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Dalla Pozza M, Abdullrahman A, Cardin CJ, Gasser G, Hall JP. Three's a crowd - stabilisation, structure, and applications of DNA triplexes. Chem Sci 2022; 13:10193-10215. [PMID: 36277639 PMCID: PMC9473520 DOI: 10.1039/d2sc01793h] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/02/2022] [Indexed: 12/16/2022] Open
Abstract
DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential - these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.
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Affiliation(s)
- Maria Dalla Pozza
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology F-75005 Paris France www.gassergroup.com
| | - Ahmad Abdullrahman
- Department of Pharmacy, Chemistry and Pharmacy Building, University of Reading Whiteknights Campus Reading Berkshire RG6 6AD UK
| | - Christine J Cardin
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6AD UK
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology F-75005 Paris France www.gassergroup.com
| | - James P Hall
- Department of Pharmacy, Chemistry and Pharmacy Building, University of Reading Whiteknights Campus Reading Berkshire RG6 6AD UK
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2
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Affiliation(s)
- Xin‐Xin Peng
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
- Spin-X Institute, School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510641 P. R. China
- Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials Guangzhou 510641 P. R. China
| | - Jun‐Long Zhang
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Chengfu Road 292, Haidian district Beijing 100871 R. P. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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3
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Ragab MS, Shehata MR, Shoukry MM, Haukka M, Ragheb MA. Oxidative DNA cleavage mediated by a new unexpected [Pd(BAPP)][PdCl 4] complex (BAPP = 1,4-bis(3-aminopropyl)piperazine): crystal structure, DNA binding and cytotoxic behavior. RSC Adv 2022; 12:1871-1884. [PMID: 35425175 PMCID: PMC8979008 DOI: 10.1039/d1ra07793g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
A novel Pd(ii) double complex, [Pd(BAPP)][PdCl4], containing the 1,4-bis(3-aminopropyl)piperazine (BAPP) ligand is investigated. X-ray crystallography of a single crystal confirmed the structure of the [Pd(BAPP)][PdCl4] complex. The spectroscopic behavior was also elucidated using elemental analysis, nuclear magnetic resonance and Fourier-transform infrared spectroscopy, and mass spectrometry. The antimicrobial susceptibility of the [Pd(BAPP)][PdCl4] complex against all tested microbial strains was lower than that of the BAPP ligand except for C. albicans. The cytotoxic impacts of the BAPP ligand and its [Pd(BAPP)][PdCl4] complex were evaluated in vitro for HepG2, CaCo-2 and MCF7 cell lines as well as the WI-38 normal cell line. The anticancer activity was markedly improved by the complexation. The [Pd(BAPP)][PdCl4] complex could selectively inhibit the tested cancer cells in a safe way to the non-tumorigenic cell (WI-38). From the DNA binding studies with ultraviolet-visible spectrophotometry, the [Pd(BAPP)][PdCl4] complex interacts more efficiently with the calf thymus DNA than its BAPP ligand through the intercalative binding mode. In the absence of an external reductant, the [Pd(BAPP)][PdCl4] complex cleaved the intact supercoiled pBR322 DNA under physiological conditions in a concentration-dependent manner. Additionally, electrophoretic experiments were performed in the presence of different radical scavengers, namely DMSO, NaN3 and KI, and ruled out the hydrolytic mechanistic pathway of the reaction and suggested that the oxidative mechanism is the preferred one. The results of the binding affinity of the [Pd(BAPP)][PdCl4] complex to human DNA were modeled using a molecular docking study showing that the complex interacts more strongly with human DNA than the ligand. Finally, an in vitro pharmacokinetic study was assessed through in silico ADME predictions.
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Affiliation(s)
- Mona S Ragab
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt
| | - Mohamed R Shehata
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt
| | - Mohamed M Shoukry
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt
| | - Matti Haukka
- Department of Chemistry, University of Jyväskylä P.O. Box 35 FI-40014 Jyväskylä Finland
| | - Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University Giza Egypt
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4
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Fernández-Fariña S, González-Barcia LM, Romero MJ, García-Tojal J, Maneiro M, Seco JM, Zaragoza G, Martínez-Calvo M, González-Noya AM, Pedrido R. Conversion of a double-tetranuclear cluster silver helicate into a dihelicate via a rare desulfurization process. Inorg Chem Front 2022. [DOI: 10.1039/d1qi01308d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show the first example of a bisthiosemicarbazone silver double-tetranuclear cluster helicate [Ag4L2]2 obtained by electrochemical synthesis which undergoes a rare desulfurization process giving rise to a cationic silver dihelicate [Ag2(H2L)2]SO4.
