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Yang Z, Hu L, Ning K, Wu Y, Liang J. A fluorescence sensor for thiram detection based on DNA-templated silver nanoclusters without metal ion-mediator. Food Chem 2023; 413:135428. [PMID: 36758384 DOI: 10.1016/j.foodchem.2023.135428] [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: 10/14/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
In this work, we firstly found a strong competitive interaction between thiram and silver atoms of DNA-templated silver nanoclusters (DNA-AgNCs), leading to fluorescence quenching of DNA-AgNCs without additional metal ion-mediator. Furthermore, this thiram-induced fluorescence quenching phenomenon was used to develop a sensor for thiram detection. This fluorescence sensor exhibited good linearity with thiram concentration from 0.20 to 2.0 μM and 0.012-0.20 μM under optimized conditions, with a low detection limit of 0.2 μM and 0.01 μM, respectively. Moreover, this sensor showed superior selectivity towards thiram, and its practicability was verified in apples and soil. This study provides a convenient and rapid "mix and detect" approach for thiram detection within 10 min, suggesting its potential for rapid on-site evaluation of thiram in real samples.
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Affiliation(s)
- Ziyan Yang
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Lingling Hu
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Keke Ning
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yuan Wu
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Jiangong Liang
- College of Science, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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2
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Guan M, Guo Y, Yan X, Si X, Peng X, Lei Y, Shen X, Luo L, He H. Silver ions involved fluorescence "on-off" responses of gold nanoclusters system for determination of carbendazim residues in fruit samples. Food Chem 2022; 386:132836. [PMID: 35381539 DOI: 10.1016/j.foodchem.2022.132836] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/08/2022] [Accepted: 03/26/2022] [Indexed: 11/27/2022]
Abstract
Herein, a fluorescence "on-off" system was developed for monitoring carbendazim (CBZ) residues in fruit samples, based on glutathione-gold nanoclusters (GSH-Au NCs) and silver ions (Ag+). First, the fluorescence intensity of GSH-Au NCs was greatly enhanced (turn on) with aggregation-induced emission enhancement (AIEE) effect in the presence of Ag+, then fluorescence quenching occurred (turn off) with adding CBZ by the chelation between CBZ and Ag+. The quenching degree was well linearly dependent on CBZ concentration covering from 0.5 to 20 μM. Moreover, the GSH-Au NCs-Ag+ system exhibited superior selectivity towards CBZ and was sensitive for the determination of CBZ in apple and orange juices with a low detection limit of 0.12 μM. The recoveries of CBZ spiked in fruit samples ranged from 81.0 % to 111.4% with the relative standard deviations less than 6.6%, demonstrating its great potential for monitoring CBZ residues in fruit samples.
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Affiliation(s)
- Mengting Guan
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yue Guo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Xiaoxia Yan
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Xiaojing Si
- Department of Food Science, Shanghai Business School, Shanghai 200235, PR China
| | - Xitian Peng
- Institute of Agricultural Quality Standards and Testing Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, PR China
| | - Yunyi Lei
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Xia Shen
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Liqiang Luo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Haibo He
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China.
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3
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Escher D, Müller J. Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson-Crick Edge. Chemistry 2020; 26:16043-16048. [PMID: 32627879 PMCID: PMC7756626 DOI: 10.1002/chem.202002803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 12/18/2022]
Abstract
DNA duplexes comprising 6‐(1H‐pyrazol‐1‐yl)‐9H‐purine (6PP), 1‐deaza‐6PP (1D6PP), 7‐deaza‐6PP (7D6PP) and 1,7‐dideaza‐6PP (1,7D6PP) 2′‐deoxyribonucleosides, respectively, were investigated towards their ability to form metal‐mediated base pairs in the presence of AgI. In 6PP and 7D6PP, the AgI ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in 1D6PP and 1,7D6PP, so that in 1D6PP an AgI coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the AgI‐binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of AgI, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1‐ or N7‐coordination is preferred in purine‐based metal‐mediated base pairs.
