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Wu ZH, Zhu X, Yang Q, Zagranyarski Y, Mishra K, Strickfaden H, Wong RP, Basché T, Koynov K, Bonn M, Li C, Liu X, Müllen K. Near-Infrared Perylenecarboximide Fluorophores for Live-Cell Super-Resolution Imaging. J Am Chem Soc 2024; 146:7135-7139. [PMID: 38441879 PMCID: PMC10958508 DOI: 10.1021/jacs.3c13368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Organic near-infrared (NIR) photoblinking fluorophores are highly desirable for live-cell super-resolution imaging based on single-molecule localization microscopy (SMLM). Herein we introduce a novel small chromophore, PMIP, through the fusion of perylenecarboximide with 2,2-dimetheylpyrimidine. PMIP exhibits an emission maximum at 732 nm with a high fluorescence quantum yield of 60% in the wavelength range of 700-1000 nm and excellent photoblinking without any additives. With resorcinol-functionalized PMIP (PMIP-OH), NIR SMLM imaging of lysosomes is demonstrated for the first time in living mammalian cells under physiological conditions. Moreover, metabolically labeled nascent DNA is site-specifically detected using azido-functionalized PMIP (PMIP-N3) via click chemistry, thereby enabling the super-resolution imaging of nascent DNA in phosphate-buffered saline with a 9-fold improvement in spatial resolution. These results indicate the potential of PMIP-based NIR blinking fluorophores for biological applications of SMLM.
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Affiliation(s)
- Ze-Hua Wu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Xingfu Zhu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Qiqi Yang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yulian Zagranyarski
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Krishna Mishra
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
| | | | - Ronald P. Wong
- Institute
of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Thomas Basché
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Kaloian Koynov
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Chen Li
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Xiaomin Liu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Klaus Müllen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Chemistry, Johannes Gutenberg-University, 55099 Mainz, Germany
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2
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Alcalde-Ordóñez A, Barreiro-Piñeiro N, McGorman B, Gómez-González J, Bouzada D, Rivadulla F, Vázquez ME, Kellett A, Martínez-Costas J, López MV. A copper(ii) peptide helicate selectively cleaves DNA replication foci in mammalian cells. Chem Sci 2023; 14:14082-14091. [PMID: 38098723 PMCID: PMC10718067 DOI: 10.1039/d3sc03303a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/25/2023] [Indexed: 12/17/2023] Open
Abstract
The use of copper-based artificial nucleases as potential anticancer agents has been hampered by their poor selectivity in the oxidative DNA cleavage process. An alternative strategy to solve this problem is to design systems capable of selectively damaging noncanonical DNA structures that play crucial roles in the cell cycle. We designed an oligocationic CuII peptide helicate that selectively binds and cleaves DNA three-way junctions (3WJs) and induces oxidative DNA damage via a ROS-mediated pathway both in vitro and in cellulo, specifically at DNA replication foci of the cell nucleus, where this DNA structure is transiently generated. To our knowledge, this is the first example of a targeted chemical nuclease that can discriminate with high selectivity 3WJs from other forms of DNA both in vitro and in mammalian cells. Since the DNA replication process is deregulated in cancer cells, this approach may pave the way for the development of a new class of anticancer agents based on copper-based artificial nucleases.
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Affiliation(s)
- Ana Alcalde-Ordóñez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Natalia Barreiro-Piñeiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Bríonna McGorman
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), 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), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Francisco Rivadulla
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Física, Universidade de Santiago de Compostela 15782 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 15782 Santiago de Compostela Spain
| | - Andrew Kellett
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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3
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Gibney A, de Paiva REF, Singh V, Fox R, Thompson D, Hennessy J, Slator C, McKenzie CJ, Johansson P, McKee V, Westerlund F, Kellett A. A Click Chemistry-Based Artificial Metallo-Nuclease. Angew Chem Int Ed Engl 2023; 62:e202305759. [PMID: 37338105 DOI: 10.1002/anie.202305759] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023]
Abstract
Artificial metallo-nucleases (AMNs) are promising DNA damaging drug candidates. Here, we demonstrate how the 1,2,3-triazole linker produced by the Cu-catalysed azide-alkyne cycloaddition (CuAAC) reaction can be directed to build Cu-binding AMN scaffolds. We selected biologically inert reaction partners tris(azidomethyl)mesitylene and ethynyl-thiophene to develop TC-Thio, a bioactive C3 -symmetric ligand in which three thiophene-triazole moieties are positioned around a central mesitylene core. The ligand was characterised by X-ray crystallography and forms multinuclear CuII and CuI complexes identified by mass spectrometry and rationalised by density functional theory (DFT). Upon Cu coordination, CuII -TC-Thio becomes a potent DNA binding and cleaving agent. Mechanistic studies reveal DNA recognition occurs exclusively at the minor groove with subsequent oxidative damage promoted through a superoxide- and peroxide-dependent pathway. Single molecule imaging of DNA isolated from peripheral blood mononuclear cells shows that the complex has comparable activity to the clinical drug temozolomide, causing DNA damage that is recognised by a combination of base excision repair (BER) enzymes.