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Affiliation(s)
- Sandra Fernández-Fariña
- Departamento de Química Inorgánica, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Luis M. González-Barcia
- Departamento de Química Inorgánica, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María J. Romero
- Departamento de Química Inorgánica, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Javier García-Tojal
- Departamento de Química, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Marcelino Maneiro
- Departamento de Química Inorgánica, Facultade de Ciencias, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - José M. Seco
- Departamento de Química Orgánica, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Guillermo Zaragoza
- Unidade de Difracción de Raios X, Edificio CACTUS, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, 15782, Spain
| | - Miguel Martínez-Calvo
- Departamento de Química Inorgánica, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ana M. González-Noya
- Departamento de Química Inorgánica, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rosa Pedrido
- Departamento de Química Inorgánica, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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5
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Takezawa Y, Sakakibara S, Shionoya M. Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting. Chemistry 2021; 27:16626-16633. [PMID: 34623721 DOI: 10.1002/chem.202102977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 11/12/2022]
Abstract
DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, Ubpy -3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand NiII (bpy)3 complex at the junction core (ΔTm =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside Ubpy -2, the degree of the NiII -mediated stabilization observed with Ubpy -3 was comparable to that of Ubpy -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of NiII ions. Furthermore, NiII -mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of NiII (bpy)3 complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shiori Sakakibara
- 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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6
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van der Westhuizen D, Bezuidenhout DI, Munro OQ. Cancer molecular biology and strategies for the design of cytotoxic gold(I) and gold(III) complexes: a tutorial review. Dalton Trans 2021; 50:17413-17437. [PMID: 34693422 DOI: 10.1039/d1dt02783b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This tutorial review highlights key principles underpinning the design of selected metallodrugs to target specific biological macromolecules (DNA and proteins). The review commences with a descriptive overview of the eukaryotic cell cycle and the molecular biology of cancer, particularly apoptosis, which is provided as a necessary foundation for the discovery, design, and targeting of metal-based anticancer agents. Drugs which target DNA have been highlighted and clinically approved metallodrugs discussed. A brief history of the development of mainly gold-based metallodrugs is presented prior to addressing ligand systems for stabilizing and adding functionality to bio-active gold(I) and gold(III) complexes, particularly in the burgeoning field of anticancer metallodrugs. Concepts such as multi-modal and selective cytotoxic agents are covered where necessary for selected compounds. The emerging role of carbenes as the ligand system of choice to achieve these goals for gold-based metallodrug candidates is highlighted prior to closing the review with comments on some future directions that this research field might follow. The latter section ultimately emphasizes the importance of understanding the fate of metal complexes in cells to garner key mechanistic insights.
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Affiliation(s)
- Danielle van der Westhuizen
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Daniela I Bezuidenhout
- Laboratory of Inorganic Chemistry, Environmental and Chemical Engineering, University of Oulu, P. O. Box 3000, 90014 Oulu, Finland.
| | - Orde Q Munro
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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7
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Melidis L, Hill HJ, Coltman NJ, Davies SP, Winczura K, Chauhan T, Craig JS, Garai A, Hooper CAJ, Egan RT, McKeating JA, Hodges NJ, Stamataki Z, Grzechnik P, Hannon MJ. Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:18292-18299. [PMID: 38505190 PMCID: PMC10947172 DOI: 10.1002/ange.202104179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 01/09/2023]
Abstract
The untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with molecular dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5' UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel anti-viral agents.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Harriet J. Hill
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Scott P. Davies
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kinga Winczura
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Tasha Chauhan
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - James S. Craig
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Aditya Garai
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Ross T. Egan
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jane A. McKeating
- Nuffield Department of Medicine & Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI)Oxford UniversityOxfordOX3 7BNUK
| | - Nikolas J. Hodges
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Zania Stamataki
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Pawel Grzechnik
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Michael J. Hannon
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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8
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Melidis L, Hill HJ, Coltman NJ, Davies SP, Winczura K, Chauhan T, Craig JS, Garai A, Hooper CAJ, Egan RT, McKeating JA, Hodges NJ, Stamataki Z, Grzechnik P, Hannon MJ. Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication*. Angew Chem Int Ed Engl 2021; 60:18144-18151. [PMID: 33915014 PMCID: PMC8222931 DOI: 10.1002/anie.202104179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 12/13/2022]
Abstract
The untranslated regions (UTRs) of viral genomes contain a variety of conserved yet dynamic structures crucial for viral replication, providing drug targets for the development of broad spectrum anti-virals. We combine in vitro RNA analysis with molecular dynamics simulations to build the first 3D models of the structure and dynamics of key regions of the 5' UTR of the SARS-CoV-2 genome. Furthermore, we determine the binding of metallo-supramolecular helicates (cylinders) to this RNA structure. These nano-size agents are uniquely able to thread through RNA junctions and we identify their binding to a 3-base bulge and the central cross 4-way junction located in stem loop 5. Finally, we show these RNA-binding cylinders suppress SARS-CoV-2 replication, highlighting their potential as novel anti-viral agents.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Harriet J. Hill
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Scott P. Davies
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kinga Winczura
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Tasha Chauhan
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - James S. Craig
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Aditya Garai
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | | | - Ross T. Egan
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jane A. McKeating
- Nuffield Department of Medicine & Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI)Oxford UniversityOxfordOX3 7BNUK
| | - Nikolas J. Hodges
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Zania Stamataki
- Institute of Immunology and ImmunotherapyUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Pawel Grzechnik
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Michael J. Hannon
- Physical Sciences for Health CentreUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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9
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van der Westhuizen D, Slabber CA, Fernandes MA, Joubert DF, Kleinhans G, van der Westhuizen CJ, Stander A, Munro OQ, Bezuidenhout DI. A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation. Chemistry 2021; 27:8295-8307. [PMID: 33822431 PMCID: PMC8251726 DOI: 10.1002/chem.202100598] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 12/13/2022]
Abstract
The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) AuI -CNC pincer complex suitable for oxidation to the redox-stable [AuIII (CNC)Cl]+ cation. Although the ligand salt and the [AuIII (CNC)Cl]+ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the AuIII complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [AuIII (CNC)Cl]+ complex behaves as a partial DNA intercalator. In silico screening indicated that the [AuIII (CNC)Cl]+ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the AuIII ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.