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Affiliation(s)
- Daniela Escher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
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4
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Flamme M, Levi-Acobas F, Hensel S, Naskar S, Röthlisberger P, Sarac I, Gasser G, Müller J, Hollenstein M. Enzymatic Construction of Artificial Base Pairs: The Effect of Metal Shielding. Chembiochem 2020; 21:3398-3409. [PMID: 32673442 DOI: 10.1002/cbic.202000402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Th formation of metal base pairs is a versatile method for the introduction of metal cations into nucleic acids that has been used in numerous applications including the construction of metal nanowires, development of energy, charge-transfer devices and expansion of the genetic alphabet. As an alternative, enzymatic construction of metal base pairs is an alluring strategy that grants access to longer sequences and offers the possibility of using such unnatural base pairs (UBPs) in SELEX experiments for the identification of functional nucleic acids. This method remains rather underexplored, and a better understanding of the key parameters in the design of efficient nucleotides is required. We have investigated the effect of methylation of the imidazole nucleoside (dImnMe TP) on the efficiency of the enzymatic construction of metal base pairs. The presence of methyl substituents on dImTP facilitates the polymerase-driven formation of dIm4Me -AgI -dIm and dIm2Me TP-CrIII -dIm base pairs. Steric factors rather than the basicity of the imidazole nucleobase appear to govern the enzymatic formation of such metal base pairs. We also demonstrate the compatibility of other metal cations rarely considered in the construction of artificial metal bases by enzymatic DNA synthesis under both primer extension reaction and PCR conditions. These findings open up new directions for the design of nucleotide analogues for the development of metal base pairs.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France.,Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l'École de Médecine, 75006, Paris, France.,Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 11, rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Susanne Hensel
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Shuvankar Naskar
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 11, rue Pierre et Marie Curie, 75005, Paris, France
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 30, 48149, Münster, Germany
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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5
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Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
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Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
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6
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Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
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7
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Ni G, Du Y, Tang F, Liu J, Zhao H, Chen Q. Review of α-nucleosides: from discovery, synthesis to properties and potential applications. RSC Adv 2019; 9:14302-14320. [PMID: 35519323 PMCID: PMC9064229 DOI: 10.1039/c9ra01399g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/29/2019] [Indexed: 02/05/2023] Open
Abstract
Nucleic acids play an important role in the genetic process of organisms; nucleosides, the building block of nucleic acids, typically exist in nature in a β configuration. As an anomer of β-nucleoside, α-nucleoside is extremely rare in nature. Because of their unique and interesting properties such as high stability, specific parallel double-stranded structure and some other biochemical properties, α-nucleosides have attracted wide attention. Various methods including but not limited to the mercuri procedure, fusion reaction and Vorbrüggen glycosylation have been used to synthesize α-nucleosides and their derivatives. However, to the best of our knowledge, there is no review that has summarized these works. Therefore, we systematically review the discovery, synthesis, properties, and potential applications of α-nucleosides in this article and look to provide a reference for subsequent studies in the coming years.
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Affiliation(s)
- Guangcheng Ni
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Yuqi Du
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Fan Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Jiang Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
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8
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Platinum(II) and palladium(II) complexes of tridentate hydrazone-based ligands as selective guanine quadruplex binders. J Inorg Biochem 2017; 175:58-66. [DOI: 10.1016/j.jinorgbio.2017.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/24/2017] [Accepted: 07/02/2017] [Indexed: 12/19/2022]
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9
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Schweizer K, Léon JC, Ravoo BJ, Müller J. Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes. J Inorg Biochem 2016; 160:256-63. [DOI: 10.1016/j.jinorgbio.2016.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/08/2016] [Accepted: 03/12/2016] [Indexed: 12/26/2022]
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10
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Asiani KR, Williams H, Bird L, Jenner M, Searle MS, Hobman JL, Scott DJ, Soultanas P. SilE is an intrinsically disordered periplasmic "molecular sponge" involved in bacterial silver resistance. Mol Microbiol 2016; 101:731-42. [PMID: 27085056 PMCID: PMC5008109 DOI: 10.1111/mmi.13399] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2016] [Indexed: 12/28/2022]
Abstract
Ag(+) resistance was initially found on the Salmonella enetrica serovar Typhimurium multi-resistance plasmid pMG101 from burns patients in 1975. The putative model of Ag(+) resistance, encoded by the sil operon from pMG101, involves export of Ag(+) via an ATPase (SilP), an effluxer complex (SilCFBA) and a periplasmic chaperon of Ag(+) (SilE). SilE is predicted to be intrinsically disordered. We tested this hypothesis using structural and biophysical studies and show that SilE is an intrinsically disordered protein in its free apo-form but folds to a compact structure upon optimal binding to six Ag(+) ions in its holo-form. Sequence analyses and site-directed mutagenesis established the importance of histidine and methionine containing motifs for Ag(+) -binding, and identified a nucleation core that initiates Ag(+) -mediated folding of SilE. We conclude that SilE is a molecular sponge for absorbing metal ions.
