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Biniuri Y, Shpilt Z, Albada B, Vázquez-González M, Wolff M, Hazan C, Golub E, Gelman D, Willner I. A Bis-Zn 2+ -Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer: An ATPase-Mimicking Nucleoapzyme. Chembiochem 2019; 21:53-58. [PMID: 30908871 DOI: 10.1002/cbic.201900182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 11/09/2022]
Abstract
Catalytic nucleic acids consisting of a bis-Zn2+ -pyridyl-salen-type ([di-ZnII 3,5 bis(pyridinylimino) benzoic acid]) complex conjugated to the ATP aptamer act as ATPase-mimicking catalysts (nucleoapzymes). Direct linking of the Zn2+ complex to the 3'- or 5'-end of the aptamer (nucleoapzymes I and II) or its conjugation to the 3'- or 5'-end of the aptamer through bis-thymidine spacers (nucleoapzymes III and IV) provided a set of nucleoapzymes exhibiting variable catalytic activities. Whereas the separated bis-Zn2+ -pyridyl-salen-type catalyst and the ATP aptamer do not show any noticeable catalytic activity, the 3'-catalyst-modified nucleoapzyme (nucleoapzyme IV) and, specifically, the nucleoapzyme consisting of the catalyst linked to the 3'-position through the spacer (nucleoapzyme III) reveal enhanced catalytic features in relation to the analogous nucleoapzyme substituted at the 5'-position (kcat =4.37 and 6.88 min-1 , respectively). Evaluation of the binding properties of ATP to the different nucleoapzyme and complementary molecular dynamics simulations suggest that the distance separating the active site from the substrate linked to the aptamer binding site controls the catalytic activities of the different nucleoapzymes.
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Affiliation(s)
- Yonatan Biniuri
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Zohar Shpilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands
| | | | - Mariusz Wolff
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Carina Hazan
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Eyal Golub
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Dimitri Gelman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
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Bencze ES, Zonta C, Mancin F, Prins LJ, Scrimin P. Distance between Metal Centres Affects Catalytic Efficiency of Dinuclear CoIII
Complexes in the Hydrolysis of a Phosphate Diester. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Eva Szusanna Bencze
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Cristiano Zonta
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Leonard J. Prins
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Paolo Scrimin
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
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Jiang B, Cai S, Xie J, Feng FM. Nuclease Activity of Diaza-Crown Ether Complexes of Cerium(III) with Different Functional Groups as Side Arms. PROGRESS IN REACTION KINETICS AND MECHANISM 2018. [DOI: 10.3184/146867818x15161889114448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cerium(III) complexes of two ligands of a diaza-crown ether with different functional groups as side arms were synthesised and characterised. The catalytic ability of the cerium(III) complexes for pUC19 DNA cleavage was investigated and compared using agarose gel electrophoresis. The results indicate that the catalytic activity of the complex CeL2 [L2 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diacetamide] with two carbamoylmethyl groups is significantly higher than the complex CeL1 [L1 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diethanol] with two hydroxyethyl groups under the same conditions. The optimum catalytic concentrations of CeL1 and CeL2 were 7.69 × 10−5 and 3.08 × 10−5 mol L−1 respectively and excessively high concentrations of the complexes can reduce their catalytic efficiency due to the formation of inactive μ-hydroxo dimers. The optimum catalytic acidities of CeL1 and CeL2 were pH 7.0 and 7.5 respectively and excessively high pH of the reaction system can reduce the catalytic efficiency of the complexes due to the formation of cerium(III) hydroxide. DNA cleavage promoted by the two complexes takes place via the same hydrolytic pathway and so the activity difference of the two complexes is attributed to the stability of the complexes, rather than the catalytic mechanism.
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Affiliation(s)
- Bingying Jiang
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
| | - Shulan Cai
- College of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Jiaqing Xie
- College of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Fa-Mei Feng
- College of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
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Chen JLY, Pezzato C, Scrimin P, Prins LJ. Chiral Nanozymes-Gold Nanoparticle-Based Transphosphorylation Catalysts Capable of Enantiomeric Discrimination. Chemistry 2016; 22:7028-32. [PMID: 26919202 DOI: 10.1002/chem.201600853] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/08/2022]
Abstract
Enantioselectivity in RNA cleavage by a synthetic metalloenzyme has been demonstrated for the first time. Thiols containing chiral Zn(II) -binding head groups have been self-assembled on the surface of gold nanoparticles. This results in the spontaneous formation of chiral bimetallic catalytic sites that display different activities (kcat ) towards the enantiomers of an RNA model substrate. Substrate selectivity is observed when the nanozyme is applied to the cleavage of the dinucleotides UpU, GpG, ApA, and CpC, and remarkable differences in reactivity are observed for the cleavage of the enantiomerically pure dinucleotide UpU.
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Affiliation(s)
- Jack L-Y Chen
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Cristian Pezzato
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Paolo Scrimin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy.
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Tirel EY, Williams NH. Enhancing Phosphate Diester Cleavage by a Zinc Complex through Controlling Nucleophile Coordination. Chemistry 2015; 21:7053-6. [PMID: 25787696 DOI: 10.1002/chem.201500619] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 11/11/2022]
Abstract
Metal-ion complexes are the most effective artificial catalysts capable of cleaving phosphate diesters under mild aqueous conditions. A central strategy for making these complexes highly reactive has been to use ligand-based alcohols that are coordinated to the ion, providing an ionised nucleophile under neutral conditions but at the expense of deactivating it. We have created a highly reactive Zn complex that is 350-fold more reactive than an alcohol analogue by preventing the nucleophile binding to the metal ion. This strategy successfully delivers the benefits of efficient nucleophile delivery without strongly deactivating the metal ion Lewis acidity nor the oxyanion nucleophilicity. Varying the leaving group reveals that the transition state of the reaction is much further advanced than the reaction with hydroxide.
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Affiliation(s)
- Emmanuel Y Tirel
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF (UK)
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