51
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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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52
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Chen YW, Satange R, Wu PC, Jhan CR, Chang CK, Chung KR, Waring MJ, Lin SW, Hsieh LC, Hou MH. Co II(Chromomycin)₂ Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex. Int J Mol Sci 2018; 19:ijms19092796. [PMID: 30227633 PMCID: PMC6164834 DOI: 10.3390/ijms19092796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/07/2018] [Indexed: 01/07/2023] Open
Abstract
We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (CoII)-mediated dimer of chromomycin A3, CoII(Chro)₂. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for CoII(Chro)₂. In addition, water hydration and divalent metal ion (CoII) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions.
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Affiliation(s)
- Yu-Wen Chen
- Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
| | - Pei-Ching Wu
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Cyong-Ru Jhan
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
| | - Kuang-Ren Chung
- Department of Plant Pathology, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Michael J Waring
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Li-Ching Hsieh
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Advanced Plant Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan.
| | - Ming-Hon Hou
- Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan.
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung 402, Taiwan.
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.
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53
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Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory. Int J Mol Sci 2018; 19:ijms19082346. [PMID: 30096923 PMCID: PMC6122091 DOI: 10.3390/ijms19082346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.
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54
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Schmidt OP, Benz AS, Mata G, Luedtke NW. HgII binds to C-T mismatches with high affinity. Nucleic Acids Res 2018; 46:6470-6479. [PMID: 29901748 PMCID: PMC6061796 DOI: 10.1093/nar/gky499] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/04/2018] [Accepted: 06/11/2018] [Indexed: 02/07/2023] Open
Abstract
Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C-T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C-T mismatches (kon ≈ 105 M-1 s-1, koff ≈ 10-3 s-1) as compared to T-T mismatches (kon ≈ 104 M-1 s-1, koff ≈ 10-4 s-1), resulting in very similar equilibrium binding affinities for both types of 'all natural' metallo base pairs (Kd ≈ 10-150 nM). These results are in contrast to thermal denaturation analyses, where duplexes containing T-T mismatches exhibited much larger increases in thermal stability upon addition of HgII (ΔTm = 6-19°C), as compared to those containing C-T mismatches (ΔTm = 1-4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C-HgII-T base pairs, our results demonstrate that fluorescent nucleobase analogs enable highly sensitive detection and characterization of metal-mediated base pairs - even in situations where metal binding has little or no impact on the thermal stability of the duplex.
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Affiliation(s)
- Olivia P Schmidt
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Andrea S Benz
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Guillaume Mata
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Nathan W Luedtke
- University of Zurich, Department of Chemistry, Zurich, Switzerland
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55
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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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56
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Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the enzymatic incorporation of an imidazole nucleotide into DNA. Org Biomol Chem 2018; 15:4449-4455. [PMID: 28485736 DOI: 10.1039/c7ob00858a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with an additional, artificial base pair is of high relevance for numerous applications in synthetic biology. The enzymatic construction of metal base pairs is an alluring strategy that would ensure orthogonality to canonical nucleic acids. So far, very little is known on the enzymatic fabrication of metal base pairs. Here, we report on the synthesis and the enzymatic incorporation of an imidazole nucleotide into DNA. The imidazole nucleotide dIm is known to form highly stable dIm-Ag+-dIm artificial base pairs that cause minimal structural perturbation of DNA duplexes and was considered to be an ideal candidate for the enzymatic construction of metal base pairs. We demonstrate that dImTP is incorporated with high efficiency and selectivity opposite a templating dIm nucleotide by the Kf exo-. The presence of Mn2+, and to a smaller extent Ag+, enhances the efficiency of this polymerization reaction, however, without being strictly required. In addition, multiple incorporation events could be observed, albeit with modest efficiency. We demonstrate that the dIm-Mn+-dIm cannot be constructed by DNA polymerases and suggest that parameters other than stability of a metal base pair and its impact on the structure of DNA duplexes govern the enzymatic formation of artificial metal base pairs.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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57
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Schneider B, Božíková P, Nečasová I, Čech P, Svozil D, Černý J. A DNA structural alphabet provides new insight into DNA flexibility. Acta Crystallogr D Struct Biol 2018; 74:52-64. [PMID: 29372899 PMCID: PMC5786007 DOI: 10.1107/s2059798318000050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/02/2018] [Indexed: 11/10/2022] Open
Abstract
DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson-Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Paulína Božíková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Iva Nečasová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czechia
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czechia
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
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58
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Du K, Niu S, Chen X, Zhang P. A novel highly selective ratiometric fluorescent sensor for relay recognition of Zn 2+ and H 2 PO 4 −. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2017.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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59
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Jash B, Müller J. Metal-Mediated Base Pairs: From Characterization to Application. Chemistry 2017; 23:17166-17178. [PMID: 28833684 DOI: 10.1002/chem.201703518] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/11/2022]
Abstract
The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.