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Affiliation(s)
- Karishma R Asiani
- School of Biosciences, University of Nottingham, Sutton, Bonington, LE12 5RD, United Kingdom
| | - Huw Williams
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Louise Bird
- Oxford Protein Production Factory, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton, Bonington, LE12 5RD, United Kingdom
| | - David J Scott
- School of Biosciences, University of Nottingham, Sutton, Bonington, LE12 5RD, United Kingdom.,ISIS Neutron and Muon Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom
| | - Panos Soultanas
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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11
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Bag SS, Talukdar S, Anjali S. Regioselective and stereoselective route to N2-β-tetrazolyl unnatural nucleosides via SN2 reaction at the anomeric center of Hoffer’s chlorosugar. Bioorg Med Chem Lett 2016; 26:2044-50. [DOI: 10.1016/j.bmcl.2016.02.078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/17/2016] [Accepted: 02/26/2016] [Indexed: 10/22/2022]
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12
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Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs. Bioinorg Chem Appl 2016; 2016:7485125. [PMID: 27034627 PMCID: PMC4791510 DOI: 10.1155/2016/7485125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/22/2015] [Accepted: 12/27/2015] [Indexed: 11/18/2022] Open
Abstract
A series of DNA double helices containing different numbers of silver(I)-mediated base pairs involving the artificial nucleobases imidazole or 2-methylimidazole has been applied for the generation of DNA-templated silver nanoclusters. The original Ag(I)-containing nucleic acids as well as the resulting nanoclusters and nanoparticles have been characterized by means of UV/Vis spectroscopy, circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM). The results show for the first time that metal-mediated base pairs can be used for the templated growth of metal nanoclusters.
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13
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Withers JM, Telfer SG, Filichev VV. Towards metal-mediated g-quartet analogues: 1,2,4-triazole nucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:277-88. [PMID: 25774720 DOI: 10.1080/15257770.2014.990156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We proposed that metal-coordinating nucleotides could be used to control the assembly of G-quadruplexes through the formation of an artificial metal-centered quartet. Several guanine-rich DNA sequences containing 1,2,4-triazole-functionalized nucleotides were investigated. These oligonucleotides were designed to form quartets mediated by metal-triazole bonding both on the surface of and within the G-quadruplex core. In contrast to duplex studies in which 1,2,4-triazole nucleosides serve as a mimic of Watson-Crick base-pairs, our results show that these nucleosides are not suitable components of an artificial metal-centered quartet.
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Affiliation(s)
- Jamie M Withers
- a Institute of Fundamental Sciences , Massey University , Palmerston North , New Zealand
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14
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Litau S, Müller J. A tridentate “click” nucleoside for metal-mediated base pairing. J Inorg Biochem 2015; 148:116-20. [DOI: 10.1016/j.jinorgbio.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 12/15/2022]
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15
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4-(2′-Pyridyl)imidazole as an artificial nucleobase in highly stabilizing Ag(I)-mediated base pairs. J Biol Inorg Chem 2015; 20:895-903. [DOI: 10.1007/s00775-015-1274-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/28/2015] [Indexed: 11/26/2022]
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16
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Tanaka Y, Kondo J, Sychrovský V, Šebera J, Dairaku T, Saneyoshi H, Urata H, Torigoe H, Ono A. Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs. Chem Commun (Camb) 2015; 51:17343-60. [DOI: 10.1039/c5cc02693h] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this feature article, recent progress and future perspectives of metal-mediated base-pairs such as T–Hg(ii)–T and C–Ag(i)–C are presented.
