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Tomczyk MD, Kuźnik N, Walczak K. Cyclen-based artificial nucleases: Three decades of development (1989–2022). Part a – Hydrolysis of phosphate esters. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Lisi D, Vezzoni CA, Casnati A, Sansone F, Salvio R. Intra- and Intermolecular Cooperativity in the Catalytic Activity of Phosphodiester Cleavage by Self-Assembled Systems Based on Guanidinylated Calix[4]arenes. Chemistry 2023; 29:e202203213. [PMID: 36382737 DOI: 10.1002/chem.202203213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022]
Abstract
The calix[4]arene scaffold, blocked in the cone conformation through alkylation with long alkyl chains, and decorated at the upper rim with four guanidine or arginine units, effectively catalyzes the cleavage of the phosphodiester bond of DNA and RNA model compounds in water. An exhaustive kinetic investigation unequivocally points to the existence of spontaneous aggregation phenomena, driven by hydrophobic effect, occurring at different critical concentrations that depend on the identity of the compound. A pronounced superiority of the assembled structures compared with the monomers in solution was observed. Moreover, the catalytically active units, clustered on the macrocyclic tetrafunctional scaffold, were proved to efficiently cooperate in the catalytic mechanism and result in improved reaction rates compared to those of the monofunctional model compounds. The kinetic analysis is also integrated and corroborated with further experiments based on fluorescence spectroscopy and light scattering. The advantage of the supramolecular assemblies based on tetrafunctional calixarenes leads to believe that the active units can cooperate not only intramolecularly but also intermolecularly. The molecules in the aggregates can probably mold, flex and rearrange but, at the same time, keep an ordered structure that favors phosphodiester bond cleavage. This dynamic preorganization can allow the catalytic units to reach a better fitting with the substrates and perform a superior catalytic activity.
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Affiliation(s)
- Daniele Lisi
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Roma, Italy
| | - Carlo Alberto Vezzoni
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Francesco Sansone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Roma, Italy.,ISB - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185, Roma, Italy
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Czescik J, Mancin F, Strömberg R, Scrimin P. The Mechanism of Cleavage of RNA Phosphodiesters by a Gold Nanoparticle Nanozyme. Chemistry 2021; 27:8143-8148. [PMID: 33780067 PMCID: PMC8251847 DOI: 10.1002/chem.202100299] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 01/08/2023]
Abstract
The cleavage of uridine 3'-phosphodiesters bearing alcohols with pKa 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.
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Affiliation(s)
- Joanna Czescik
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
- Current address: School of Life and Health SciencesAston UniversityB4 7ETBirminghamUK
| | - Fabrizio Mancin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
| | | | - Paolo Scrimin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
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Zubenko AD, Fedorova OA. Aromatic and heteroaromatic azacrown compounds: advantages and disadvantages of rigid macrocyclic ligands. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4913] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Current approaches to the synthesis of aromatic and heteroaromatic azamacrocycles and their derivatives are summarized and systematized. The relationship between the structure of azacrown compounds and their complexation behaviour towards metal cations is analyzed. The diversity of practical applications of azamacrocyclic derivatives in medicine, biology and analytical and organic chemistry, as well as for the design of molecular devices is demonstrated.
The bibliography includes 307 references.
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Guo X, Li M, Zhao R, Yang Y, Wang R, Wu F, Jia L, Zhang Y, Wang L, Qu Z, Wang F, Zhu Y, Hao R, Zhang X, Song H. Structural and positional impact on DNAzyme-based electrochemical sensors for metal ions. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 21:102035. [DOI: 10.1016/j.nano.2019.102035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/24/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
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Murtola M, Ghidini A, Virta P, Strömberg R. Zinc Ion-Dependent Peptide Nucleic Acid-Based Artificial Enzyme that Cleaves RNA-Bulge Size and Sequence Dependence. Molecules 2017; 22:molecules22111856. [PMID: 29109368 PMCID: PMC6150328 DOI: 10.3390/molecules22111856] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 11/17/2022] Open
Abstract
In this report, we investigate the efficiency and selectivity of a Zn2+-dependent peptide nucleic acid-based artificial ribonuclease (PNAzyme) that cleaves RNA target sequences. The target RNAs are varied to form different sizes (3 and 4 nucleotides, nt) and sequences in the bulge formed upon binding to the PNAzyme. PNAzyme-promoted cleavage of the target RNAs was observed and variation of the substrate showed a clear dependence on the sequence and size of the bulge. For targets that form 4-nt bulges, we identified systems with an improved efficacy (an estimated half-life of ca 7–8 h as compared to 11–12 h for sequences studied earlier) as well as systems with an improved site selectivity (up to over 70% cleavage at a single site as compared to 50–60% with previous targets sequences). For targets forming 3-nt bulges, the enhancement compared to previous systems was even more pronounced. Compared to a starting point of targets forming 3-nt AAA bulges (half-lives of ca 21–24 h), we could identify target sequences that were cleaved with half-lives three times lower (ca 7–8 h), i.e., at rates similar to those found for the fastest 4-nt bulge system. In addition, with the 3-nt bulge RNA target site selectivity was improved even further to reach well over 80% cleavage at a specific site.
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Affiliation(s)
- Merita Murtola
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
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