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Affiliation(s)
- Alex Gibney
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Raphael E F de Paiva
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Vandana Singh
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Fox
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Damien Thompson
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, Department of Physics, University of Limerick, Ireland
| | - Joseph Hennessy
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Creina Slator
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Christine J McKenzie
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Pegah Johansson
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Sweden
| | - Vickie McKee
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew Kellett
- SSPC, the, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
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4
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Detinis Zur T, Deek J, Ebenstein Y. Single-molecule approaches for DNA damage detection and repair: A focus on Repair Assisted Damage Detection (RADD). DNA Repair (Amst) 2023; 129:103533. [PMID: 37467630 PMCID: PMC10496029 DOI: 10.1016/j.dnarep.2023.103533] [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: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023]
Abstract
The human genome is continually exposed to various stressors, which can result in DNA damage, mutations, and diseases. Among the different types of DNA damage, single-strand lesions are commonly induced by external stressors and metabolic processes. Accurate detection and quantification of DNA damage are crucial for understanding repair mechanisms, assessing environmental impacts, and evaluating response to therapy. However, traditional techniques have limitations in sensitivity and the ability to detect multiple types of damage. In recent years, single-molecule fluorescence approaches have emerged as powerful tools for precisely localizing and quantifying DNA damage. Repair Assisted Damage Detection (RADD) is a single-molecule technique that employs specific repair enzymes to excise damaged bases and incorporates fluorescently labeled nucleotides to visualize the damage. This technique provides valuable insights into repair efficiency and sequence-specific damage. In this review, we discuss the principles and applications of RADD assays, highlighting their potential for enhancing our understanding of DNA damage and repair processes.
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Affiliation(s)
- Tahir Detinis Zur
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jasline Deek
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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5
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Ahmad MG, Balamurali MM, Chanda K. Click-derived multifunctional metal complexes for diverse applications. Chem Soc Rev 2023; 52:5051-5087. [PMID: 37431583 DOI: 10.1039/d3cs00343d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The Click reaction that involves Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) serves as the most potent and highly dependable tool for the development of many complex architectures. It has paved the way for the synthesis of numerous drug molecules with enhanced synthetic flexibility, reliability, specificity and modularity. It is all about bringing two different molecular entities together to achieve the required molecular properties. The utilization of Click chemistry has been well demonstrated in organic synthesis, particularly in reactions that involve biocompatible precursors. In pharmaceutical research, Click chemistry is extensively utilized for drug delivery applications. The exhibited bio-compatibility and dormancy towards other biological components under cellular environments makes Click chemistry an identified boon in bio-medical research. In this review, various click-derived transition metal complexes are discussed in terms of their applications and uniqueness. The scope of this chemistry towards other streams of applied sciences is also discussed.
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Affiliation(s)
- Md Gulzar Ahmad
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
| | - M M Balamurali
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai 600127, Tamilnadu, India.
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
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6
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Singh V, Johansson P, Ekedahl E, Lin YL, Hammarsten O, Westerlund F. Quantification of single-strand DNA lesions caused by the topoisomerase II poison etoposide using single DNA molecule imaging. Biochem Biophys Res Commun 2022; 594:57-62. [DOI: 10.1016/j.bbrc.2022.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/11/2022] [Indexed: 11/02/2022]
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7
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Banasiak A, Zuin Fantoni N, Kellett A, Colleran J. Mapping the DNA Damaging Effects of Polypyridyl Copper Complexes with DNA Electrochemical Biosensors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030645. [PMID: 35163909 PMCID: PMC8838702 DOI: 10.3390/molecules27030645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/18/2021] [Accepted: 01/01/2022] [Indexed: 12/22/2022]
Abstract
Several classes of copper complexes are known to induce oxidative DNA damage that mediates cell death. These compounds are potentially useful anticancer agents and detailed investigation can reveal the mode of DNA interaction, binding strength, and type of oxidative lesion formed. We recently reported the development of a DNA electrochemical biosensor employed to quantify the DNA cleavage activity of the well-studied [Cu(phen)2]2+ chemical nuclease. However, to validate the broader compatibility of this sensor for use with more diverse—and biologically compatible—copper complexes, and to probe its use from a drug discovery perspective, analysis involving new compound libraries is required. Here, we report on the DNA binding and quantitative cleavage activity of the [Cu(TPMA)(N,N)]2+ class (where TPMA = tris-2-pyridylmethylamine) using a DNA electrochemical biosensor. TPMA is a tripodal copper caging ligand, while N,N represents a bidentate planar phenanthrene ligand capable of enhancing DNA interactions through intercalation. All complexes exhibited electroactivity and interact with DNA through partial (or semi-) intercalation but predominantly through electrostatic attraction. Although TPMA provides excellent solution stability, the bulky ligand enforces a non-planar geometry on the complex, which sterically impedes full interaction. [Cu(TPMA)(phen)]2+ and [Cu(TPMA)(DPQ)]2+ cleaved 39% and 48% of the DNA strands from the biosensor surface, respectively, while complexes [Cu(TPMA)(bipy)]2+ and [Cu(TPMA)(PD)]2+ exhibit comparatively moderate nuclease efficacy (ca. 26%). Comparing the nuclease activities of [Cu(TPMA)(phen)] 2+ and [Cu(phen)2]2+ (ca. 23%) confirms the presence of TPMA significantly enhances chemical nuclease activity. Therefore, the use of this DNA electrochemical biosensor is compatible with copper(II) polypyridyl complexes and reveals TPMA complexes as a promising class of DNA damaging agent with tuneable activity due to coordinated ancillary phenanthrene ligands.