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Affiliation(s)
- Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences
- Tokushima Bunri University
- Tokushima
- Japan
- Graduate School of Pharmaceutical Sciences
| | - Jiro Kondo
- Department of Materials and Life Sciences
- Faculty of Science and Technology
- Sophia University
- Chiyoda-ku
- Japan
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Institute of Physics
| | - Takenori Dairaku
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai
- Japan
| | - Hisao Saneyoshi
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
| | - Hidehito Urata
- Osaka University of Pharmaceutical Sciences
- Takatsuki
- Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry
- Faculty of Science
- Tokyo University of Science
- Shinjuku-ku
- Japan
| | - Akira Ono
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
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17
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Mei H, Ingale SA, Seela F. Imidazolo-dC metal-mediated base pairs: purine nucleosides capture two Ag(+) ions and form a duplex with the stability of a covalent DNA cross-link. Chemistry 2014; 20:16248-57. [PMID: 25336305 DOI: 10.1002/chem.201404422] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Indexed: 12/13/2022]
Abstract
8-Phenylimidazolo-dC ((ph) ImidC, 2) forms metal-mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent "purine" 2'-deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6. Owing to the ease of nucleobase deprotonation, the new Ag(+) -mediated base pair containing a "purine" skeleton is much stronger than that derived from the pyrrolo- [3,4-d]pyrimidine system ((ph) PyrdC, 1). The silver-mediated (ph) ImidC-(ph) ImidC base pair fits well into the DNA double helix and has the stability of a covalent cross-link. The formation of such artificial metal base pairs might not be limited to DNA but may be applicable to other nucleic acids such as RNA, PNA and GNA as well as other biopolymers.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857; Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
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18
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Hensel S, Megger N, Schweizer K, Müller J. Second generation silver(I)-mediated imidazole base pairs. Beilstein J Org Chem 2014; 10:2139-44. [PMID: 25246972 PMCID: PMC4168905 DOI: 10.3762/bjoc.10.221] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/27/2014] [Indexed: 12/15/2022] Open
Abstract
The imidazole-Ag(I)-imidazole base pair is one of the best-investigated artificial metal-mediated base pairs. We show here that its stability can be further improved by formally replacing the imidazole moiety by a 2-methylimidazole or 4-methylimidazole moiety. A comparison of the thermal stability of several double helices shows that the addition of one equivalent of Ag(I) leads to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair.
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Affiliation(s)
- Susanne Hensel
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Nicole Megger
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Kristina Schweizer
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
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Richters T, Krug O, Kösters J, Hepp A, Müller J. A family of "click" nucleosides for metal-mediated base pairing: unravelling the principles of highly stabilizing metal-mediated base pairs. Chemistry 2014; 20:7811-8. [PMID: 24838942 DOI: 10.1002/chem.201402221] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 12/12/2022]
Abstract
A family of artificial nucleosides has been developed by applying the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition. Starting from 2-deoxy-β-D-glycosyl azide as a common precursor, three bidentate nucleosides have been synthesized. The 1,2,3-triazole involved in all three nucleobases is complemented by 1,2,4-triazole (TriTri), pyrazole (TriPyr), or pyridine (TriPy). Molecular structures of two metal complexes indicate that metal-mediated base pairs of TriPyr may not be fully planar. An investigation of DNA oligonucleotide duplexes comprising the new "click" nucleosides showed that they can bind Ag(I) to form metal-mediated base pairs. In particular the mispair formed from TriPy and the previously established imidazole nucleoside is significantly stabilized in the presence of Ag(I). A comparison of different oligonucleotide sequences allowed the determination of general factors involved in the stabilization of nucleic acids duplexes with metal-mediated base pairs.