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Affiliation(s)
- Biswarup Jash
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
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60
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Liu H, Cai C, Haruehanroengra P, Yao Q, Chen Y, Yang C, Luo Q, Wu B, Li J, Ma J, Sheng J, Gan J. Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex. Nucleic Acids Res 2017; 45:2910-2918. [PMID: 27998930 PMCID: PMC5389650 DOI: 10.1093/nar/gkw1296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
Abstract
Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C–HgII–T containing duplex, three T–HgII–T containing duplexes and one native duplex containing T–T pair without HgII. Our structures suggest that both C–T and T–T pairs are flexible in interacting with the HgII ion with various binding modes including N3–HgII–N3, N4–HgII–N3, O2–HgII–N3 and N3–HgII–O4. Our studies also reveal that the overall conformations of the C–HgII–T and T–HgII–T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C–HgII–T or T–HgII–T containing DNA nanodevices in the future.
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Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chen Cai
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
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61
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Liu H, Shen F, Haruehanroengra P, Yao Q, Cheng Y, Chen Y, Yang C, Zhang J, Wu B, Luo Q, Cui R, Li J, Ma J, Sheng J, Gan J. A DNA Structure Containing AgI
-Mediated G:G and C:C Base Pairs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704891] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Fusheng Shen
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yunshan Cheng
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
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62
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Liu H, Shen F, Haruehanroengra P, Yao Q, Cheng Y, Chen Y, Yang C, Zhang J, Wu B, Luo Q, Cui R, Li J, Ma J, Sheng J, Gan J. A DNA Structure Containing AgI
-Mediated G:G and C:C Base Pairs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201704891] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Fusheng Shen
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yunshan Cheng
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
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63
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A metallo-DNA nanowire with uninterrupted one-dimensional silver array. Nat Chem 2017; 9:956-960. [DOI: 10.1038/nchem.2808] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 05/24/2017] [Indexed: 12/11/2022]
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64
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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65
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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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66
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Mandal S, Müller J. Metal-mediated DNA assembly with ligand-based nucleosides. Curr Opin Chem Biol 2017; 37:71-79. [PMID: 28214670 DOI: 10.1016/j.cbpa.2017.01.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/22/2017] [Accepted: 01/24/2017] [Indexed: 01/12/2023]
Abstract
Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the formation of predesigned metal arrays. This article offers an overview of structural aspects of metal-mediated base pairs, reviews recent advances in the field of metal-mediated base pairing and presents potential applications of the resulting metal-modified nucleic acids. It particularly focuses on recently developed metal-mediated base pairs with purine-derived nucleosides, gives an overview of metal-responsive systems relying on metal-mediated base pairs and summarizes various applications beyond metal-ion sensors.
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Affiliation(s)
- Soham Mandal
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany(*)
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany(*).
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67
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Jash B, Scharf P, Sandmann N, Fonseca Guerra C, Megger DA, Müller J. A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases. Chem Sci 2017; 8:1337-1343. [PMID: 28451274 PMCID: PMC5360170 DOI: 10.1039/c6sc03482a] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/12/2016] [Indexed: 12/17/2022] Open
Abstract
A nucleoside analogue comprising the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag+-mediated base pair between P and cytosine, whereas the presence of Ag+ strongly destabilizes nucleic acids comprising an artificial base pair between P and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations. The molecular beacon significantly extends the application spectrum of nucleic acids with metal-mediated base pairs. It is of potential use in the detection of single-nucleotide polymorphisms.
