1
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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2
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Wang M, Tsukamoto M, Sergeyev VG, Zinchenko A. Metal Ions Sensing by Biodots Prepared from DNA, RNA, and Nucleotides. BIOSENSORS 2021; 11:333. [PMID: 34562923 PMCID: PMC8466223 DOI: 10.3390/bios11090333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 01/20/2023]
Abstract
Nucleic acids that exhibit a high affinity toward noble and transition metal ions have attracted growing attention in the fields of metal ion sensing, toxic metal ion removal, and the construction of functional metal nanostructures. In this study, fluorescent nanoparticles (biodots) were synthesized from DNA, RNA, and RNA nucleotides (AMP, GMP, UMP, and CMP) using a hydrothermal (HT) method, in order to study their metal ion sensing characteristics. The fluorescent properties of biodots differ markedly between those prepared from purine and pyrimidine nucleobases. All biodots demonstrate a high sensitivity to the presence of mercury cations (Hg2+), while biodots prepared from DNA, RNA, and guanosine monophosphate (GMP) are also sensitive to Ag+ and Cu2+ ions, but to a lesser extent. The obtained results show that biodots inherit the metal ion recognition properties of nucleobases, while the nucleobase composition of biodot precursors affects metal ion sensitivity and selectivity. A linear response of biodot fluorescence to Hg2+ concentration in solution was observed for AMP and GMP biodots in the range 0-250 μM, which can be used for the analytic detection of mercury ion concentration. A facile paper strip test was also developed that allows visual detection of mercury ions in solutions.
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Affiliation(s)
- Maofei Wang
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
| | - Masaki Tsukamoto
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
| | - Vladimir G. Sergeyev
- Department of Chemistry, Lomonosov Moscow State University, 119899 Moscow, Russia;
| | - Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan;
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3
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Tan J, Zhao M, Wang J, Li Z, Liang L, Zhang L, Yuan Q, Tan W. Regulation of Protein Activity and Cellular Functions Mediated by Molecularly Evolved Nucleic Acids. Angew Chem Int Ed Engl 2019; 58:1621-1625. [PMID: 30556364 PMCID: PMC6442720 DOI: 10.1002/anie.201809010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/07/2018] [Indexed: 01/05/2023]
Abstract
Regulation of protein activity is essential for revealing the molecular mechanisms of biological processes. DNA and RNA achieve many uniquely efficient functions, such as genetic expression and regulation. The chemical capability to synthesize artificial nucleotides can expand the chemical space of nucleic acid libraries and further increase the functional diversity of nucleic acids. Herein, a versatile method has been developed for modular expansion of the chemical space of nucleic acid libraries, thus enabling the generation of aptamers able to regulate protein activity. Specifically, an aptamer that targets integrin alpha3 was identified and this aptamer can inhibit cell adhesion and migration. Overall, this chemical-design-assisted in vitro selection approach enables the generation of functional nucleic acids for elucidating the molecular basis of biological activities and uncovering a novel basis for the rational design of new protein-inhibitor pharmaceuticals.
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Affiliation(s)
- Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China,
| | - Mengmeng Zhao
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Ling Liang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China
| | - Liqin Zhang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China,
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082 China, Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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4
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Tan J, Zhao M, Wang J, Li Z, Liang L, Zhang L, Yuan Q, Tan W. Regulation of Protein Activity and Cellular Functions Mediated by Molecularly Evolved Nucleic Acids. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Mengmeng Zhao
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 China
| | - Ling Liang
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Liqin Zhang
- Department of Chemistry and Department of Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute and McKnight Brain Institute University of Florida Gainesville FL 32611-7200 USA
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL) Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
- Department of Chemistry and Department of Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute and McKnight Brain Institute University of Florida Gainesville FL 32611-7200 USA
- Institute of Molecular Medicine (IMM) Renji Hospital Shanghai Jiao Tong University School of Medicine College of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai China
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5
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Application of Heteronuclear NMR Spectroscopy to Bioinorganic and Medicinal Chemistry ☆. REFERENCE MODULE IN CHEMISTRY, MOLECULAR SCIENCES AND CHEMICAL ENGINEERING 2018. [PMCID: PMC7157447 DOI: 10.1016/b978-0-12-409547-2.10947-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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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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7
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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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8
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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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9
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Terrón A, Tomàs L, Bauzá A, García-Raso A, Fiol JJ, Molins E, Frontera A. The first X-ray structure of a silver–nucleotide complex: interaction of ion Ag(i) with cytidine-5′-monophosphate. CrystEngComm 2017. [DOI: 10.1039/c7ce01400g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The synthesis and X-ray characterization of an unprecedented complex of Ag(i) with cytidine-5′-monophosphate (HCMP) is reported. The coordination of Ag(i) to HCMP is via both the N3 and O2 atoms of two cytosine moieties and the phosphate group, generating a MOF.