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Affiliation(s)
- Tim Richters
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149 Münster (Germany), Fax: (+49) 251-8336007
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Richters T, Müller J. A Metal-Mediated Base Pair with a [2+1] Coordination Environment. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201301491] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Kumbhar S, Johannsen S, Sigel RK, Waller MP, Müller J. A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs. J Inorg Biochem 2013; 127:203-10. [DOI: 10.1016/j.jinorgbio.2013.03.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/18/2013] [Accepted: 03/18/2013] [Indexed: 01/04/2023]
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Radunsky C, Megger DA, Hepp A, Kösters J, Freisinger E, Müller J. A Family of Hydrazone-Based Nucleosides for Use in Metal-Mediated Base Pairs. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Megger N, Johannsen S, Müller J, Sigel RKO. Synthesis and acid-base properties of an imidazole-containing nucleotide analog, 1-(2'-deoxy-β-D-ribofuranosyl)imidazole 5'-monophosphate (dImMP(2-)). Chem Biodivers 2013; 9:2050-63. [PMID: 22976990 DOI: 10.1002/cbdv.201100437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Deletion of the substituted pyrimidine ring in purine-2'-deoxynucleoside 5'-monophosphates leads to the artificial nucleotide analog dImMP(2-). This analog can be incorporated into DNA to yield, upon addition of Ag(+) ions, a molecular wire. Here, we measured the acidity constants of H(2)(dImMP)(±) having one proton at N(3) and one at the PO(3)(2-) group by potentiometric pH titrations in aqueous solution. The micro acidity constants show that N(3) is somewhat more basic than PO(3)(2-) and, consequently, the (H·dImMP)(-) tautomer with the proton at N(3) dominates to ca. 75%. The calculated micro acidity constants are confirmed by (31)P- and (1)H-NMR chemical shifts. The assembled data allow many quantitative comparisons, e.g., the N(3)-protonated and thus positively charged imidazole residue facilitates deprotonation of the P(O)(2)(OH)(-) group by 0.3 pK units. Information on the intrinsic site basicities also allows predictions about metal-ion binding; e.g., Mg(2+) and Mn(2+) will primarily coordinate to the phosphate group, whereas Ni(2+) and Cu(2+) will preferably bind to N(3). Macrochelate formation for these metal ions is also predicted. The micro acidity constant for N(3)H(+) deprotonation in the (H·dImMP·H)(±) species (pk(a) 6.46) and the M(n+)-binding properties are of relevance for understanding the behavior of dImMP units present in DNA hairpins and metalated duplexes.
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Affiliation(s)
- Nicole Megger
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstrasse 28/30, D-48149 Münster
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Megger DA, Megger N, Müller J. Metal-mediated base pairs in nucleic acids with purine- and pyrimidine-derived nucleosides. Met Ions Life Sci 2012; 10:295-317. [PMID: 22210344 DOI: 10.1007/978-94-007-2172-2_11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Metal-mediated base pairs are transition metal complexes formed from complementary nucleosides within nucleic acid double helices. Instead of relying on hydrogen bonds, they are stabilized by coordinative bonds. The nucleosides acting as ligands do not necessarily have to be artificial. In fact, several examples are known of naturally occurring nucleobases (e.g., thymine, cytosine) capable of forming stable metal-mediated base pairs that are highly selective towards certain metal ions. This chapter provides a comprehensive overview of metal-mediated base pairs formed from natural nucleosides or from closely related artificial nucleosides that are pyrimidine or purine derivatives. It addresses the different strategies that lead to the development of these base pairs. The article focuses on structural models for metal-mediated base pairs, their experimental characterization within a nucleic acid, and on their possible applications.