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Affiliation(s)
| | - Cathryn A. Slabber
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Manuel A. Fernandes
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniël F. Joubert
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - George Kleinhans
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
| | - C. Johan van der Westhuizen
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
- Future Production: ChemicalsPharmaceutical Technologies Research GroupCouncil for Scientific and Industrial Research (CSIR)0184PretoriaSouth Africa
| | - André Stander
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - Orde Q. Munro
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniela I. Bezuidenhout
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Laboratory of Inorganic ChemistryEnvironmental and Chemical EngineeringUniversity of Oulu3000OuluFinland
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10
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Dey N, Haynes CJE. Supramolecular Coordination Complexes as Optical Biosensors. Chempluschem 2021; 86:418-433. [PMID: 33665986 DOI: 10.1002/cplu.202100004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/15/2021] [Indexed: 12/11/2022]
Abstract
In recent years, luminescent supramolecular coordination complexes (SCCs), including 2D-metallacycles and 3D-metallacages have been utilised for biomolecular analysis. Unlike small-molecular probes, the dimensions, size, shape, and flexibility of these complexes can easily be tuned by combining ligands designed with particular geometries, symmetries and denticity with metal ions with strong geometrical binding preferences. The well-defined cavities that result, in combination with the other non-covalent interactions that can be programmed into the ligand design, facilitate great selectivity towards guest binding. In this Review we will discuss the application of luminescent metallacycles and cages in the binding and detection of a wide range of biomolecules, such as carbohydrates, proteins, amino acids, and biogenic amines. We aim to explore the effect of the structural diversity of SCCs on the extent of biomolecular sensing, expressed in terms of sensitivity, selectivity and detection range.
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Affiliation(s)
- Nilanjan Dey
- Graduate School of Science, Kyoto University, Japan
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11
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Gómez-González J, Pérez Y, Sciortino G, Roldan-Martín L, Martínez-Costas J, Maréchal JD, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*. Angew Chem Int Ed Engl 2021; 60:8859-8866. [PMID: 33290612 DOI: 10.1002/anie.202013039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/12/2020] [Indexed: 01/03/2023]
Abstract
Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as FeII and CoII . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled FeII helicate was internalized and selectively stains DNA replication factories in functional cells.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Yolanda Pérez
- NMR Facility, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Lorena Roldan-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
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12
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Gómez‐González J, Pérez Y, Sciortino G, Roldan‐Martín L, Martínez‐Costas J, Maréchal J, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jacobo Gómez‐González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
| | - Yolanda Pérez
- NMR Facility Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Giuseppe Sciortino
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola Spain
- Institute of Chemical Research of Catalonia (ICIQ) Avgda. Països Catalans, 16 43007 Tarragona Spain
| | | | - José Martínez‐Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Bioquímica y Biología Molecular Universidade de Santiago de Compostela Spain
| | | | - Ignacio Alfonso
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Inorgánica Universidade de Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
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13
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Eskandari A, Kundu A, Ghosh S, Suntharalingam K. A Triangular Platinum(II) Multinuclear Complex with Cytotoxicity Towards Breast Cancer Stem Cells. Angew Chem Int Ed Engl 2019; 58:12059-12064. [DOI: 10.1002/anie.201905389] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Arvin Eskandari
- Department of ChemistryKing's College London London SE1 1DB UK
| | - Arunangshu Kundu
- Department of ChemistryGauhati University Guwahati Assam 781014 India
| | - Sushobhan Ghosh
- Department of ChemistryGauhati University Guwahati Assam 781014 India
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14
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Lejault P, Duskova K, Bernhard C, Valverde IE, Romieu A, Monchaud D. The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900870] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Pauline Lejault
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Katerina Duskova
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Claire Bernhard
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Ibai E. Valverde
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - Anthony Romieu
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
| | - David Monchaud
- CNRS UMR6302, Université Bourgogne Franche-Comté (UBFC); Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB); 9, Avenue Alain Savary 21078 Dijon France
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15
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Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
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Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
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16
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Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
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17
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Eskandari A, Kundu A, Ghosh S, Suntharalingam K. A Triangular Platinum(II) Multinuclear Complex with Cytotoxicity Towards Breast Cancer Stem Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Arvin Eskandari
- Department of ChemistryKing's College London London SE1 1DB UK
| | - Arunangshu Kundu
- Department of ChemistryGauhati University Guwahati Assam 781014 India
| | - Sushobhan Ghosh
- Department of ChemistryGauhati University Guwahati Assam 781014 India
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18
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van Rixel VHS, Busemann A, Wissingh MF, Hopkins SL, Siewert B, van de Griend C, Siegler MA, Marzo T, Papi F, Ferraroni M, Gratteri P, Bazzicalupi C, Messori L, Bonnet S. Induction of a Four-Way Junction Structure in the DNA Palindromic Hexanucleotide 5'-d(CGTACG)-3' by a Mononuclear Platinum Complex. Angew Chem Int Ed Engl 2019; 58:9378-9382. [PMID: 31046177 PMCID: PMC6618160 DOI: 10.1002/anie.201814532] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 12/22/2022]
Abstract
Four-way junctions (4WJs) are supramolecular DNA assemblies comprising four interacting DNA strands that in biology are involved in DNA-damage repair. In this study, a new mononuclear platinum(II) complex 1 was prepared that is capable of driving the crystallization of the DNA oligomer 5'-d(CGTACG)-3' specifically into a 4WJ-like motif. In the crystal structure of the 1-CGTACG adduct, the distorted-square-planar platinum complex binds to the core of the 4WJ-like motif through π-π stacking and hydrogen bonding, without forming any platinum-nitrogen coordination bonds. Our observations suggest that the specific molecular properties of the metal complex are crucially responsible for triggering the selective assembly of this peculiar DNA superstructure.