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Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
- NRW Graduate School of Chemistry , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany
| | - Philipp Scharf
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
| | - Nikolas Sandmann
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry , Amsterdam Center for Multiscale Modeling (ACMM) , VU Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands .
| | - Dominik A Megger
- Medizinisches Proteom-Center , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
- NRW Graduate School of Chemistry , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany
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68
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Terrón A, Moreno-Vachiano B, Bauzá A, García-Raso A, Fiol JJ, Barceló-Oliver M, Molins E, Frontera A. X-ray Crystal Structure of a Metalled Double-Helix Generated by Infinite and Consecutive C*-AgI
-C* (C*:N1
-Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions. Chemistry 2017; 23:2103-2108. [DOI: 10.1002/chem.201604331] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Angel Terrón
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Blas Moreno-Vachiano
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Antonio Bauzá
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Angel García-Raso
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Juan Jesús Fiol
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Miquel Barceló-Oliver
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC); Campus de la Universitat Autònoma de Barcelona 08193 Bellaterra Spain
| | - Antonio Frontera
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
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69
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Guo X, Ingale SA, Yang H, He Y, Seela F. MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents. Org Biomol Chem 2017; 15:870-883. [PMID: 28045181 DOI: 10.1039/c6ob02560a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–HgII–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.
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Affiliation(s)
- Xiurong Guo
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Yang He
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
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70
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Mandal S, Hebenbrock M, Müller J. Ein zweikerniges Quecksilber(II)-vermitteltes Basenpaar in DNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
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71
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Mandal S, Hebenbrock M, Müller J. A Dinuclear Mercury(II)-Mediated Base Pair in DNA. Angew Chem Int Ed Engl 2016; 55:15520-15523. [PMID: 27862734 DOI: 10.1002/anie.201608354] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/30/2016] [Indexed: 11/08/2022]
Abstract
The first dinuclear metal-mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N6 -ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N-M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of HgII and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T-HgII2 -ϵA base pair. This metal-mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature-dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.
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Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
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72
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Schmidt OP, Mata G, Luedtke NW. Fluorescent Base Analogue Reveals T-HgII-T Base Pairs Have High Kinetic Stabilities That Perturb DNA Metabolism. J Am Chem Soc 2016; 138:14733-14739. [DOI: 10.1021/jacs.6b09044] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Olivia P. Schmidt
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Guillaume Mata
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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73
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Kobayashi T, Takezawa Y, Sakamoto A, Shionoya M. Enzymatic synthesis of ligand-bearing DNAs for metal-mediated base pairing utilising a template-independent polymerase. Chem Commun (Camb) 2016; 52:3762-5. [PMID: 26810253 DOI: 10.1039/c5cc10039a] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have developed a novel method to synthesise artificial ligand-bearing DNAs utilising a template-independent DNA polymerase. Hydroxypyridone ligand-bearing nucleotides () were successively appended to DNA primers by the enzyme. The resulting strands, tailed with nucleotides, formed Cu(II)-mediated metallo-DNA duplexes through the formation of metal-mediated artificial base pairs (H-Cu(II)-H).
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Affiliation(s)
- Teruki Kobayashi
- 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.
| | - Akira Sakamoto
- 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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74
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Kumar J, Pratibha, Verma S. Crystallographic signatures of silver-purine frameworks with an azide functionality. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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75
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Bauzá A, Terrón A, Barceló-Oliver M, García-Raso A, Frontera A. On the importance of antiparallel C O⋯C–F interactions in N1-(3-hydroxypropyl)-5-fluorouracilate–Hg(II) complex: A combined X-ray and DFT study. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.04.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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76
