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Nakano E, Takeuchi S, Ono R, Tsujimoto M, Masaki T, Nishigori C. Xeroderma Pigmentosum Diagnosis Using a Flow Cytometry-Based Nucleotide Excision Repair Assay. J Invest Dermatol 2017; 138:467-470. [PMID: 29024689 DOI: 10.1016/j.jid.2017.08.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/16/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Eiji Nakano
- Department of Dermatology, the Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Seiji Takeuchi
- Department of Dermatology, the Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Ryusuke Ono
- Department of Dermatology, the Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Mariko Tsujimoto
- Department of Dermatology, the Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Taro Masaki
- Department of Dermatology, the Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Chikako Nishigori
- Department of Dermatology, the Graduate School of Medicine, Kobe University, Kobe, Japan.
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Jia N, Nakazawa Y, Guo C, Shimada M, Sethi M, Takahashi Y, Ueda H, Nagayama Y, Ogi T. A rapid, comprehensive system for assaying DNA repair activity and cytotoxic effects of DNA-damaging reagents. Nat Protoc 2014; 10:12-24. [PMID: 25474029 DOI: 10.1038/nprot.2014.194] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA repair systems protect cells from genomic instability and carcinogenesis. Therefore, assays for measuring DNA repair activity are valuable, not only for clinical diagnoses of DNA repair deficiency disorders but also for basic research and anticancer drug development. Two commonly used assays are UDS (unscheduled DNA synthesis, requiring a precise measurement of an extremely small amount of repair DNA synthesis) and RRS (recovery of RNA synthesis after DNA damage). Both UDS and RRS are major endpoints for assessing the activity of nucleotide excision repair (NER), the most versatile DNA repair process. Conventional UDS and RRS assays are laborious and time-consuming, as they measure the incorporation of radiolabeled nucleosides associated with NER. Here we describe a comprehensive protocol for monitoring nonradioactive UDS and RRS by studying the incorporation of alkyne-conjugated nucleoside analogs followed by a fluorescent azide-coupling click-chemistry reaction. The system is also suitable for quick measurement of cell sensitivity to DNA-damaging reagents and for lentivirus-based complementation assays, which can be used to systematically determine the pathogenic genes associated with DNA repair deficiency disorders. A typical UDS or RRS assay using primary fibroblasts, including a virus complementation test, takes 1 week to complete.
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Affiliation(s)
- Nan Jia
- 1] Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan. [2] Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki University, Nagasaki, Japan. [3] Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Yuka Nakazawa
- 1] Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki University, Nagasaki, Japan. [2] Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Chaowan Guo
- 1] Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki University, Nagasaki, Japan. [2] Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Mayuko Shimada
- 1] Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki University, Nagasaki, Japan. [2] Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Mieran Sethi
- St. John's Institute of Dermatology, Guy's and St. Thomas' Hospital, London, UK
| | - Yoshito Takahashi
- Innovative Beauty Science Laboratory, Kanebo Cosmetics Inc., Odawara, Japan
| | - Hiroshi Ueda
- Department of Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yuji Nagayama
- Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Tomoo Ogi
- 1] Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki University, Nagasaki, Japan. [2] Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. [3] Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Japan
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Hasegawa M, Iwai S, Kuraoka I. A non-isotopic assay uses bromouridine and RNA synthesis to detect DNA damage responses. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2010; 699:62-6. [DOI: 10.1016/j.mrgentox.2010.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/20/2010] [Accepted: 04/07/2010] [Indexed: 10/19/2022]
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Nakazawa Y, Yamashita S, Lehmann AR, Ogi T. A semi-automated non-radioactive system for measuring recovery of RNA synthesis and unscheduled DNA synthesis using ethynyluracil derivatives. DNA Repair (Amst) 2010; 9:506-16. [PMID: 20171149 DOI: 10.1016/j.dnarep.2010.01.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 01/22/2010] [Accepted: 01/23/2010] [Indexed: 01/03/2023]
Abstract
Nucleotide excision repair (NER) removes the major UV-photolesions from cellular DNA. In humans, compromised NER activity is the cause of several photosensitive diseases, one of which is the skin-cancer predisposition disorder, xeroderma pigmentosum (XP). Two assays commonly used in measurement of NER activity are 'unscheduled DNA synthesis (UDS)', and 'recovery of RNA synthesis (RRS)', the latter being a specific measure of the transcription-coupled repair sub-pathway of NER. Both assays are key techniques for research in NER as well as in diagnoses of NER-related disorders. Until very recently, reliable methods for these assays involved measurements of incorporation of radio-labeled nucleosides. We have established non-radioactive procedures for determining UDS and RRS levels by incorporation of recently developed alkyne-conjugated nucleoside analogues, 5-ethynyl-2'-deoxyuridine (EdU) and 5-ethynyuridine (EU). EdU and EU are respectively used as alternatives for (3)H-thymidine in UDS and for (3)H-uridine in RRS. Based on these alkyne-nucleosides and an integrated image analyser, we have developed a semi-automated assay system for NER-activity. We demonstrate the utility of this system for NER-activity assessments of lymphoblastoid samples as well as primary fibroblasts. Potential use of the system for large-scale siRNA-screening for novel NER defects as well as for routine XP diagnosis are also considered.
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Affiliation(s)
- Yuka Nakazawa
- Department of Molecular Medicine, Atomic Bomb Disease Institute, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
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