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Affiliation(s)
- Vincent H. S. van Rixel
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Anja Busemann
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Mathijs F. Wissingh
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Samantha L. Hopkins
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Bianka Siewert
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | - Corjan van de Griend
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
| | | | - Tiziano Marzo
- Department of PharmacyUniversity of PisaVia Bonanno Pisano 656126PisaItaly
| | - Francesco Papi
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI)Italy
| | - Marta Ferraroni
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI)Italy
| | - Paola Gratteri
- Department NEUROFARBA—Pharmaceutical and Nutraceutical sectionLaboratory of Molecular Modeling Cheminformatics and QSARUniversity of FlorenceVia Ugo Schiff 650019Sesto Fiorentino (FI)Italy
| | - Carla Bazzicalupi
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI)Italy
| | - Luigi Messori
- Department of Chemistry “Ugo Schiff”University of FlorenceItaly
| | - Sylvestre Bonnet
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 55, PO Box 95022333CCLeidenThe Netherlands
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19
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Guyon L, Pirrotta M, Duskova K, Granzhan A, Teulade-Fichou MP, Monchaud D. TWJ-Screen: an isothermal screening assay to assess ligand/DNA junction interactions in vitro. Nucleic Acids Res 2019; 46:e16. [PMID: 29149299 PMCID: PMC5815093 DOI: 10.1093/nar/gkx1118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
The quest for chemicals able to operate at selected genomic loci in a spatiotemporally controlled manner is desirable to create manageable DNA damages. Mounting evidence now shows that alternative DNA structures, including G-quadruplexes and branched DNA (or DNA junctions), might hamper proper progression of replication fork, thus triggering DNA damages and genomic instability. Therefore, small molecules that stabilize these DNA structures are currently scrutinized as a promising way to create genomic defects that cannot be dealt with properly by cancer cells. While much emphasis has been recently given to G-quadruplexes and related ligands, we report herein on three-way DNA junctions (TWJ) and related ligands. We first highlight the biological implications of TWJ and their strategic relevance as triggers for replicative stress. Then, we describe a new in vitro high-throughput screening assay, TWJ-Screen, which allows for identifying TWJ ligands with both high affinity and selectivity for TWJ over other DNA structures (duplexes and quadruplexes), in a convenient and unbiased manner as demonstrated by the screening of a library of 25 compounds from different chemical families. TWJ-Screen thus represents a reliable mean to uncover molecular tools able to foster replicative stress through an innovative approach, thus providing new strategic opportunities to combat cancers.
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Affiliation(s)
- Ludivine Guyon
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Marc Pirrotta
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Katerina Duskova
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, 91405 Orsay, France
| | | | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
- To whom correspondence should be addressed. Tel: +33 380 399 043; Fax: 33 380 396 117;
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20
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van Rixel VHS, Busemann A, Wissingh MF, Hopkins SL, Siewert B, van de Griend C, Siegler MA, Marzo T, Papi F, Ferraroni M, Gratteri P, Bazzicalupi C, Messori L, Bonnet S. Induction of a Four‐Way Junction Structure in the DNA Palindromic Hexanucleotide 5′‐d(CGTACG)‐3′ by a Mononuclear Platinum Complex. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Vincent H. S. van Rixel
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Anja Busemann
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Mathijs F. Wissingh
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Samantha L. Hopkins
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Bianka Siewert
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | - Corjan van de Griend
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
| | | | - Tiziano Marzo
- Department of PharmacyUniversity of Pisa Via Bonanno Pisano 6 56126 Pisa Italy
| | - Francesco Papi
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Marta Ferraroni
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Paola Gratteri
- Department NEUROFARBA—Pharmaceutical and Nutraceutical sectionLaboratory of Molecular Modeling Cheminformatics and QSARUniversity of Florence Via Ugo Schiff 6 50019 Sesto Fiorentino (FI) Italy
| | - Carla Bazzicalupi
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Luigi Messori
- Department of Chemistry “Ugo Schiff”University of Florence Italy
| | - Sylvestre Bonnet
- Leiden Institute of ChemistryLeiden University Einsteinweg 55, PO Box 9502 2333CC Leiden The Netherlands
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21
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Kellett A, Molphy Z, Slator C, McKee V, Farrell NP. Molecular methods for assessment of non-covalent metallodrug-DNA interactions. Chem Soc Rev 2019; 48:971-988. [PMID: 30714595 PMCID: PMC6657641 DOI: 10.1039/c8cs00157j] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Herein we provide an accessible account of molecular methods to probe inorganic–nucleic acid interactions. Techniques are described using copper(ii) and platinum(ii) complexes prepared in our laboratories.
The binding of small molecule metallodrugs to discrete regions of nucleic acids is an important branch of medicinal chemistry and the nature of these interactions, allied with sequence selectivity, forms part of the backbone of modern medicinal inorganic chemistry research. In this tutorial review we describe a range of molecular methods currently employed within our laboratories to explore novel metallodrug–DNA interactions. At the outset, an introduction to DNA from a structural perspective is provided along with descriptions of non-covalent DNA recognition focusing on intercalation, insertion, and phosphate binding. Molecular methods, described from a non-expert perspective, to identify non-covalent and pre-associative nucleic acid recognition are then demonstrated using a variety of techniques including direct (non-optical) and indirect (optical) methods. Direct methods include: X-ray crystallography; NMR spectroscopy; mass spectrometry; and viscosity while indirect approaches detail: competitive inhibition experiments; fluorescence and absorbance spectroscopy; circular dichroism; and electrophoresis-based techniques. For each method described we provide an overview of the technique, a detailed examination of results obtained and relevant follow-on of advanced biophysical/analytical techniques. To achieve this, a selection of relevant copper(ii) and platinum(ii) complexes developed within our laboratories are discussed and are compared, where possible, to classical DNA binding agents. Applying these molecular methods enables us to determine structure–activity factors important to rational metallodrug design. In many cases, combinations of molecular methods are required to comprehensively elucidate new metallodrug–DNA interactions and, from a drug discovery perspective, coupling this data with cellular responses helps to inform understanding of how metallodrug–DNA binding interactions manifest cytotoxic action.