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Taherpour S, Golubev O, Lönnberg T. On the feasibility of recognition of nucleic acid sequences by metal-ion-carrying oligonucleotides. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.01.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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77
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The effect of chemical modification of DNA base on binding of HgII and AgI in metal-mediated base pairs. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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78
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79
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Nishiyama K, Takezawa Y, Shionoya M. pH-Dependence of the thermal stability of metallo-DNA duplexes containing ligand-type 5-hydroxyuracil nucleobases. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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80
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Helical Aggregates of Building Blocks Formed In Situ from Five Components. Chempluschem 2016; 81:1326-1332. [DOI: 10.1002/cplu.201600419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 01/06/2023]
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81
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Lippert B, Sanz Miguel PJ. The Renaissance of Metal-Pyrimidine Nucleobase Coordination Chemistry. Acc Chem Res 2016; 49:1537-45. [PMID: 27472006 DOI: 10.1021/acs.accounts.6b00253] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The significance of metal ions for the function and properties of DNA and RNA, long seen primarily under biological aspects and medicinal uses, has recently gained a renewed momentum. This is a consequence of the advent of novel applications in the fields of materials science, biotechnology, and analytical sensor chemistry that relate to the designed incorporation of transition metal ions into nucleic acid base pairs. Ag(+) and Hg(2+) ions, binding to pyrimidine (pym) nucleobases, represent major players in this development. Interestingly, these metal ions were the ones that some 60 years ago started the field! At the same time, the mentioned metal ions had demonstrated a "special relationship" with the pym nucleobases cytosine, thymine, and uracil! Parallel work conducted with oligonucleotides and model nucleobases fostered numerous significant details of these interactions, in particular when X-ray crystallography was involved, correcting earlier views occasionally. Our own activities during the past three to four decades have focused on, among others, the coordination chemistry of transition and main-group metal ions with pym model nucleobases, with an emphasis on Pt(II) and Pd(II). It has always been our goal to deduce, if possible, the potential relevance of our findings for biological processes. It is interesting to put our data, in particular for trans-a2Pt(II) (a = NH3 or amine), into perspective with those of other metal ions, notably Ag(+) and Hg(2+). Irrespective of major differences in kinetics and lability/inertness between d(8) and d(10) metal ions, there is also a lot of similarity in structural aspects as a result of the preferred linear coordination geometry of these species. Moreover, the apparent clustering of metal ions to the pym nucleobases, which is presumably essential for the formation of nanoclusters on oligonucleotide scaffolds, is impressively reflected in model systems, as are reasons for inter-nucleobase cross-links containing more than a single metal ion. The present understanding of these interrelationships is a consequence of intensive research carried out during the last 60 years by numerous laboratories. For space restrictions in this Account, it was impossible to adequately highlight the valuable contributions of all of the researchers in the field of metal-pym nucleobase interactions. Explicitly this refers to colleagues not cited in the references, e.g., R. Stuart Tobias, Robert Bau, R. Bruce Martin, Colin J. L. Lock, Katsuyuki Aoki, Helmut Sigel, and Michael J. Clarke, among others.
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Affiliation(s)
- Bernhard Lippert
- Fakultät
für Chemie und Chemische Biologie (CCB), Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Pablo J. Sanz Miguel
- Departamento
de Química Inorgánica, Instituto de Síntesis
Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
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82
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Zhang Y, Qian C, Zeng GM, Tang L, Zhang C, Zhu Y, Feng CL, Liu YY. Effects of Functionalized Electrodes and Gold Nanoparticle Carrier Signal Amplification on an Electrochemical DNA Sensing Strategy. ChemElectroChem 2016. [DOI: 10.1002/celc.201600362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yi Zhang
- College of Environmental Science and Engineering; Hunan University; Changsha P.R. China
- Key Laboratory of Environmental Biology & Pollution Control; Hunan University, Ministry of Education; Changsha P.R. China
- Department of Chemistry; University of Science and Technology of China; Hefei P.R. China
| | - Chen Qian
- Department of Chemistry; University of Science and Technology of China; Hefei P.R. China
| | - Guang Ming Zeng
- College of Environmental Science and Engineering; Hunan University; Changsha P.R. China
- Key Laboratory of Environmental Biology & Pollution Control; Hunan University, Ministry of Education; Changsha P.R. China
| | - Lin Tang
- College of Environmental Science and Engineering; Hunan University; Changsha P.R. China
- Key Laboratory of Environmental Biology & Pollution Control; Hunan University, Ministry of Education; Changsha P.R. China
| | - Chang Zhang
- College of Environmental Science and Engineering; Hunan University; Changsha P.R. China