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Petrovec K, Ravoo BJ, Müller J. Cooperative formation of silver(i)-mediated base pairs. Chem Commun (Camb) 2012; 48:11844-6. [DOI: 10.1039/c2cc36169h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Impact of histidine residue on chelating ability of 2'-deoxyriboadenosine. J Inorg Biochem 2011; 105:1212-9. [PMID: 21723807 DOI: 10.1016/j.jinorgbio.2011.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 05/20/2011] [Accepted: 05/20/2011] [Indexed: 11/22/2022]
Abstract
Copper(II) complexes with a new chelator-type nucleoside-histidine modified 2'-deoxyriboadenosine (N-[(9-β-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine) were studied by potentiometric and spectroscopic (UV-visible, CD, EPR) techniques, in conjunction with computer modeling optimization. The ligand can act as bidentate or tridentate depending on pH range. In acidic pH a very stable dimeric complex Cu(2)L(2) predominates with coordination spheres of both metal ions composed of oxygen atoms from carboxylic groups, one oxygen atom from ureido group and two nitrogen atoms derived from purine base and histidine ring. Above pH 5, deprotonation of carbamoyl nitrogens leads to the formation of CuL(2), Cu(2)L(2)H(-1) and Cu(2)L(2)H(-2) species. The CuL(2)H(-1) and CuL(2)H(-2) complexes with three or four nitrogens in Cu(II) coordination sphere have been detected in alkaline medium. Our findings suggest that N-[(9-beta-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine chelates copper(II) ions very efficiently. The resulting complex might be used as an alternative base-pairing mode in which hydrogen-bonded base pairs present in natural DNA are replaced by metal-mediated ones.
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Megger DA, Fonseca Guerra C, Hoffmann J, Brutschy B, Bickelhaupt FM, Müller J. Contiguous Metal‐Mediated Base Pairs Comprising Two Ag
I
Ions. Chemistry 2011; 17:6533-44. [DOI: 10.1002/chem.201002944] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/12/2011] [Indexed: 12/28/2022]
Affiliation(s)
- Dominik A. Megger
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jan Hoffmann
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - Bernhard Brutschy
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jens Müller
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
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Huang R, Zhou X, Peng Y, Yang X, Xu T, Liu Y. Nucleosides from the marine sponge Callyspongia SP. Chem Nat Compd 2011. [DOI: 10.1007/s10600-011-9815-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Megger N, Welte L, Zamora F, Müller J. Metal-mediated aggregation of DNA comprising 2,2′-bipyridine nucleoside, an asymmetrically substituted chiral bidentate ligand. Dalton Trans 2011; 40:1802-7. [DOI: 10.1039/c0dt01569e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Seubert K, Guerra CF, Bickelhaupt FM, Müller J. Chimeric GNA/DNA metal-mediated base pairs. Chem Commun (Camb) 2011; 47:11041-3. [DOI: 10.1039/c1cc13774c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chen X, Zu Y, Xie H, Kemas AM, Gao Z. Coordination of mercury(ii) to gold nanoparticle associated nitrotriazole towards sensitive colorimetric detection of mercuric ion with a tunable dynamic range. Analyst 2011; 136:1690-6. [DOI: 10.1039/c0an00903b] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Megger DA, Muller J. Silver(I)-mediated cytosine self-pairing is preferred over hoogsteen-type base pairs with the artificial nucleobase 1,3-dideaza-6-nitropurine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 29:27-38. [PMID: 20391190 DOI: 10.1080/15257770903451579] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A 2'-deoxyribonucleoside containing 1,3-dideaza-6-nitropurine was synthesized and incorporated into oligonucleotides. The acid-base properties of this nucleoside and the corresponding N9-methylated derivative were investigated by pD-dependent (1)H NMR spectroscopy. A possible formation of Hoogsteen-type base pairs with cytosine was studied by ultraviolet (UV) and circular dichroism (CD) spectroscopy in the presence and absence of Ag(I) and under neutral and acidic conditions, respectively. In each case, no indication for the formation of Hoogsteen-type base pairs was obtained, which is attributed to the higher affinity of cytosine to form self-complementary hemi-protonated base pairs under acidic conditions and metal-mediated homo base pairs in presence of Ag(I), respectively.