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Affiliation(s)
- Angel Terrón
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Llorenç Tomàs
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Angel García-Raso
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Juan J. Fiol
- Departament de Química
- Universitat de les Illes Balears
- 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
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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10
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Sigel A, Operschall BP, Matera-Witkiewicz A, Świątek-Kozłowska J, Sigel H. Acid–base and metal ion-binding properties of thiopyrimidine derivatives. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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UV fragmentation and ultrafast dynamics of trinuclear silver/1-methylthymine and silver/1-methyluracil metal-base pairs in an ion trap. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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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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13
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Nosenko Y, Riehn C, Niedner-Schatteburg G. Self-pairing of 1-methylthymine mediated by two and three Ag(i) ions: a gas phase study using infrared dissociation spectroscopy and density functional theory. Phys Chem Chem Phys 2016; 18:8491-501. [DOI: 10.1039/c5cp07016c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Metal base pairs comprised of silver dimer or trimer and two thymines were studied by IR dissociation spectroscopy and density functional theory.
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Affiliation(s)
- Yevgeniy Nosenko
- Fachbereich Chemie and Forschungszentrum OPTIMAS
- Technische Universität Kaiserslautern
- Kaiserslautern 67663
- Germany
| | - Christoph Riehn
- Fachbereich Chemie and Forschungszentrum OPTIMAS
- Technische Universität Kaiserslautern
- Kaiserslautern 67663
- Germany
| | - Gereon Niedner-Schatteburg
- Fachbereich Chemie and Forschungszentrum OPTIMAS
- Technische Universität Kaiserslautern
- Kaiserslautern 67663
- Germany
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14
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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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15
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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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16
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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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17
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18
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Litau S, Müller J. A tridentate “click” nucleoside for metal-mediated base pairing. J Inorg Biochem 2015; 148:116-20. [DOI: 10.1016/j.jinorgbio.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 12/15/2022]
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19
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4-(2′-Pyridyl)imidazole as an artificial nucleobase in highly stabilizing Ag(I)-mediated base pairs. J Biol Inorg Chem 2015; 20:895-903. [DOI: 10.1007/s00775-015-1274-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/28/2015] [Indexed: 11/26/2022]
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20
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Fortino M, Marino T, Russo N. Theoretical Study of Silver-Ion-Mediated Base Pairs: The Case of C–Ag–C and C–Ag–A Systems. J Phys Chem A 2014; 119:5153-7. [DOI: 10.1021/jp5096739] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mariagrazia Fortino
- Dipartimento di Chimica e
Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e
Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
| | - Nino Russo
- Dipartimento di Chimica e
Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
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21
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Hensel S, Megger N, Schweizer K, Müller J. Second generation silver(I)-mediated imidazole base pairs. Beilstein J Org Chem 2014; 10:2139-44. [PMID: 25246972 PMCID: PMC4168905 DOI: 10.3762/bjoc.10.221] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/27/2014] [Indexed: 12/15/2022] Open
Abstract
The imidazole-Ag(I)-imidazole base pair is one of the best-investigated artificial metal-mediated base pairs. We show here that its stability can be further improved by formally replacing the imidazole moiety by a 2-methylimidazole or 4-methylimidazole moiety. A comparison of the thermal stability of several double helices shows that the addition of one equivalent of Ag(I) leads to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair.