- Key Laboratory of Environmental Biology & Pollution Control; Hunan University, Ministry of Education; Changsha P.R. China
| | - Yuan Zhu
- College of Environmental Science and Engineering; Hunan University; Changsha P.R. China
- Key Laboratory of Environmental Biology & Pollution Control; Hunan University, Ministry of Education; Changsha P.R. China
| | - Chong Ling Feng
- Research Center of Environmental Science and Engineering; Center South University of Forestry and Technology; Changsha P.R. China
| | - Yuan Yuan Liu
- College of Environmental Science and Engineering; Hunan University; Changsha P.R. China
- Key Laboratory of Environmental Biology & Pollution Control; Hunan University, Ministry of Education; Changsha P.R. China
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83
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Dairaku T, Furuita K, Sato H, Šebera J, Nakashima K, Kondo J, Yamanaka D, Kondo Y, Okamoto I, Ono A, Sychrovský V, Kojima C, Tanaka Y. Structure Determination of an AgI-Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with1H/15N/109Ag NMR Spectroscopy. Chemistry 2016; 22:13028-31. [DOI: 10.1002/chem.201603048] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Takenori Dairaku
- School of Pharmaceutical Sciences; Ohu University; 31-1 Misumido, Tomita-machi, Koriyama Fukushima 963-8611 Japan
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Kyoko Furuita
- Institute for Protein Research; Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Hajime Sato
- Application, Bruker BioSpin K. K.; 3-9 Moriya-cho, Kanagawa-ku, Yokohama Kanagawa 221-0022 Japan
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, v.v.i.; Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Katsuyuki Nakashima
- Faculty of Phamaceutical Scienes; Tokushima Bunri University; Yamashiro-cho Tokushima 770-8514 Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences; Faculty of Science and Technology, Sophia University; 7-1 Kioi-cho, Chiyoda-ku Tokyo 102-8554 Japan
| | - Daichi Yamanaka
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Yoshinori Kondo
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Itaru Okamoto
- Department of Material & Life Chemistry, Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
| | - Akira Ono
- Department of Material & Life Chemistry, Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, v.v.i.; Flemingovo náměstí 2 16610 Praha 6 Czech Republic
- Czech Technical University in Prague; Faculty of Electrical Engineering, Department of Electrotechnology; Technická 2 166 27 Praha 6 Czech Republic
| | - Chojiro Kojima
- Institute for Protein Research; Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
- Faculty of Phamaceutical Scienes; Tokushima Bunri University; Yamashiro-cho Tokushima 770-8514 Japan
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84
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Chu-mong K, Thammakhet C, Thavarungkul P, Kanatharana P, Buranachai C. A FRET based aptasensor coupled with non-enzymatic signal amplification for mercury (II) ion detection. Talanta 2016; 155:305-13. [DOI: 10.1016/j.talanta.2016.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 12/30/2022]
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85
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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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86
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Mandal S, Wang C, Prajapati RK, Kösters J, Verma S, Chi L, Müller J. Metal-Mediated Assembly of 1,N6-Ethenoadenine: From Surfaces to DNA Duplexes. Inorg Chem 2016; 55:7041-50. [DOI: 10.1021/acs.inorgchem.6b00927] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Can Wang
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
| | - Rajneesh K. Prajapati
- Department of Chemistry, DST Thematic Unit of Excellence
on Soft Nanofabrication, Indian Institute of Technology−Kanpur, Kanpur, Uttar Pradesh 208016, India
| | | | - Sandeep Verma
- Department of Chemistry, DST Thematic Unit of Excellence
on Soft Nanofabrication, Indian Institute of Technology−Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Lifeng Chi
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Institute
of Functional Nano and Soft Materials, Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai
Road, Suzhou, 215123 Jiangsu, People’s Republic of China
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87
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Ukale D, Shinde VS, Lönnberg T. 5-Mercuricytosine: An Organometallic Janus Nucleobase. Chemistry 2016; 22:7917-23. [PMID: 27113075 DOI: 10.1002/chem.201600851] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/10/2022]
Abstract
The base-pairing properties of 5-mercuricytosine have been explored at the monomer level by NMR titrations and at the oligonucleotide level by melting temperature measurements. The NMR studies revealed a relatively high affinity for guanine, hypoxanthine, and uridine, that is, bases that are deprotonated upon coordination of Hg(II) . Within an oligonucleotide duplex, 5-mercuricytosine formed Hg(II) -mediated base pairs with thymine and guanine. In the former case, the duplex formed was as stable as the respective duplex comprising solely Watson-Crick base pairs. Based on detailed thermodynamic analysis of the melting curves, the stabilization by the Hg(II) -mediated base pairs may be attributed to a comparatively low entropic penalty of hybridization.
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Affiliation(s)
- Dattatraya Ukale
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland.,Department of Chemistry, Savirtibai Phule Pune University, Pune, 411007, India
| | - Vaishali S Shinde
- Department of Chemistry, Savirtibai Phule Pune University, Pune, 411007, India
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland.