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Affiliation(s)
- Dominik A Megger
- Westfalische Wilhelms-Universitat Munster, Institut fur Anorganische und Analytische Chemie, Munster, Germany
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Megger DA, Kösters J, Hepp A, Müller J. Silver(I) and Mercury(II) Complexes with 1-Methyl-1,2,4-triazole as Models for Metal-Mediated Base Pairs - Formation of Discrete Complexes in Solution vs. One- and Two-Dimensional Coordination Polymers in the Solid State. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.201000509] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Solution structure of a DNA double helix with consecutive metal-mediated base pairs. Nat Chem 2010; 2:229-34. [PMID: 21124482 DOI: 10.1038/nchem.512] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 12/03/2009] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of Ag(i) ions, a duplex comprising three imidazole-Ag(+)-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from ¹J(¹⁵N,¹⁰⁷/¹⁰⁹Ag) couplings upon incorporation of ¹⁵N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs.
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Takezawa Y, Maeda W, Tanaka K, Shionoya M. Discrete self-assembly of iron(III) ions inside triple-stranded artificial DNA. Angew Chem Int Ed Engl 2009; 48:1081-4. [PMID: 19115350 DOI: 10.1002/anie.200804654] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Takezawa Y, Maeda W, Tanaka K, Shionoya M. Discrete Self-Assembly of Iron(III) Ions inside Triple-Stranded Artificial DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804654] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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41
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Schlegel MK, Zhang L, Pagano N, Meggers E. Metal-mediated base pairing within the simplified nucleic acid GNA. Org Biomol Chem 2008; 7:476-82. [PMID: 19156312 DOI: 10.1039/b816142a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydroxypyridone and pyridopurine homo- and hetero-base pairs have been investigated in the context of duplex GNA (glycol nucleic acid). Phosphoramidites for automated GNA solid phase synthesis were synthesized economically in a few steps starting from commercially available enantiopure glycidol. Similar to their behavior in DNA, the hydroxypyridone and pyridopurine homo-base pairs display a metal-dependent base pairing, with the hydroxypyridone base pair exhibiting a preference for copper(II) ions and the pyridopurine a preference for nickel(II) ions. However, these metallo-base pairs show modulated properties in GNA with respect to metal-dependent pairing stabilities and metal selectivities. Most interestingly, the hydroxypyridone homo-base pair and hydroxypyridone-pyridopurine hetero-base pair are particularly well accommodated in the GNA duplex and form copper(II)-dependent base pairs that are more stable compared to a Watson-Crick A:T base pair at the same position by nearly 20 degrees C and 24 degrees C, respectively. The structure of the copper(II)-hydroxypyridone homo-base pair is discussed based on a recent metallo-GNA duplex crystal structure.
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Affiliation(s)
- Mark K Schlegel
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany
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Affiliation(s)
- Jens Müller
- Faculty of Chemistry, Dortmund University of Technology, Otto‐Hahn‐Str. 6, 44227 Dortmund, Germany, Fax: +49 231 755 3797
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Takezawa Y, Tanaka K, Yori M, Tashiro S, Shiro M, Shionoya M. Soft metal-mediated base pairing with novel synthetic nucleosides possessing an O,S-donor ligand. J Org Chem 2008; 73:6092-8. [PMID: 18630968 DOI: 10.1021/jo800587d] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal-mediated base pairing with artificial ligand-bearing nucleosides allows site-selective metal incorporation inside DNA duplexes. In particular, this strategy has provided a general way of discrete, heterogeneous metal arrays in a programmable manner. To increase the kind of metallo-building blocks, we have newly synthesized two artificial nucleosides which have an O, S-donor ligand as the nucleobase moiety, mercaptopyridone ( M) and hydroxypyridinethione ( S). These nucleosides were found to efficiently form metal-mediated base pairs with soft transition metal ions such as Pd (2+) and Pt (2+).
