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Abstract
The comet assay is an effective method for identifying DNA breaks and alkali-labile sites induced by genotoxins. Performed as a single-cell electrophoresis, this assay is especially simplistic, and the results are easily reproducible. DNA breakage can be quantitatively assessed by the induced comet tail regions, which can be measured using a variety of comet software. This protocol will finish within approximately two hours with adequate preparation, and digitized images can be taken using a confocal or standard fluorescence microscopes after staining the cell nucleus with a DNA dye.
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Affiliation(s)
- Kade D Walsh
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Takamitsu A Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
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Castro C, Carvalho A, Gaivão I, Lima-Brito J. Evaluation of copper-induced DNA damage in Vitis vinifera L. using Comet-FISH. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:6600-6610. [PMID: 33006094 DOI: 10.1007/s11356-020-10995-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The contamination of soils and water with copper (Cu) can compromise the crops production and quality. Fungicides containing Cu are widely and intensively used in viticulture contributing to environmental contamination and genotoxicity in Vitis vinifera L. Despite the difficulty in reproducing field conditions in the laboratory, hydroponic solutions enriched with Cu (1, 10, 25 and 50 μM) were used in forced V. vinifera cuttings to evaluate the DNA damage in leaves of four wine-producing varieties ('Tinta Barroca', 'Tinto Cão', 'Malvasia Fina' and 'Viosinho'). Alkaline comet assay followed by fluorescence in situ hybridisation (Comet-FISH) was performed with the 45S ribosomal DNA (rDNA) and telomeric [(TTTAGGG)n] sequences as probes. This study aimed to evaluate the tolerance of the four varieties to different concentrations of Cu and to determine which genomic regions were more prone to DNA damage. The comet assay revealed comets of categories 0 to 4 in all varieties. The DNA damage increased significantly (p < 0.001) with the Cu concentration. 'Tinto Cão' appeared to be the most sensitive variety because it had the highest DNA damage increase in 50 μM Cu relative to the control. Comet-FISH was only performed on slides of the control and 50 μM Cu treatments. Comets of all varieties treated with 50 μM Cu showed rDNA hybridisation on the head, 'halo' and tail (category III), and their frequency was significantly higher than that of control. The frequency of category III comets hybridised with the telomeric probe was only significantly different from the control in 'Malvasia Fina' and 'Tinta Barroca'. Comet-FISH revealed partial damage on rDNA and telomeric DNA in response to Cu but also in control, confirming the high sensitivity of these genomic regions to DNA fragmentation.
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Affiliation(s)
- Cláudia Castro
- Biosystems & Integrative Sciences Institute-University of Tras-os-Montes and Alto Douro (BioISI-UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Ana Carvalho
- Biosystems & Integrative Sciences Institute-University of Tras-os-Montes and Alto Douro (BioISI-UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal.
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Tras-os-Montes and Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal.
- Department of Genetics and Biotechnology, Blocos Laboratoriais, A1.09, University of Tras-os-Montes and Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal.
| | - Isabel Gaivão
- Department of Genetics and Biotechnology, Blocos Laboratoriais, A1.09, University of Tras-os-Montes and Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
- Animal and Veterinary Research Centre (CECAV), University of Tras-os-Montes and Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - José Lima-Brito
- Biosystems & Integrative Sciences Institute-University of Tras-os-Montes and Alto Douro (BioISI-UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Tras-os-Montes and Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
- Department of Genetics and Biotechnology, Blocos Laboratoriais, A1.09, University of Tras-os-Montes and Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
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Abstract
The genome integrity of living organisms is constantly threatened by endogenous cellular metabolic processes and environmental agents. To quantify these low, physiologically relevant levels of DNA damage, a single-cell gel electrophoresis (comet) combined with strand-specific fluorescence in situ hybridization (FISH)-based approach has been developed. This approach enables the quantification of low levels of specific DNA lesions in each strand of the selected sequence at the single-molecule sensitivity, as well as in the genome overall in single cells. In this method, the percentage of DNA in the comet tail is used to quantify lesions in the genome overall. Lesions in the respective strands of the designated sequence are analyzed using strand-specific FISH probes. These probes targeting the 3' and 5' termini of the selected sequence are conjugated with two distinct fluorophores. Following the comet-FISH assay, the two termini of the designated sequence are visualized as two spots with different colors, under a fluorescence microscope. Separated spots indicate a damage strand, while adjacent or colocalized spots imply an intact strand. Any DNA lesions or DNA modifications, which can be converted into strand breaks enzymatically or chemically, can be quantified by this method. The comet-FISH approach described here can be applied to the study of the molecular mechanisms of various repair pathways, as well as in drug screening to develop inhibitors for specific repair pathways.
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Koppen G, Azqueta A, Pourrut B, Brunborg G, Collins AR, Langie SAS. The next three decades of the comet assay: a report of the 11th International Comet Assay Workshop. Mutagenesis 2017; 32:397-408. [DOI: 10.1093/mutage/gex002] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gudrun Koppen
- Environmental Risk and Health unit, Flemish Institute of Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium,
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, and IdiSNA, Navarra Institute for Health Research, C/Irunlarrea 1, 31009 Pamplona, Spain,
| | - Bertrand Pourrut
- ISA Lille – LGCgE, University of Lille Nord de France, 48 boulevard Vauban, 59046 Lille, France,
| | - Gunnar Brunborg
- Department of Molecular Biology, Norwegian Institute of Public Health, PO Box 4404 Nydalen, Oslo, Norway and
| | - Andrew R. Collins
- Department of Nutrition, University of Oslo, PB 1046 Blindern, Oslo, Norway
| | - Sabine A. S. Langie
- Environmental Risk and Health unit, Flemish Institute of Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium,
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Araldi RP, de Melo TC, Mendes TB, de Sá Júnior PL, Nozima BHN, Ito ET, de Carvalho RF, de Souza EB, de Cassia Stocco R. Using the comet and micronucleus assays for genotoxicity studies: A review. Biomed Pharmacother 2015; 72:74-82. [DOI: 10.1016/j.biopha.2015.04.004] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/03/2015] [Indexed: 12/20/2022] Open
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