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88
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Léon JC, Sinha I, Müller J. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes. Int J Mol Sci 2016; 17:554. [PMID: 27089326 PMCID: PMC4849010 DOI: 10.3390/ijms17040554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase.
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Affiliation(s)
- J Christian Léon
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| | - Indranil Sinha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
- NRW Graduate School of Chemistry, 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.
- NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
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89
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Wang W, Kang TS, Chan PWH, Lu JJ, Chen XP, Leung CH, Ma DL. A label-free G-quadruplex-based mercury detection assay employing the exonuclease III-mediated cleavage of T-Hg 2+-T mismatched DNA. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2015; 16:065004. [PMID: 27877846 PMCID: PMC5069990 DOI: 10.1088/1468-6996/16/6/065004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 05/30/2023]
Abstract
We report herein the use of an exonuclease III and G-quadruplex probe to construct a G-quadruplex-based luminescence detection platform for Hg2+. Unlike common DNA-based Hg2+ detection methods, when using the dsDNA probe to monitor the hairpin formation, the intercalation of the dsDNA probe may be influenced by the distortion of dsDNA. This 'mix-and-detect' methodology utilized the G-quadruplex probe as the signal transducer and is simple, rapid, convenient to use and can detect down to 20 nM of Hg2+.
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Affiliation(s)
- Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Philip Wai Hong Chan
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xiu-Ping Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- Partner State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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90
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Sinha I, Hepp A, Kösters J, Müller J. Metal complexes of 6-pyrazolylpurine derivatives as models for metal-mediated base pairs. J Inorg Biochem 2015; 153:355-360. [DOI: 10.1016/j.jinorgbio.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/10/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022]
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91
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Scharf P, Jash B, Kuriappan JA, Waller MP, Müller J. Sequence-Dependent Duplex Stabilization upon Formation of a Metal-Mediated Base Pair. Chemistry 2015; 22:295-301. [PMID: 26584591 DOI: 10.1002/chem.201503405] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 12/20/2022]
Abstract
An artificial nucleoside surrogate with 1H-imidazo[4,5-f][1,10]phenanthroline (P) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal-mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag(I) -mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B-DNA duplex.
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Affiliation(s)
- Philipp Scharf
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster (Germany).,Current address: University of Iceland, Science Institute, Dunhagi 3, 107 Reykjavík (Iceland)
| | - Biswarup Jash
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster (Germany).,Westfälische Wilhelms-Universität Münster, Graduate School of Chemistry, Corrensstrasse 28/30, 48149 Münster (Germany)
| | - Jissy A Kuriappan
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Corrensstrasse 40, 48149 Münster (Germany)
| | - Mark P Waller
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Corrensstrasse 40, 48149 Münster (Germany)
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster (Germany). .,Westfälische Wilhelms-Universität Münster, Graduate School of Chemistry, Corrensstrasse 28/30, 48149 Münster (Germany).
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92
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Dairaku T, Furuita K, Sato H, Kondo Y, Kojima C, Ono A, Tanaka Y. Exploring a DNA Sequence for the Three-Dimensional Structure Determination of a Silver(I)-Mediated C-C Base Pair in a DNA Duplex By (1)H NMR Spectroscopy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:877-900. [PMID: 26576739 DOI: 10.1080/15257770.2015.1088160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recently, we discovered novel silver(I)-mediated cytosine-cytosine base pair (C-Ag(I)-C) in DNA duplexes. To understand the properties of these base pairs, we searched for a DNA sequence that can be used in NMR structure determination. After extensive sequence optimizations, a non-symmetric 15-base-paired DNA duplex with a single C-Ag(I)-C base pair flanked by 14 A-T base pairs was selected. In spite of its challenging length for NMR measurements (30 independent residues) with small sequence variation, we could assign most non-exchangeable protons (254 out of 270) and imino protons for structure determination.