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Affiliation(s)
- Andrew Kellett
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Zara Molphy
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Creina Slator
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Vickie McKee
- School of Chemical Sciences and the National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland. and Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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22
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Singh K, Kumari S, Jana A, Bhowmick S, Das P, Das N. Self-assembled neutral [2+2] platinacycles showing minimal DNA interactions. Polyhedron 2019. [DOI: 10.1016/j.poly.2018.09.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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24
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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25
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Miron CE, Fleischel O, Petitjean A. To Loop or Not to Loop: Influence of Hinge Flexibility on Self-Assembly Outcomes for Acridine-Based Triazolylpyridine Chelates with Zinc(II), Iron(II), and Copper(II). Chemistry 2018; 24:17318-17326. [PMID: 30252967 DOI: 10.1002/chem.201803732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/05/2018] [Indexed: 11/07/2022]
Abstract
Coordination-driven self-assembly has been established as an effective strategy for the efficient construction of intricate architectures in both natural and artificial systems, for applications ranging from gene regulation to metal-organic frameworks. Central to these systems is the need for carefully designed organic ligands, generally with rigid components, that can undergo self-assembly with metal ions in a predictable manner. Herein, we report the synthesis and study of three novel organic ligands that feature 3,6-disubstituted acridine as a rigid spacer connected to two 2-(1,2,3-triazol-4-yl)pyridine "click" chelates through hinges of the same length but differing flexibility. The flexibility of these "three-atom" hinges was modulated by i) moving from secondary to tertiary amide functional groups and ii) replacing an sp2 amide carbon with an sp3 methylene carbon. In an effort to understand the role of hinge flexibility in directing self-assembly into mononuclear loops or dinuclear cylinders, the impact of these changes on self-assembly outcomes with zinc(II), iron(II), and copper(II) ions is described.
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Affiliation(s)
- Caitlin E Miron
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L3N6, Canada
| | | | - Anne Petitjean
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L3N6, Canada
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26
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Molphy Z, Montagner D, Bhat SS, Slator C, Long C, Erxleben A, Kellett A. A phosphate-targeted dinuclear Cu(II) complex combining major groove binding and oxidative DNA cleavage. Nucleic Acids Res 2018; 46:9918-9931. [PMID: 30239938 PMCID: PMC6212767 DOI: 10.1093/nar/gky806] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/05/2018] [Accepted: 09/05/2018] [Indexed: 12/18/2022] Open
Abstract
Free radical generation is an inevitable consequence of aerobic existence and is implicated in a wide variety of pathological conditions including cancer, cardiovascular disease, ageing and neurodegenerative disorder. Free radicals can, however, be used to our advantage since their production is catalysed by synthetic inorganic molecules-termed artificial metallonucleases-that cut DNA strands by oxidative cleavage reactions. Here, we report the rational design and DNA binding interactions of a novel di-Cu2+ artificial metallonuclease [Cu2(tetra-(2-pyridyl)-NMe-naphthalene)Cl4] (Cu2TPNap). Cu2TPNap is a high-affinity binder of duplex DNA with an apparent binding constant (Kapp) of 107 M(bp)-1. The agent binds non-intercalatively in the major groove causing condensation and G-C specific destabilization. Artificial metallonuclease activity occurs in the absence of exogenous reductant, is dependent on superoxide and hydrogen peroxide, and gives rise to single strand DNA breaks. Pre-associative molecular docking studies with the 8-mer d(GGGGCCCC)2, a model for poly[d(G-C)2], identified selective major groove incorporation of the complex with ancillary Cu2+-phosphate backbone binding. Molecular mechanics methods then showed the d(GGGGCCCC)2 adduct to relax about the complex and this interaction is supported by UV melting experiments where poly[d(G-C)2] is selectively destabilized.
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Affiliation(s)
- Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Diego Montagner
- Department of Chemistry, Maynooth University, Maynooth, Kildare, Ireland
| | - Satish S Bhat
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Conor Long
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Andrea Erxleben
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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27
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Díaz DE, Llanos L, Arce P, Lorca R, Guerrero J, Costamagna J, Aravena D, Ferraudi G, Oliver A, Lappin AG, Lemus L. Steric and Electronic Factors Affecting the Conformation of Bimetallic CuI
Complexes: Effect of the Aliphatic Spacer of Tetracoordinating Schiff-Base Ligands. Chemistry 2018; 24:13839-13849. [DOI: 10.1002/chem.201802290] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Daniel E. Díaz
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
| | - Leonel Llanos
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
| | - Pablo Arce
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
| | - Romina Lorca
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
| | - Juan Guerrero
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
| | - Juan Costamagna
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
| | - Daniel Aravena
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
| | - Guillermo Ferraudi
- Department of Chemistry and Biochemistry; University of Notre Dame; 46556-5670 Notre Dame IN USA
| | - Allen Oliver
- Department of Chemistry and Biochemistry; University of Notre Dame; 46556-5670 Notre Dame IN USA
| | - A. Graham Lappin
- Department of Chemistry and Biochemistry; University of Notre Dame; 46556-5670 Notre Dame IN USA
| | - Luis Lemus
- Facultad de Química y Biología, Departamento de Química de los, Materiales; Universidad de Santiago de Chile; Av. Libertador Bernardo O'Higgins 3363, Estación Central Santiago Chile
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28
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Xue C, Zhang SX, Ouyang CH, Chang D, Salena BJ, Li Y, Wu ZS. Target-Induced Catalytic Assembly of Y-Shaped DNA and Its Application for In Situ Imaging of MicroRNAs. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804741] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Shu-Xin Zhang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Chang-He Ouyang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Dingran Chang
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine; McMaster University; 1280 Main St. W. Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
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29
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Xue C, Zhang SX, Ouyang CH, Chang D, Salena BJ, Li Y, Wu ZS. Target-Induced Catalytic Assembly of Y-Shaped DNA and Its Application for In Situ Imaging of MicroRNAs. Angew Chem Int Ed Engl 2018; 57:9739-9743. [PMID: 29901854 DOI: 10.1002/anie.201804741] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/04/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Shu-Xin Zhang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Chang-He Ouyang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Dingran Chang
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine; McMaster University; 1280 Main St. W. Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
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30
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Baltierra-Jasso LE, Morten MJ, Magennis SW. Sub-Ensemble Monitoring of DNA Strand Displacement Using Multiparameter Single-Molecule FRET. Chemphyschem 2018; 19:551-555. [PMID: 29316151 DOI: 10.1002/cphc.201800012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Indexed: 11/09/2022]
Abstract
Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here, we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of 10 m-1 s-1 . We also followed the displacement from a DNA three-way junction (3WJ) by ssDNA. The presence of three internal mismatched bases in the middle of the invading strand did not prevent displacement from the 3WJ, but reduced the second-order rate constant by about 50 %. We attribute strand exchange in the dsDNA and 3WJ to a zero-toehold pathway from the blunt-ended duplex arms. The single-molecule approach demonstrated here will be useful for studying complex DNA networks.
