1
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Zhang K, Fu B, Zou G, Yang W, Yan S, Tian T, Zhou X. Determination of 5-formyluracil via oxime-based nucleotide-metal coordination. Chembiochem 2022; 23:e202200355. [PMID: 35849116 DOI: 10.1002/cbic.202200355] [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: 06/21/2022] [Revised: 07/18/2022] [Indexed: 11/08/2022]
Abstract
In this article, a small chemical molecule was synthesized, and its ability to regulate activities of DNA polymerase was tested. In addition, we also used isothermal amplification technology to detect the content of 5-formyluracil sites in irradiated genomic DNA, which confirmed its capability for the detection of 5-formyluracil content in general samples. This study presents the first example of the determination of 5fU based on coordination chemistry.
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Affiliation(s)
- Kaiyuan Zhang
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Boshi Fu
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Guangrong Zou
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Wei Yang
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Shen Yan
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Tian Tian
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Xiang Zhou
- Wuhan University, College of Chemistry and Molecular Sciences, Luojia Shan, 430072, Wuhan, CHINA
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2
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Wang J, Wicher B, Méndez-Ardoy A, Li X, Pecastaings G, Buffeteau T, Bassani DM, Maurizot V, Huc I. Loading Linear Arrays of Cu II Inside Aromatic Amide Helices. Angew Chem Int Ed Engl 2021; 60:18461-18466. [PMID: 34014599 PMCID: PMC8456862 DOI: 10.1002/anie.202104734] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/12/2021] [Indexed: 12/25/2022]
Abstract
The very stable helices of 8-amino-2-quinolinecarboxylic acid oligoamides are shown to uptake CuII ions in their cavity through deprotonation of their amide functions with minimal alteration of their shape, unlike most metallo-organic structures which generally differ from their organic precursors. The outcome is the formation of intramolecular linear arrays of a defined number of CuII centers (up to sixteen in this study) at a 3 Å distance, forming a molecular mimic of a metal wire completely surrounded by an organic sheath. The helices pack in the solid state so that the arrays of CuII extend intermolecularly. Conductive-AFM and cyclic voltammetry suggest that electrons are transported throughout the metal-loaded helices in contrast with hole transport observed for analogous foldamers devoid of metal ions.
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Affiliation(s)
- Jinhua Wang
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780, Poznan, Poland
| | - Alejandro Méndez-Ardoy
- ISM (UMR 5255), Univ. Bordeaux, CNRS, 351, Cours de la Libération, 33405, Talence, France
| | - Xuesong Li
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Gilles Pecastaings
- LCPO (UMR 5629), Bordeaux INP, CNRS, 16, Av. Pey-Berland, 33600, Pessac, France
- CRPP (UMR 5031), Univ. Bordeaux, CNRS, 115 Avenue du Dr Albert Schweitzer, 33600, Pessac, France
| | - Thierry Buffeteau
- ISM (UMR 5255), Univ. Bordeaux, CNRS, 351, Cours de la Libération, 33405, Talence, France
| | - Dario M Bassani
- ISM (UMR 5255), Univ. Bordeaux, CNRS, 351, Cours de la Libération, 33405, Talence, France
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Ivan Huc
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600, Pessac, France
- Department of Pharmacy, Ludwig-Maximilians-Universität, Butenandstraße 5-13, 81377, Munich, Germany
- Cluster of Excellence e-conversion, 85748, Garching, Germany
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3
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Wang J, Wicher B, Méndez‐Ardoy A, Li X, Pecastaings G, Buffeteau T, Bassani DM, Maurizot V, Huc I. Loading Linear Arrays of Cu
II
Inside Aromatic Amide Helices. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104734] [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)
- Jinhua Wang
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
| | - Barbara Wicher
- Department of Chemical Technology of Drugs Poznan University of Medical Sciences Grunwaldzka 6 60-780 Poznan Poland
| | | | - Xuesong Li
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
| | - Gilles Pecastaings
- LCPO (UMR 5629) Bordeaux INP CNRS 16, Av. Pey-Berland 33600 Pessac France
- CRPP (UMR 5031) Univ. Bordeaux CNRS 115 Avenue du Dr Albert Schweitzer 33600 Pessac France
| | - Thierry Buffeteau
- ISM (UMR 5255) Univ. Bordeaux CNRS 351, Cours de la Libération 33405 Talence France
| | - Dario M. Bassani
- ISM (UMR 5255) Univ. Bordeaux CNRS 351, Cours de la Libération 33405 Talence France
| | - Victor Maurizot
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
| | - Ivan Huc
- CBMN (UMR 5248) Univ. Bordeaux CNRS Bordeaux INP 2 rue Robert Escarpit 33600 Pessac France
- Department of Pharmacy Ludwig-Maximilians-Universität Butenandstraße 5–13 81377 Munich Germany
- Cluster of Excellence e-conversion 85748 Garching Germany
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4
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Nakagawa O, Aoyama H, Fujii A, Kishimoto Y, Obika S. Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids. Chemistry 2021; 27:3842-3848. [PMID: 33274789 DOI: 10.1002/chem.202004819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of AgI ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of AgI -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing AgI -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of AgI -mediated base pairs in the central region. The bent duplex structure induced by the addition of AgI ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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5
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Naskar S, Müller J. Light-Induced Formation of Thymine-Containing Mercury(II)-Mediated Base Pairs. Chemistry 2019; 25:16214-16218. [PMID: 31682036 PMCID: PMC6972992 DOI: 10.1002/chem.201903789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/14/2019] [Indexed: 12/16/2022]
Abstract
By applying caged thymidine residues, DNA duplexes were created in which HgII‐mediated base pair formation can be triggered by irradiation with light. When a bidentate ligand was used as the complementary nucleobase, an unprecedented stepwise formation of different metal‐mediated base pairs was achieved.