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Affiliation(s)
- Susanne Hensel
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Nicole Megger
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Kristina Schweizer
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
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Lee SJ, Michel SLJ. Structural metal sites in nonclassical zinc finger proteins involved in transcriptional and translational regulation. Acc Chem Res 2014; 47:2643-50. [PMID: 25098749 DOI: 10.1021/ar500182d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zinc finger (ZF) proteins are a large family of metalloproteins that utilize zinc for structural purposes. Zinc coordinates to a combination of cysteine thiol and histidine imidazole residues within the ZF polypeptide sequence resulting in a folded and functional protein. Initially, a single class of ZFs were identified. These ZFs, now referred to as the "classical" ZFs, utilize a Cys2His2 (CCHH) ligand set to bind zinc. Upon Zn coordination, the classical ZFs fold into a structure made up of an α helix and an antiparallel β sheet. When folded, classical ZFs recognize and bind to specific DNA targets and function as transcription factors. With the advent of genome sequencing and proteomics, many additional classes of ZFs were identified based upon their primary amino acid sequences. At least 13 additional classes of ZFs are known, and collectively these "nonclassical" ZFs differ in the ligand set involved in Zn(II) coordination, the organization of the ligands within the polypeptide sequence and the macromolecular targets. Some nonclassical ZFs are DNA binding "transcription factors", while others are involved in RNA regulation and protein recognition. Much less is known about these nonclassical ZFs with regards to the roles of metal coordination in fold and function. This Account focuses on our laboratory's efforts to characterize two families of "nonclassical" ZFs: the Cys3His (or CCCH) ZF family and the Cys2His2Cys (or CCHHC) ZF family. Our work on the CCCH ZF family has focused on the protein Tristetraprolin (TTP), which is a key protein in regulating inflammation. TTP contains two CCCH domains that were proposed to be ZFs based upon their sequence. We have shown that while this protein can coordinate Zn(II) at the CCCH sites, it can also coordinate Fe(II) and Fe(III). Moreover, the zinc and iron bound forms of TTP are equally adept at discriminating between RNA targets, which we have demonstrated via a fluorescence anisotropy based approach. Thus, CCCH type ZFs appear to be promiscuous with respect to metal preference and a role for iron coordination in CCCH ZF function is proposed. The CCHHC family of ZFs is a small family of nonclassical ZFs that are essential for the development of the central nervous system. There are three ZFs in this family: neural zinc finger factor-1 (NZF-1), myelin transcription factor-1 (MyT1), and suppressor of tumorgenicity 18 (ST18). All three proteins contain multiple clusters of "CCHHC" domains, which are all predicted to be Zn binding domains. We have focused on a tandem-CCHHC domain construct of NZF-1, which recognizes β-RARE DNA, and we have identified key residues required for DNA recognition. Unlike classical ZFs, for which a few conserved residues are required for DNA recognition, the CCHHC class of ZFs utilize a few nonconserved residues to drive DNA recognition leading us to propose a new paradigm for ZF/DNA binding.
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Affiliation(s)
- Seung Jae Lee
- Department
of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Sarah L. J. Michel
- Department
of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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Richters T, Krug O, Kösters J, Hepp A, Müller J. A family of "click" nucleosides for metal-mediated base pairing: unravelling the principles of highly stabilizing metal-mediated base pairs. Chemistry 2014; 20:7811-8. [PMID: 24838942 DOI: 10.1002/chem.201402221] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 12/12/2022]
Abstract
A family of artificial nucleosides has been developed by applying the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition. Starting from 2-deoxy-β-D-glycosyl azide as a common precursor, three bidentate nucleosides have been synthesized. The 1,2,3-triazole involved in all three nucleobases is complemented by 1,2,4-triazole (TriTri), pyrazole (TriPyr), or pyridine (TriPy). Molecular structures of two metal complexes indicate that metal-mediated base pairs of TriPyr may not be fully planar. An investigation of DNA oligonucleotide duplexes comprising the new "click" nucleosides showed that they can bind Ag(I) to form metal-mediated base pairs. In particular the mispair formed from TriPy and the previously established imidazole nucleoside is significantly stabilized in the presence of Ag(I). A comparison of different oligonucleotide sequences allowed the determination of general factors involved in the stabilization of nucleic acids duplexes with metal-mediated base pairs.