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Affiliation(s)
- Laura E Baltierra-Jasso
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Michael J Morten
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Steven W Magennis
- WestCHEM School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
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31
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Yang Z, Chen Y, Li G, Tian Z, Zhao L, Wu X, Ma Q, Liu M, Yang P. Supramolecular Recognition of Three Way Junction DNA by a Cationic Calix[3]carbazole. Chemistry 2018; 24:6087-6093. [PMID: 29315943 DOI: 10.1002/chem.201705564] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Indexed: 12/31/2022]
Abstract
DNA three-way junctions (TWJ-DNA) are intermediate structures in DNA replication and/or recombination. They play very important roles in biological processes, but more subtle functions are still unknown due partially to the lack of a fluorescent ligand. In this study, a cationic calix[3]carbazole (2) has been synthesized and its properties of interacting with TWJ-DNA have been evaluated by UV/Vis and fluorescence spectroscopy, circular dichroism (CD), gel electrophoresis, and 1 H NMR studies. The results show that 2 binds to the central hydrophobic cavity of TWJ-DNA. Moreover, it could selectively bind to TWJ-DNA over duplex and quadruplex DNA. Furthermore, 2 possesses the capability of serving as the TWJ-DNA probe as its trap-II excimer emission is turned on by TWJ-DNA.
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Affiliation(s)
- Zhaozheng Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. China
| | - Yan Chen
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. China
| | - Gang Li
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University), Ministry of Education, Shenyang, 110016, P. R. China
| | - Zhangmin Tian
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. China
| | - Liang Zhao
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. China
| | - Xi Wu
- Shenzhen Institute for Drug Control, Shenzhen, 518057, P. R. China
| | - Qi Ma
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University), Ministry of Education, Shenyang, 110016, P. R. China
| | - Mingzhe Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University), Ministry of Education, Shenyang, 110016, P. R. China
| | - Peng Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. China
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32
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Boga S, Bouzada D, García Peña D, Vázquez López M, Vázquez ME. Sequence-Specific DNA Recognition with Designed Peptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Boga
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Diego García Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Inorgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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33
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Fu Y, Romero MJ, Salassa L, Cheng X, Habtemariam A, Clarkson GJ, Prokes I, Rodger A, Costantini G, Sadler PJ. Os2 -Os4 Switch Controls DNA Knotting and Anticancer Activity. Angew Chem Int Ed Engl 2016; 55:8909-12. [PMID: 27240103 PMCID: PMC4982093 DOI: 10.1002/anie.201602995] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/01/2016] [Indexed: 12/19/2022]
Abstract
Dinuclear trihydroxido‐bridged osmium–arene complexes are inert and biologically inactive, but we show here that linking dihydroxido‐bridged OsII–arene fragments by a bridging di‐imine to form a metallacycle framework results in strong antiproliferative activity towards cancer cells and distinctive knotting of DNA. The shortened spacer length reduces biological activity and stability in solution towards decomposition to biologically inactive dimers. Significant differences in behavior toward plasmid DNA condensation are correlated with biological activity.
