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Takezawa Y, Shionoya M. Enzymatic synthesis of ligand-bearing oligonucleotides for the development of metal-responsive DNA materials. Org Biomol Chem 2024; 22:7259-7270. [PMID: 38967487 DOI: 10.1039/d4ob00947a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Metal-mediated artificial base pairs are some of the most promising building blocks for constructing DNA-based supramolecules and functional materials. These base pairs are formed by coordination bonds between ligand-type nucleobases and a bridging metal ion and have been exploited to develop metal-responsive DNA materials and DNA-templated metal arrays. In this review, we provide an overview of methods for the enzymatic synthesis of DNA strands containing ligand-type artificial nucleotides that form metal-mediated base pairs. Conventionally, ligand-bearing DNA oligomers have been synthesized via solid-phase synthesis using a DNA synthesizer. In recent years, there has been growing interest in enzymatic methods as an alternative approach to synthesize ligand-bearing DNA oligomers, because enzymatic reactions proceed under mild conditions and do not require protecting groups. DNA polymerases are used to incorporate ligand-bearing unnatural nucleotides into DNA, and DNA ligases are used to connect artificial DNA oligomers to natural DNA fragments. Template-independent polymerases are also utilized to post-synthetically append ligand-bearing nucleotides to DNA oligomers. In addition, enzymatic replication of DNA duplexes containing metal-mediated base pairs has been intensively studied. Enzymatic methods facilitate the synthesis of DNA strands containing ligand-bearing nucleotides at both internal and terminal positions. Enzymatically synthesized ligand-bearing DNAs have been applied to metal-dependent self-assembly of DNA structures and the allosteric control of DNAzyme activity through metal-mediated base pairing. Therefore, the enzymatic synthesis of ligand-bearing oligonucleotides holds great potential in advancing the development of various metal-responsive DNA materials, such as molecular sensors and machines, providing a versatile tool for DNA supramolecular chemistry and nanotechnology.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan.
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2
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Rajasree SC, Takezawa Y, Shionoya M. Cu II-mediated stabilisation of DNA duplexes bearing consecutive ethenoadenine lesions and its application to a metal-responsive DNAzyme. Chem Commun (Camb) 2023; 59:1006-1009. [PMID: 36524578 DOI: 10.1039/d2cc06179a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal-mediated nucleobase pairing can play a central role in the expression of metal-responsive DNA functions. We report the CuII-mediated stabilisation of DNA duplexes bearing damaged nucleobases, 1,N6-ethenoadenine (εA), as metal-binding sites, which was utilised to construct a metal-responsive DNAzyme. Consecutive incorporation of three or more εA-εA mismatch pairs allowed for CuII-dependent significant duplex stabilisation through metal-mediated εA-CuII-εA base pairing. Subsequently, a split DNAzyme with three εA-CuII-εA base pairs was strategically designed. The activity of the εA-modified DNAzyme was enhanced by 5.3-fold upon addition of CuII ions. This study demonstrates the utility of εA lesions for building metal-responsive DNA architectures.
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Affiliation(s)
- Silpa Chandran Rajasree
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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3
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Molina V, Arroyo JL, MacLeod-Carey D, Muñoz-Castro A, Morales-Verdejo C. Catalytic effect of [trans-Cu(μ-OH)(μ-dmpz)]6 on the thermal decomposition of ammonium perchlorate. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Ma J, Yang J, Yan K, Sun X, Wei W, Tian L, Wen J. Electrochemical‐Induced C(sp
3
)−H Dehydrogenative Trimerization of Pyrazolones to Tripyrazolones. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jing Ma
- Institute of Medicine and Materials Applied Technologies College of Chemistry and Chemical Engineering Qufu Normal University, Qufu Shandong 273165 P. R. China
| | - Jianjing Yang
- Institute of Medicine and Materials Applied Technologies College of Chemistry and Chemical Engineering Qufu Normal University, Qufu Shandong 273165 P. R. China
| | - Kelu Yan
- Institute of Medicine and Materials Applied Technologies College of Chemistry and Chemical Engineering Qufu Normal University, Qufu Shandong 273165 P. R. China
| | - Xue Sun
- Institute of Medicine and Materials Applied Technologies College of Chemistry and Chemical Engineering Qufu Normal University, Qufu Shandong 273165 P. R. China
| | - Wei Wei
- Institute of Medicine and Materials Applied Technologies College of Chemistry and Chemical Engineering Qufu Normal University, Qufu Shandong 273165 P. R. China
| | - Laijin Tian
- Institute of Medicine and Materials Applied Technologies College of Chemistry and Chemical Engineering Qufu Normal University, Qufu Shandong 273165 P. R. China
| | - Jiangwei Wen
- Institute of Medicine and Materials Applied Technologies College of Chemistry and Chemical Engineering Qufu Normal University, Qufu Shandong 273165 P. R. China
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5
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Light-induced formation of silver(I)-mediated base pairs in DNA: Possibilities and limitations. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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6
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Metal-mediated base pairing in DNA involving the artificial nucleobase imidazole-4-carboxylate. J Inorg Biochem 2019; 191:85-93. [DOI: 10.1016/j.jinorgbio.2018.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/18/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
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7
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Sandmann N, Bachmann J, Hepp A, Doltsinis NL, Müller J. Copper(ii)-mediated base pairing involving the artificial nucleobase 3H-imidazo[4,5-f]quinolin-5-ol. Dalton Trans 2019; 48:10505-10515. [DOI: 10.1039/c9dt02043h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A highly stabilizing Cu(ii)-mediated base pair is introduced into DNA using a large artificial nucleobase.