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Affiliation(s)
- Tim Richters
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149 Münster (Germany), Fax: (+49) 251-8336007
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Richters T, Müller J. A Metal-Mediated Base Pair with a [2+1] Coordination Environment. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201301491] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Kumbhar S, Johannsen S, Sigel RK, Waller MP, Müller J. A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs. J Inorg Biochem 2013; 127:203-10. [DOI: 10.1016/j.jinorgbio.2013.03.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/18/2013] [Accepted: 03/18/2013] [Indexed: 01/04/2023]
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26
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Buvaylo OA, Kokozay VN, Ischenko MV, Vassilyeva OY, Skelton BW. New nickel mixed-ligand complex containing 2-aminopyrimidine and 5-bromosalicylaldehyde with a one-dimensional hydrogen bonded structure. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Nosenko Y, Menges F, Riehn C, Niedner-Schatteburg G. Investigation by two-color IR dissociation spectroscopy of Hoogsteen-type binding in a metalated nucleobase pair mimic. Phys Chem Chem Phys 2013; 15:8171-8. [PMID: 23612714 DOI: 10.1039/c3cp44283g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Two Ag(I) ions, deprotonated 1-methyl-thymine (1MT-H)(-) and 1,3-dideaza-adenine (DDA), self-assemble in methanolic solution to a cationic [(Ag)2(1MT-H)(DDA)](+) complex as identified by electrospray ionization mass spectrometry. Assignment of vibrational bands and identification of the silver coordination pattern arise from comparison of one- and two-color Infrared Multiple Photon Dissociation (IRMPD) spectra (1000-4000 cm(-1)) of isolated and trapped complexes to calculated spectra from density functional theory. This approach reveals two structurally and energetically close isomers that resemble a metalated Hoogsteen-like binding motif. The two color IR/IR double resonance scheme proved in particular useful to observe weakly absorbing or weakly fragmenting vibrational modes.
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Affiliation(s)
- Yevgeniy Nosenko
- Fachbereich Chemie and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 52, Kaiserslautern 67663, Germany.
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Radunsky C, Megger DA, Hepp A, Kösters J, Freisinger E, Müller J. A Family of Hydrazone-Based Nucleosides for Use in Metal-Mediated Base Pairs. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Barceló-Oliver M, Baquero BA, Bauzá A, García-Raso Á, Vich R, Mata I, Molins E, Terrón À, Frontera A. Experimental and theoretical studies on the coordination chemistry of the N1-hexyl substituted pyrimidines (uracil, 5-fluorouracil and cytosine). Dalton Trans 2013; 42:7631-42. [DOI: 10.1039/c3dt32922d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Sinha I, Kösters J, Hepp A, Müller J. 6-Substituted purines containing thienyl or furyl substituents as artificial nucleobases for metal-mediated base pairing. Dalton Trans 2013; 42:16080-9. [DOI: 10.1039/c3dt51691a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Seubert K, Böhme D, Kösters J, Shen WZ, Freisinger E, Müller J. N-Methyl-2, 2'-Dipicolylamine Complexes as Potential Models for Metal-Mediated Base Pairs. Z Anorg Allg Chem 2012. [DOI: 10.1002/zaac.201200089] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Petrovec K, Ravoo BJ, Müller J. Cooperative formation of silver(i)-mediated base pairs. Chem Commun (Camb) 2012; 48:11844-6. [DOI: 10.1039/c2cc36169h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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