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Affiliation(s)
- Anna Banasiak
- Applied Electrochemistry Group, FOCAS Institute, Technological University Dublin, Camden Row, Dublin 8, D08 CKP1 Dublin, Ireland;
| | - Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK;
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, D09 NR58 Dublin, Ireland
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, D09 NR58 Dublin, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, D09 NR58 Dublin, Ireland
- Correspondence: (A.K.); (J.C.); Tel.: +353-1-700-5461 (A.K.); +353-1-220-5562 (J.C.)
| | - John Colleran
- Applied Electrochemistry Group, FOCAS Institute, Technological University Dublin, Camden Row, Dublin 8, D08 CKP1 Dublin, Ireland;
- Central Quad Grangegorman, School of Chemical and Pharmaceutical Sciences, Technological University Dublin, Dublin 7, D07 H6K8 Dublin, Ireland
- Correspondence: (A.K.); (J.C.); Tel.: +353-1-700-5461 (A.K.); +353-1-220-5562 (J.C.)
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8
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Copper(II) and silver(I)-1,10-phenanthroline-5,6-dione complexes interact with double-stranded DNA: further evidence of their apparent multi-modal activity towards Pseudomonas aeruginosa. J Biol Inorg Chem 2022; 27:201-213. [PMID: 35006347 PMCID: PMC8840922 DOI: 10.1007/s00775-021-01922-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/13/2021] [Indexed: 01/04/2023]
Abstract
Tackling microbial resistance requires continuous efforts for the development of new molecules with novel mechanisms of action and potent antimicrobial activity. Our group has previously identified metal-based compounds, [Ag(1,10-phenanthroline-5,6-dione)2]ClO4 (Ag-phendione) and [Cu(1,10-phenanthroline-5,6-dione)3](ClO4)2.4H2O (Cu-phendione), with efficient antimicrobial action against multidrug-resistant species. Herein, we investigated the ability of Ag-phendione and Cu-phendione to bind with double-stranded DNA using a combination of in silico and in vitro approaches. Molecular docking revealed that both phendione derivatives can interact with the DNA by hydrogen bonding, hydrophobic and electrostatic interactions. Cu-phendione exhibited the highest binding affinity to either major (− 7.9 kcal/mol) or minor (− 7.2 kcal/mol) DNA grooves. In vitro competitive quenching assays involving duplex DNA with Hoechst 33258 or ethidium bromide demonstrated that Ag-phendione and Cu-phendione preferentially bind DNA in the minor grooves. The competitive ethidium bromide displacement technique revealed Cu-phendione has a higher binding affinity to DNA (Kapp = 2.55 × 106 M−1) than Ag-phendione (Kapp = 2.79 × 105 M−1) and phendione (Kapp = 1.33 × 105 M−1). Cu-phendione induced topoisomerase I-mediated DNA relaxation of supercoiled plasmid DNA. Moreover, Cu-phendione was able to induce oxidative DNA injuries with the addition of free radical scavengers inhibiting DNA damage. Ag-phendione and Cu-phendione avidly displaced propidium iodide bound to DNA in permeabilized Pseudomonas aeruginosa cells in a dose-dependent manner as judged by flow cytometry. The treatment of P. aeruginosa with bactericidal concentrations of Cu-phendione (15 µM) induced DNA fragmentation as visualized by either agarose gel or TUNEL assays. Altogether, these results highlight a possible novel DNA-targeted mechanism by which phendione-containing complexes, in part, elicit toxicity toward the multidrug-resistant pathogen P. aeruginosa.
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