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Saneyoshi H, Tamaki K, Ohkubo A, Seio K, Sekine M. Synthesis and hybridization properties of 2′-O-(tetrazol-5-yl)ethyl-modified oligonucleotides. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.02.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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He W, Franzini RM, Achim C. Metal-Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding. PROGRESS IN INORGANIC CHEMISTRY 2008. [DOI: 10.1002/9780470144428.ch8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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46
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Müller J, Polonius FA, Freisinger E, Gil Bardají E. X-ray crystallographic study of several 2'-deoxy-beta-D-ribonucleosides with 1-deazapurine-derived aglycones. Carbohydr Res 2008; 343:397-403. [PMID: 18045576 DOI: 10.1016/j.carres.2007.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 10/19/2007] [Accepted: 11/05/2007] [Indexed: 11/25/2022]
Abstract
The 2'-deoxy-beta-D-ribonucleosides of 1,3-deazapurine (benzimidazole (1)), 1-deazapurine (both 1H-imidazo[4,5-b]pyridine (2) and 3H-imidazo[4,5-b]pyridine (3)), and 6-benzoylamino-1-deazapurine (7-benzoylamino-3H-imidazo[4,5-b]pyridine (4)) have been prepared and structurally characterized by X-ray crystallography. Especially compounds 1-3 can serve as artificial nucleosides that may substitute 2'-deoxy adenosine because they lack the exocyclic amino group and one or two of the endocyclic nitrogen atoms and hence have a much smaller potential to engage in hydrogen bonds. In the latter respect, they are candidates for nucleosides in metal-ion mediated base pairs. The unit cell of compound 3 contains two crystallographically independent molecules. Compound 4 was crystallized from methanol and water, respectively, giving rise to two different solvates. Despite the closely related aglycones, the sugar conformations in 1-4 are found to be highly variable (1: (2)T(1); 2: (3)T(2); 3: (3)E and E(4); 4: (2)E and (2)T(3)). The structures reported here confirm that there is no simple correlation between the sugar conformation and the character of the nucleoside, and they will hopefully contribute to a better understanding of the complex interplay of different effects that are in control of the conformational equilibrium.
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Affiliation(s)
- Jens Müller
- University of Dortmund, Department of Chemistry, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.
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Johannsen S, Paulus S, Düpre N, Müller J, Sigel RKO. Using in vitro transcription to construct scaffolds for one-dimensional arrays of mercuric ions. J Inorg Biochem 2008; 102:1141-51. [PMID: 18289686 DOI: 10.1016/j.jinorgbio.2007.12.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 12/22/2007] [Accepted: 12/23/2007] [Indexed: 10/22/2022]
Abstract
In vitro transcription by T7 RNA polymerase can be used to construct scaffolds for the one-dimensional arrangement of mercury(II) ions. In these constructs, the metal ions are located inside of RNA double helices. By replacing the amide protons of two oppositely located uracil residues of complementary strands, mercury(II) becomes coordinated in a linear fashion to form metal-ion mediated base pairs, analogous to the well-known thymine-Hg-thymine base pair in DNA. This is shown here by a combination of various experimental techniques, including NMR spectroscopy, dynamic light scattering, as well as UV and CD spectroscopy. A total of five different double helices, including both palindromic and non-palindromic RNA sequences and between two and twenty consecutive uracil residues, have been synthesized and shown to be able to incorporate mercury(II). The synthesis of r(GGAGU 20CUCC) demonstrates that T7 polymerase is capable of handling long continuous stretches of identical nucleotides, albeit at the cost of an increasing number of abortion products and longer oligonucleotide strands that need to be separated by polyacrylamide gel electrophoresis. This work introduces RNA into the group of nucleic acids that can form metal ion mediated base pairs. The use of such metal-modified nucleic acids has been envisaged in various fields of research, including the generation of molecular wires.
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Affiliation(s)
- Silke Johannsen
- Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Kirin SI, Yennawar HP, Williams ME. Synthesis and Characterization of CuII Complexes with Amino Acid Substituted Di(2-pyridyl)amine Ligands. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700273] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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49
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Polonius FA, Müller J. Ein durch Wasserstoffbrücken und Metallionenbindung vermitteltes, künstliches Basenpaar. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700315] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Polonius FA, Müller J. An Artificial Base Pair, Mediated by Hydrogen Bonding and Metal-Ion Binding. Angew Chem Int Ed Engl 2007; 46:5602-4. [PMID: 17585398 DOI: 10.1002/anie.200700315] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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