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Affiliation(s)
- Ying Fu
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Laboratory of Molecular Biology, Center for Cancer Research, NCI, Building 37, Room 5011, Bethesda, MD, 20892-4264, USA
| | - María J Romero
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Departamento de Química Inorgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Luca Salassa
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,CIC biomaGUNE, Paseo de Miramón 182, 20009, Donostia-San Sebastián, Spain
| | - Xi Cheng
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Guy J Clarkson
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Ivan Prokes
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Peter J Sadler
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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34
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Fu Y, Romero MJ, Salassa L, Cheng X, Habtemariam A, Clarkson GJ, Prokes I, Rodger A, Costantini G, Sadler PJ. Os2-Os4Switch Controls DNA Knotting and Anticancer Activity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ying Fu
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
- Laboratory of Molecular Biology; Center for Cancer Research, NCI; Building 37, Room 5011 Bethesda MD 20892-4264 USA
| | - María J. Romero
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
- Departamento de Química Inorgánica; Facultade de Química; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Luca Salassa
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
- CIC biomaGUNE; Paseo de Miramón 182 20009 Donostia-San Sebastián Spain
| | - Xi Cheng
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
| | | | - Guy J. Clarkson
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
| | - Ivan Prokes
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
| | - Alison Rodger
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
| | | | - Peter J. Sadler
- Department of Chemistry; University of Warwick; Coventry CV4 7AL UK
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35
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Ayhan MM, Casano G, Karoui H, Rockenbauer A, Monnier V, Hardy M, Tordo P, Bardelang D, Ouari O. EPR Studies of the Binding Properties, Guest Dynamics, and Inner-Space Dimensions of a Water-Soluble Resorcinarene Capsule. Chemistry 2015; 21:16404-10. [PMID: 26403999 DOI: 10.1002/chem.201502212] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 12/11/2022]
Abstract
Nitroxide free radicals have been used to study the inner space of one of Rebek's water-soluble capsules. EPR and (1) H NMR spectroscopy, ESI-MS, and DFT calculations showed a preference for the formation of 1:2 complexes. EPR titrations allowed us to determine binding constants (Ka ) in the order of 10(7) M(-2) . EPR spectral-shape analysis provided information on the guest rotational dynamics within the capsule. The interplay between optimum hydrogen bonding upon capsule formation and steric strain for guest accommodation highlights some degree of flexibility for guest inclusion, particularly at the center of the capsule where the hydrogen bond seam can be barely distorted or slightly disturbed.
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Affiliation(s)
- Mehmet Menaf Ayhan
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille (France).,Department of Chemistry, Gebze Technical University, P.K.:141, 41400 Gebze, Kocaeli (Turkey)
| | - Gilles Casano
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille (France)
| | - Hakim Karoui
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille (France)
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences and, Department of Physics, Budapest University of Technology and Economics, Budafoki ut 8, 1111 Budapest (Hungary)
| | - Valérie Monnier
- Aix-Marseille Université, CNRS, Spectropole, FR 1739, 13013 Marseille (France)
| | - Micaël Hardy
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille (France)
| | - Paul Tordo
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille (France)
| | - David Bardelang
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille (France)
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13013 Marseille (France).
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36
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Chen F, Fan C, Zhao Y. Inhibitory impact of 3'-terminal 2'-O-methylated small silencing RNA on target-primed polymerization and unbiased amplified quantification of the RNA in Arabidopsis thaliana. Anal Chem 2015; 87:8758-64. [PMID: 26244621 DOI: 10.1021/acs.analchem.5b01683] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
3'-terminal 2'-O-methylation has been found in several kinds of small silencing RNA, regarded as a protective mechanism against enzymatic 3' → 5' degradation and 3'-end uridylation. The influence of this modification on enzymatic polymerization, however, remains unknown. Herein, a systematic investigation is performed to explore this issue. We found these methylated small RNAs exhibited a suppression behavior in target-primed polymerization, revealing biased result for the manipulation of these small RNAs by conventional polymerization-based methodology. The related potential mechanism is investigated and discussed, which is probably ascribed to the big size of modified group and its close location to 3'-OH. Furthermore, two novel solutions each utilizing base-stacking hybridization and three-way junction structure have been proposed to realize unbiased recognition of small RNAs. On the basis of phosphorothioate against nicking, a creative amplified strategy, phosphorothioate-protected polymerization/binicking amplification, has also been developed for the unbiased quantification of methylated small RNA in Arabidopsis thaliana, demonstrating its promising potential for real sample analysis. Collectively, our studies uncover the polymerization inhibition by 3'-terminal 2'-O-methylated small RNAs with mechanistic discussion, and propose novel unbiased solutions for amplified quantification of small RNAs in real sample.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Yuquan Road, Shanghai 201800, P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
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37
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Malina J, Hannon MJ, Brabec V. Iron(II) supramolecular helicates condense plasmid DNA and inhibit vital DNA-related enzymatic activities. Chemistry 2015; 21:11189-95. [PMID: 26103944 DOI: 10.1002/chem.201501307] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 11/06/2022]
Abstract
The dinuclear iron(II) supramolecular helicates [Fe2 L3 ]Cl4 (L=C25 H20 N4 ) bind to DNA through noncovalent (i.e., hydrogen-bonding, electrostatic) interactions and exhibit antimicrobial and anticancer effects. In this study, we show that the helicates condense plasmid DNA with a much higher potency than conventional DNA-condensing agents. Notably, molecules of DNA in the presence of the M enantiomer of [Fe2 L3 ]Cl4 do not form intermolecular aggregates typically formed by other condensing agents, such as spermidine or spermine. The helicates inhibit the activity of several DNA-processing enzymes, such as RNA polymerase, DNA topoisomerase I, deoxyribonuclease I, and site-specific restriction endonucleases. However, the results also indicate that the DNA condensation induced by the helicates does not play a crucial role in these inhibition reactions. The mechanisms for the inhibitory effects of [Fe2 L3 ]Cl4 helicates on DNA-related enzymatic activities have been proposed.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Kralovopolska 135, 612 65 Brno (Czech Republic)
| | - Michael J Hannon
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT (UK)
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Kralovopolska 135, 612 65 Brno (Czech Republic).
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38
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Wu B, Li S, Lei Y, Hu H, de Sousa Amadeu N, Janiak C, Mathieson JS, Long DL, Cronin L, Yang XJ. The effect of the spacer of bis(biurea) ligands on the structure of A2 L3 -type (A=anion) phosphate complexes. Chemistry 2014; 21:2588-93. [PMID: 25504744 DOI: 10.1002/chem.201405235] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 11/08/2022]
Abstract
By tuning the length and rigidity of the spacer of bis(biurea) ligands L, three structural motifs of the A2 L3 complexes (A represents anion, here orthophosphate PO4 (3-) ), namely helicate, mesocate, and mono-bridged motif, have been assembled by coordination of the ligand to phosphate anion. Crystal structure analysis indicated that in the three complexes, each of the phosphate ions is coordinated by twelve hydrogen bonds from six surrounding urea groups. The anion coordination properties in solution have also been studied. The results further demonstrate the coordination behavior of phosphate ion, which shows strong tendency for coordination saturation and geometrical preference, thus allowing for the assembly of novel anion coordination-based structures as in transition-metal complexes.
