromberg R, Scrimin P Chemistry. 2021; 27(31):8143-8148.

PMID: 33780067 PMC: 8251847. DOI: 10.1002/chem.202100299.

References

Iranzo O, Kovalevsky A, Morrow J, Richard J . Physical and kinetic analysis of the cooperative role of metal ions in catalysis of phosphodiester cleavage by a dinuclear Zn(II) complex. J Am Chem Soc. 2003; 125(7):1988-93. DOI: 10.1021/ja027728v. View

Mancin F, Scrimin P, Tecilla P, Tonellato U . Artificial metallonucleases. Chem Commun (Camb). 2005; (20):2540-8. DOI: 10.1039/b418164f. View

Mancin F, Prins L, Pengo P, Pasquato L, Tecilla P, Scrimin P . Hydrolytic Metallo-Nanozymes: From Micelles and Vesicles to Gold Nanoparticles. Molecules. 2016; 21(8). PMC: 6272841. DOI: 10.3390/molecules21081014. View

Wolfenden R . Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes. Annu Rev Biochem. 2011; 80:645-67. DOI: 10.1146/annurev-biochem-060409-093051. View

Yang M, Richard J, Morrow J . Substrate specificity for catalysis of phosphodiester cleavage by a dinuclear Zn(II) complex. Chem Commun (Camb). 2003; (22):2832-3. DOI: 10.1039/b308644e. View

Korhonen H, Mikkola S, Williams N . The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex. Chemistry. 2011; 18(2):659-70. DOI: 10.1002/chem.201100721. View

Guarino G, Rastrelli F, Scrimin P, Mancin F . Lanthanide-based NMR: a tool to investigate component distribution in mixed-monolayer-protected nanoparticles. J Am Chem Soc. 2012; 134(17):7200-3. DOI: 10.1021/ja211030y. View

Mancin F, Scrimin P, Tecilla P . Progress in artificial metallonucleases. Chem Commun (Camb). 2012; 48(45):5545-59. DOI: 10.1039/c2cc30952a. View

Lyu Y, Morillas-Becerril L, Mancin F, Scrimin P . Hydrolytic cleavage of nerve agent simulants by gold nanozymes. J Hazard Mater. 2021; 415:125644. DOI: 10.1016/j.jhazmat.2021.125644. View

10.

Czescik J, Zamolo S, Darbre T, Rigo R, Sissi C, Pecina A . A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex. Angew Chem Int Ed Engl. 2020; 60(3):1423-1432. PMC: 7839518. DOI: 10.1002/anie.202012513. View

11.

Lonnberg H, Stromberg R, Williams A . Compelling evidence for a stepwise mechanism of the alkaline cyclisation of uridine 3'-phosphate esters. Org Biomol Chem. 2004; 2(15):2165-7. DOI: 10.1039/b406926a. View

12.

Diez-Castellnou M, Mancin F, Scrimin P . Efficient phosphodiester cleaving nanozymes resulting from multivalency and local medium polarity control. J Am Chem Soc. 2014; 136(4):1158-61. DOI: 10.1021/ja411969e. View

13.

Wang Q, Lonnberg H . Simultaneous interaction with base and phosphate moieties modulates the phosphodiester cleavage of dinucleoside 3',5'-monophosphates by dinuclear Zn2+ complexes of di(azacrown) ligands. J Am Chem Soc. 2006; 128(33):10716-28. DOI: 10.1021/ja058806s. View

14.

Fasting C, Schalley C, Weber M, Seitz O, Hecht S, Koksch B . Multivalency as a chemical organization and action principle. Angew Chem Int Ed Engl. 2012; 51(42):10472-98. DOI: 10.1002/anie.201201114. View

15.

Wang Q, Leino E, Jancso A, Szilagyi I, Gajda T, Hietamaki E . Zn2+ complexes of di- and tri-nucleating azacrown ligands as base-moiety-selective cleaving agents of RNA 3',5'-phosphodiester bonds: binding to guanine base. Chembiochem. 2008; 9(11):1739-48. DOI: 10.1002/cbic.200800095. View

16.

Korhonen H, Koivusalo T, Toivola S, Mikkola S . There is no universal mechanism for the cleavage of RNA model compounds in the presence of metal ion catalysts. Org Biomol Chem. 2013; 11(48):8324-39. DOI: 10.1039/c3ob41554f. View

17.

Wei H, Wang E . Nanomaterials with enzyme-like characteristics (nanozymes): next-generation artificial enzymes. Chem Soc Rev. 2013; 42(14):6060-93. DOI: 10.1039/c3cs35486e. View

18.

Cacciapaglia R, Di Stefano S, Mandolini L . Effective molarities in supramolecular catalysis of two-substrate reactions. Acc Chem Res. 2004; 37(2):113-22. DOI: 10.1021/ar020076v. View

19.

Manea F, Houillon F, Pasquato L, Scrimin P . Nanozymes: gold-nanoparticle-based transphosphorylation catalysts. Angew Chem Int Ed Engl. 2004; 43(45):6165-9. DOI: 10.1002/anie.200460649. View

20.

Riccardi L, Gabrielli L, Sun X, De Biasi F, Rastrelli F, Mancin F . Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition. Chem. 2017; 3(1):92-109. PMC: 5521955. DOI: 10.1016/j.chempr.2017.05.016. View