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Affiliation(s)
- Nikolas Sandmann
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jim Bachmann
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Nikos L. Doltsinis
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
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8
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Takezawa Y, Müller J, Shionoya M. Artificial DNA Base Pairing Mediated by Diverse Metal Ions. CHEM LETT 2017. [DOI: 10.1246/cl.160985] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
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9
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Molina V, Rauhalahti M, Hurtado J, Fliegl H, Sundholm D, Muñoz-Castro A. Aromaticity introduced by antiferromagnetic ligand mediated metal–metal interactions. Insights from the induced magnetic response in [Cu6(dmPz)6(OH)6]. Inorg Chem Front 2017. [DOI: 10.1039/c7qi00023e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ligand-mediated antiferromagnetic coupling induces aromatic-ring behavior.
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Affiliation(s)
- V. Molina
- Grupo de Química Inorgánica y Materiales Moleculares
- Universidad Autonoma de Chile
- Santiago
- Chile
- Liceo Politécnico Ciencia y Tecnología
| | - M. Rauhalahti
- Department of Chemistry
- University of Helsinki
- Finland
| | - J. Hurtado
- Departamento de Química
- Universidad de los Andes
- Bogotá
- Colombia
| | - H. Fliegl
- Centre for Theoretical and Computational Chemistry (CTCC)
- Department of Chemistry
- University of Oslo
- Oslo
- Norway
| | - D. Sundholm
- Department of Chemistry
- University of Helsinki
- Finland
| | - A. Muñoz-Castro
- Grupo de Química Inorgánica y Materiales Moleculares
- Universidad Autonoma de Chile
- Santiago
- Chile
- Doctorado en Fisicoquímica Molecular
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11
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Yang D, Sun P, Wei W, Meng L, He L, Fang B, Jiang W, Wang H. Metal-free iodine-catalyzed direct cross-dehydrogenative coupling (CDC) between pyrazoles and thiols. Org Chem Front 2016. [DOI: 10.1039/c6qo00407e] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A green and efficient iodine-catalyzed cross-dehydrogenative C–S coupling method for the synthesis of C-4 sulfenylated pyrazoles has been initially developed under metal-free conditions.
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Affiliation(s)
- Daoshan Yang
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Pengfei Sun
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Wei Wei
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Lingduan Meng
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Lingchao He
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Baokai Fang
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Wei Jiang
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Hua Wang
- The Key Laboratory of Life-Organic Analysis and Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- P. R. China
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12
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Batchu H, Bhattacharyya S, Kant R, Batra S. Palladium-Catalyzed Chelation-Assisted Regioselective Oxidative Dehydrogenative Homocoupling/Ortho-Hydroxylation in N-Phenylpyrazoles. J Org Chem 2015; 80:7360-74. [DOI: 10.1021/acs.joc.5b00733] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | | | - Sanjay Batra
- Academy of Scientific and Innovative Research, New Delhi, 110025, India
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13
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Su M, Tomás-Gamasa M, Carell T. DNA based multi-copper ions assembly using combined pyrazole and salen ligandosides. Chem Sci 2015; 6:632-638. [PMID: 28936312 PMCID: PMC5588782 DOI: 10.1039/c4sc01567c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/05/2014] [Indexed: 01/16/2023] Open
Abstract
The DNA structure is an ideal building block for the construction of functional nano-objects. In this direction, metal coordinating base pairs (ligandosides) are an appealing tool for the future specific functionalization of such nano-objects. We present here a study, in which we combine the metal ion coordinating pyrazole ligandoside with the interstrand crosslinking salen ligandoside system. We show that both ligandosides, when combined, are able to create stable multi-copper ion complexing DNA double helix structures in a cooperative fashion.
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Affiliation(s)
- Meng Su
- Department of Chemistry , Ludwig-Maximilians-University Munich , Butenandtstraße 5-13 , 81377 , Munich , Germany .
| | - María Tomás-Gamasa
- Department of Chemistry , Ludwig-Maximilians-University Munich , Butenandtstraße 5-13 , 81377 , Munich , Germany .
| | - Thomas Carell
- Department of Chemistry , Ludwig-Maximilians-University Munich , Butenandtstraße 5-13 , 81377 , Munich , Germany .
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