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Affiliation(s)
- Shuvankar Naskar
- 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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6
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Funai T, Aotani M, Kiriu R, Nakamura J, Miyazaki Y, Nakagawa O, Wada S, Torigoe H, Ono A, Urata H. Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases. Chembiochem 2019; 21:517-522. [DOI: 10.1002/cbic.201900450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Megumi Aotani
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Risa Kiriu
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Junko Nakamura
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Yuki Miyazaki
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Osamu Nakagawa
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
- Present address: Graduate School of Pharmaceutical SciencesOsaka University 1–6 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Shun‐ichi Wada
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Hidetaka Torigoe
- Department of Applied ChemistryFaculty of ScienceTokyo University of Science 1-3 Kagurazaka, Shinjuku-ku Tokyo 162-8601 Japan
| | - Akira Ono
- Department of Material and Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Japan
| | - Hidehito Urata
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
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7
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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: 69] [Impact Index Per Article: 13.8] [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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8
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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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9
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Fujii A, Nakagawa O, Kishimoto Y, Okuda T, Nakatsuji Y, Nozaki N, Kasahara Y, Obika S. 1,3,9-Triaza-2-oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self-Base Pairs with Three Ag I Ions in a Duplex. Chemistry 2019; 25:7443-7448. [PMID: 30843298 DOI: 10.1002/chem.201900373] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 12/23/2022]
Abstract
Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self-bases coordinated by three linearly aligned AgI ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9-triaza-2-oxophenoxazine (9-TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self-base pairs of 9-TAP could form highly stable MMBPs with three AgI ions. Nine equivalents of AgI led to the formation of three consecutive 9-TAP self-base pairs with extremely high stability. The complex structures of 9-TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self-9-TAP MMBPs with three AgI ions are expected to be applicable to new DNA nanotechnologies.
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Affiliation(s)
- Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
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10
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Nakagawa O, Fujii A, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. 2'-O,4'-C-Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex. Chembiochem 2018; 19:2372-2379. [PMID: 30168891 DOI: 10.1002/cbic.201800448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Indexed: 11/08/2022]
Abstract
The 2'-O,4'-C-methylene-bridged or locked nucleic acid (2',4'-BNA/LNA), with an N-type sugar conformation, effectively improves duplex-forming ability. 2',4'-BNA/LNA is widely used to improve gene knockdown in nucleic acid based therapies and is used in gene diagnosis. Metal-mediated base pairs (MMBPs), such as thymine (T)-HgII -T and cytosine (C)-AgI -C have been developed and used as attractive tools in DNA nanotechnology studies. This study aimed to investigate the application of 2',4'-BNA/LNA in the field of MMBPs. 2',4'-BNA/LNA with 5-methylcytosine stabilized the MMBP of C with AgI ions. Moreover, the 2',4'-BNA/LNA sugar significantly improved the duplex-forming ability of the DNA/DNA complex, relative to that by the unmodified sugar. These results suggest that the sugar conformation is important for improving the stability of duplex-containing MMBPs. The results indicate that 2',4'-BNA/LNA can be applied not only to nucleic acid based therapies, but also to MMBP technologies.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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11
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Jash B, Müller J. Concomitant Site-Specific Incorporation of Silver(I) and Mercury(II) Ions into a DNA Duplex. Chemistry 2018; 24:10636-10640. [DOI: 10.1002/chem.201802470] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
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