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Akamatsu K, Satoh K, Shikazono N, Saito T. Proximity Estimation and Quantification of Ionizing Radiation-induced DNA Lesions in Aqueous Media using Fluorescence Spectroscopy. Radiat Res 2024; 201:150-159. [PMID: 38155317 DOI: 10.1667/rade-23-00145.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/12/2023] [Indexed: 12/30/2023]
Abstract
Clustered DNA damage (cluster) or a multiply damaged site, which is a region with two or more lesions within one or two helical turns, has a high mutagenic potential and causes cell death. We quantified fluorophore-labeled lesions and estimated their proximity through fluorescence anisotropy measurements depending on Förster resonance energy transfer (FRET) among the fluorophores close to each other. pUC19 plasmid DNA (2,686 base pairs) dissolved in water or 0.2 M Tris-HCl buffer at a concentration of 10 μg/μL was irradiated by several ionizing radiations with varying linear energy transfers (LET, 0.2-1890 keV/μm). Electrophilic carbonyls (aldehydes and ketones) at abasic sites (APs) produced in DNA were labeled with Alexa Fluor 488 fluorescent dyes with an O-amino functional group. Regardless of the presence or absence of the buffer, AP yields (the number of APs/base pair/Gy) tended to decrease with increasing LET, and the ratio of the AP yield (in 0.2 M Tris-HCl/in water) was less than 0.1 in the LET range of 0.2-200 keV/μm. However, in a higher LET range, the ratios were greater than 0.1. At a low dose, fluorescence anisotropy decreased with increasing LET in 0.2 M Tris-HCl, whereas, in water, this LET dependence was almost insignificant. These findings suggest that 1. the damage distribution on a DNA molecule formed by indirect effects (e.g., by hydroxyl radicals) does not depend on radiation quality and 2. greater LET radiation is more likely to produce a cluster and/or to produce a cluster with shorter distances between lesions by direct effects. This FRET-based proximity estimation of DNA lesions will contribute not only to the identification of clusters and their complexity in a whole genome, but also to the study of their repair mechanism by single-molecular level fluorescence microscopy.
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Affiliation(s)
- Ken Akamatsu
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Katsuya Satoh
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Naoya Shikazono
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Takeshi Saito
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan, Osaka 590-0494, Japan
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Formation of clustered DNA damage in vivo upon irradiation with ionizing radiation: Visualization and analysis with atomic force microscopy. Proc Natl Acad Sci U S A 2022; 119:e2119132119. [PMID: 35324325 PMCID: PMC9060515 DOI: 10.1073/pnas.2119132119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA damage causes loss of or alterations in genetic information, resulting in cell death or mutations. Ionizing radiations produce local, multiple DNA damage sites called clustered DNA damage. In this study, a complete protocol was established to analyze the damage complexity of clustered DNA damage, wherein damage-containing genomic DNA fragments were selectively concentrated via pulldown, and clustered DNA damage was visualized by atomic force microscopy. It was found that X-rays and Fe ion beams caused clustered DNA damage. Fe ion beams also produced clustered DNA damage with high complexity. Fe ion beam–induced complex DNA double-strand breaks (DSBs) containing one or more base lesion(s) near the DSB end were refractory to repair, implying their lethal effects. Clustered DNA damage is related to the biological effects of ionizing radiation. However, its precise yield and complexity (i.e., number of lesions per damaged site) in vivo remain unknown. To better understand the consequences of clustered DNA damage, a method was established to evaluate its yield and complexity in irradiated cells by atomic force microscopy. This was achieved by isolating and concentrating damaged DNA fragments from purified genomic DNA. It was found that X-rays and Fe ion beams caused clustered DNA damage in human TK6 cells, whereas Fenton's reagents did it less efficiently, highlighting clustered DNA damage as a signature of ionizing radiation. Moreover, Fe ion beams produced clustered DNA damage with high complexity. Remarkably, Fe ion beam–induced complex DNA double-strand breaks (DSBs) containing one or more base lesion(s) near the DSB end were refractory to repair, implying the lethal effect of complex DSBs.
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Akamatsu K, Shikazono N, Saito T. Fluorescence anisotropy study of radiation-induced DNA damage clustering based on FRET. Anal Bioanal Chem 2020; 413:1185-1192. [PMID: 33245399 DOI: 10.1007/s00216-020-03082-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/01/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022]
Abstract
A clustered DNA damage site (cluster), in which two or more lesions exist within a few helical turns, is believed to be a key factor determining the fate of a living cell exposed to a DNA damaging agent such as ionizing radiation. However, the structural details of a cluster such as the number of included lesions and their proximity are unknown. Herein, we develop a method to characterize a cluster by fluorescence anisotropy measurements based on Förster resonance energy transfer (homo-FRET). Plasmid DNA (pUC19) was irradiated with 2.0 and 0.52 MeV/u 4He2+, or 0.37 MeV/u 12C5+ ion beams (linear energy transfer: ~ 70, ~ 150, ~ 760 keV/μm, respectively) and 60Co γ-rays as a standard (~ 0.2 keV/μm) in the solid state. The irradiated DNA was labeled with an aminooxyl fluorophore (Alexa Fluor 488) to the aldehyde/ketone moieties such as apurinic/apyrimidinic sites. Homo-FRET analyses provided the apparent base separation values between lesions in a cluster produced by each ion beam track as 21.1, 19.4, and 18.7 base pairs. The production frequency of a cluster increases with increasing linear energy transfer of radiation. Our results demonstrate that homo-FRET analysis has the potential to discover the qualitative and the quantitative differences of the clusters produced not only by a variety of ionizing radiation but also by other DNA damaging agents.