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Affiliation(s)
- Biao Wu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710069 (P. R. China).
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40
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Mishra A, Chang Lee S, Kaushik N, Cook TR, Choi EH, Kumar Kaushik N, Stang PJ, Chi KW. Self-assembled supramolecular hetero-bimetallacycles for anticancer potency by intracellular release. Chemistry 2014; 20:14410-20. [PMID: 25209962 PMCID: PMC5796531 DOI: 10.1002/chem.201403372] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Indexed: 11/09/2022]
Abstract
Two new tetracationic hetero-bimetallacycles, compounds 4 and 5, have been constructed from an N,N'-bis(4-(pyridin-4-ylethynyl)phenyl)pyridine-2,6-dicarboxamide ligand (1), and cis-blocked complexes [M(dppf)(OTf)2 ] (dppf=1,1'-bis(diphenylphosphino)ferrocene; OTf=trifluoromethanesulfonate; M=Pd (2), Pt (3)) in CH3 NO2 /CH2 Cl2 (1:1) solvent. Both complexes were isolated with adequate yields as triflate salts and were then characterized using (1) H, (13) C, and (31) P NMR spectroscopy, elemental analysis, UV/Vis spectroscopy, and high-resolution electrospray mass spectrometry (HR-ESMS). The molecular structure of 4 was determined by molecular mechanics force-field calculations. The cytotoxic effect of both new complexes were analyzed against T98G (brain tumor), KB (head and neck cancer), SNU-80 (thyroid cancer), and HEK-293 non-malignant cell lines. The cytotoxicity of complexes 4 and 5 were found to be considerably more effective against cancer cells than reference drug cisplatin. Annexin-V/PI staining, caspase-3/7 activity, and the reduction in mitochondrial membrane potential justify a significant level of apoptosis in complex-treated cells.
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Affiliation(s)
- Anurag Mishra
- Department of Chemistry, University of Ulsan, Ulsan 680-749 (Republic of Korea)
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41
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Barros SA, Chenoweth DM. Recognition of nucleic acid junctions using triptycene-based molecules. Angew Chem Int Ed Engl 2014; 53:13746-50. [PMID: 25257803 DOI: 10.1002/anie.201407061] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/09/2014] [Indexed: 12/24/2022]
Abstract
The modulation of nucleic acids by small molecules is an essential process across the kingdoms of life. Targeting nucleic acids with small molecules represents a significant challenge at the forefront of chemical biology. Nucleic acid junctions are ubiquitous structural motifs in nature and in designed materials. Herein, we describe a new class of structure-specific nucleic acid junction stabilizers based on a triptycene scaffold. Triptycenes provide significant stabilization of DNA and RNA three-way junctions, providing a new scaffold for the development of nucleic acid junction binders with enhanced recognition properties. Additionally, we report cytotoxicity and cell uptake data in two human ovarian carcinoma cell lines.
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Affiliation(s)
- Stephanie A Barros
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104 (USA)
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42
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Barros SA, Chenoweth DM. Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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43
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Wu L, Zhao C, Ren J, Qu X. Label-free Electrochemiluminescent Enantioselective Sensor for Distinguishing between Chiral Metallosupramolecular Complexes. Chemistry 2014; 20:11675-9. [DOI: 10.1002/chem.201403481] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Indexed: 02/04/2023]
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44
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Boer DR, Wu L, Lincoln P, Coll M. Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes. Angew Chem Int Ed Engl 2014; 53:1949-52. [DOI: 10.1002/anie.201308070] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/15/2013] [Indexed: 11/07/2022]
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45
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Boer DR, Wu L, Lincoln P, Coll M. Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Cámara V, Masciocchi N, Gil-Rubio J, Vicente J. Triple Helicates with Golden Strands: Self-Assembly of M2Au6Complexes from Gold(I) Metallaligands and Iron(II), Cobalt(II) or Zinc(II) Cations. Chemistry 2013; 20:1389-402. [DOI: 10.1002/chem.201303744] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 11/05/2022]
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47
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Phongtongpasuk S, Paulus S, Schnabl J, Sigel RKO, Spingler B, Hannon MJ, Freisinger E. Binding of a Designed Anti-Cancer Drug to the Central Cavity of an RNA Three-Way Junction. Angew Chem Int Ed Engl 2013; 52:11513-6. [DOI: 10.1002/anie.201305079] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Indexed: 11/08/2022]
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Phongtongpasuk S, Paulus S, Schnabl J, Sigel RKO, Spingler B, Hannon MJ, Freisinger E. Binding of a Designed Anti-Cancer Drug to the Central Cavity of an RNA Three-Way Junction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bilbeisi RA, Zarra S, Feltham HLC, Jameson GNL, Clegg JK, Brooker S, Nitschke JR. Guest Binding Subtly Influences Spin Crossover in an FeII4L4Capsule. Chemistry 2013; 19:8058-62. [DOI: 10.1002/chem.201300805] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 11/08/2022]
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Duprey JLHA, Takezawa Y, Shionoya M. Metal-locked DNA three-way junction. Angew Chem Int Ed Engl 2012; 52:1212-6. [PMID: 23238966 DOI: 10.1002/anie.201207338] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Indexed: 02/04/2023]
Affiliation(s)
- Jean-Louis H A Duprey
- 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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