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Affiliation(s)
- Takenori Dairaku
- a Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku , Sendai , Miyagi , Japan
| | - Kyoko Furuita
- b Institute for Protein Research, Osaka University , Suita , Osaka , Japan
| | - Hajime Sato
- c Bruker BioSpin K.K. , Yokohama , Kanagawa , Japan
| | - Yoshinori Kondo
- a Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku , Sendai , Miyagi , Japan
| | - Chojiro Kojima
- b Institute for Protein Research, Osaka University , Suita , Osaka , Japan
| | - Akira Ono
- d Department of Material & Life Chemistry , Kangawa University, Kanagawa-ku , Yokohama , Kanagawa , Japan
| | - Yoshiyuki Tanaka
- a Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Aoba-ku , Sendai , Miyagi , Japan.,e Laboratory of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University , Yamashiro-cho , Tokushima , Japan
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93
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Kondo J, Tada Y, Dairaku T, Saneyoshi H, Okamoto I, Tanaka Y, Ono A. High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs. Angew Chem Int Ed Engl 2015; 54:13323-6. [DOI: 10.1002/anie.201507894] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Yoshinari Tada
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
| | - Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Itaru Okamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro‐cho, 770‐8514 Tokushima (Japan)
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
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94
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Deng W, Zheng B, Ding W, Zhu H, Liang HJ. Metal-Triggered DNA Folding by Different Mechanisms. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1503051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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95
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Mandal S, Hepp A, Müller J. Unprecedented dinuclear silver(I)-mediated base pair involving the DNA lesion 1,N(6)-ethenoadenine. Dalton Trans 2015; 44:3540-3. [PMID: 25478946 DOI: 10.1039/c4dt02663b] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The DNA lesion 1,N(6)-ethenoadenine (εA) has been investigated with respect to its metal-binding properties. A synthetic DNA duplex comprising an εA : εA mispair readily forms doubly silver(I)-mediated base pairs εA-Ag(I)2-εA, representing the first example for a dinuclear metal-mediated homo base pair of a purine derivative. It also constitutes the first example for a Hoogsteen-type metal-mediated homo base pair within a B-DNA duplex.
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Affiliation(s)
- Soham Mandal
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149 Münster, Germany.
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96
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Tan X, Litau S, Zhang X, Müller J. Single-Molecule Force Spectroscopy of an Artificial DNA Duplex Comprising a Silver(I)-Mediated Base Pair. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11305-11310. [PMID: 26421907 DOI: 10.1021/acs.langmuir.5b03183] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule force spectroscopy measurements of a DNA duplex comprising an artificial metal-mediated base pair are reported. The measurements reveal that DNA duplexes comprising one central imidazole:imidazole mispair rupture at lower forces than a related duplex with canonical base pairs only. In contrast, DNA duplexes with one central imidazole-Ag(+)-imidazole base pair (formed by the addition of Ag(+) to the aforementioned duplex with the mispair) rupture at higher forces. These measurements indicate for the first time that the increase in thermal stability of a nucleic acid duplex that is observed upon the formation of a metal-mediated base pair is accompanied by a concomitant mechanical stabilization. In fact, the mechanical stabilization even exceeds the thermal one. This result indicates that nucleic acids with metal-mediated base pairs should be ideal building blocks for rigid functionalized DNA nano-objects.
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Affiliation(s)
- Xinxin Tan
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Stefanie Litau
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster , Corrensstr. 28/30, 48149 Münster, Germany
| | - Xi Zhang
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster , Corrensstr. 28/30, 48149 Münster, Germany
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97
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Espinosa Leal LA, Karpenko A, Swasey S, Gwinn EG, Rojas-Cervellera V, Rovira C, Lopez-Acevedo O. The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers. J Phys Chem Lett 2015; 6:4061-6. [PMID: 26722777 DOI: 10.1021/acs.jpclett.5b01864] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.
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Affiliation(s)
| | - Alexander Karpenko
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
| | - Steven Swasey
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Elisabeth G Gwinn
- Department of Physics, University of California , Santa Barbara, California 93106-9510, United States
| | - Victor Rojas-Cervellera
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Olga Lopez-Acevedo
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
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98
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Kondo J, Tada Y, Dairaku T, Saneyoshi H, Okamoto I, Tanaka Y, Ono A. High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507894] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Yoshinari Tada
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
| | - Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Itaru Okamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro‐cho, 770‐8514 Tokushima (Japan)
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
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99
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Takezawa Y, Nishiyama K, Mashima T, Katahira M, Shionoya M. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination. Chemistry 2015; 21:14713-6. [DOI: 10.1002/chem.201502772] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/11/2022]
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100
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