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Affiliation(s)
- Ken Akamatsu
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, 619-0215, Kyoto, Japan.
| | - Naoya Shikazono
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, 619-0215, Kyoto, Japan
| | - Takeshi Saito
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan, Osaka, 590-0494, Japan
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Du Y, Hase Y, Satoh K, Shikazono N. Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining. JOURNAL OF RADIATION RESEARCH 2020; 61:639-647. [PMID: 32766789 PMCID: PMC7482170 DOI: 10.1093/jrr/rraa059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/01/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
Abstract
To investigate the involvement of the non-homologous end joining (NHEJ) pathway in plant mutagenesis by ionizing radiation, we conducted a genome-wide characterization of the mutations induced by gamma rays in NHEJ-deficient Arabidopsis mutants (AtKu70-/- and AtLig4-/-). Although both mutants were more sensitive to gamma rays than the wild-type control, the AtKu70-/- mutant was slightly more sensitive than the AtLig4-/- mutant. Single-base substitutions (SBSs) were the predominant mutations in the wild-type control, whereas deletions (≥2 bp) and complex-type mutations [i.e. more than two SBSs or short insertion and deletions (InDels) separated by fewer than 10 bp] were frequently induced in the mutants. Single-base deletions were the most frequent deletions in the wild-type control, whereas the most common deletions in the mutants were 11-30 bp. The apparent microhomology at the rejoined sites of deletions peaked at 2 bp in the wild-type control, but was 3-4 bp in the mutants. This suggests the involvement of alternative end joining and single-strand annealing pathways involving increased microhomology for rejoining DNA ends. Complex-type mutations comprising short InDels were frequently detected in the mutants, but not in the wild-type control. Accordingly, NHEJ is more precise than the backup pathways, and is the main pathway for rejoining the broken DNA ends induced by ionizing radiation in plants.
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Affiliation(s)
- Yan Du
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Yoshihiro Hase
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
- Corresponding author. Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan. Tel: +81-27-346-9032; Fax: +81-27-346-9688;
| | - Katsuya Satoh
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Naoya Shikazono
- Kansai Photon Science Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
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Wang L, Zhao H, He D, Wu Y, Jin L, Li G, Su N, Li H, Xing XH. Insights into the molecular-level effects of atmospheric and room-temperature plasma on mononucleotides and single-stranded homo- and hetero-oligonucleotides. Sci Rep 2020; 10:14298. [PMID: 32868795 PMCID: PMC7459345 DOI: 10.1038/s41598-020-71152-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/09/2020] [Indexed: 01/18/2023] Open
Abstract
Atmospheric and room-temperature plasma (ARTP) has been successfully developed as a useful mutation tool for mutation breeding of various microbes and plants as well animals by genetic alterations. However, understanding of the molecular mechanisms underlying the biological responses to ARTP irradiation is still limited. Therefore, to gain a molecular understanding of how irradiation with ARTP damages DNA, we irradiated the artificially synthesized mononucleotides of dATP, dTTP, dGTP, and dCTP, and the oligonucleotides of dA8, dT8, dG8, dC8, and dA2dT2dG2dC2 as chemical building blocks of DNA with ARTP for 1-4 min, identified the mononucleotide products using 31P- and 1H-nuclear magnetic resonance spectroscopy (NMR), and identified the oligonucleotide products using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) during ARTP treatment. The observed 31P-and 1H-NMR spectrum signals for the plasma-treated and untreated mononucleotides indicated that dATP was less stable to plasma irradiation than the other mononucleotides. The oligonucleotides after treatment with ARTP were found to have been broken into small fragments as shown by mass spectrometry, with the cleaved bonds and produced fragments identified according to their expected spectral m/z values or molecular weights derived from their m/z values. The stabilities of the oligonucleotides differed to ARTP irradiation, with dT8 being the most stable and was more beneficial to stabilizing single-stranded oligonucleotide structures compared to the other base groups (A, G, and C). This was consistent with the average potential energy level obtained by the molecular dynamic simulation of the oligonucleotides, i.e., dT8 > dC8 > dA8 > dG8 > dA2dT2dG2dC2. In summary, we found that ARTP treatment caused various structural changes to the oligonucleotides that may account for the wide and successful applications reported for ARTP-induced mutation breeding of various organisms.
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Affiliation(s)
- Liyan Wang
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
- Biobreeding Center, Wuxi Research Institute of Applied Technologies, Tsinghua University, Wuxi, 214072, People's Republic of China
- TmaxTree Biotechnology Co. Ltd., Luoyang, 471023, People's Republic of China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Dong He
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Lihua Jin
- College of Bioengineering, Beijing Polytechnic, Beijing, 100176, People's Republic of China
| | - Guo Li
- Department of Engineering Physics, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Nan Su
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Heping Li
- Department of Engineering Physics, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China.
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China.
- Center for Synthetic and System Biology, Tsinghua University, Beijing, People's Republic of China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, People's Republic of China.
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Matsuya Y, Nakano T, Kai T, Shikazono N, Akamatsu K, Yoshii Y, Sato T. A Simplified Cluster Analysis of Electron Track Structure for Estimating Complex DNA Damage Yields. Int J Mol Sci 2020; 21:ijms21051701. [PMID: 32131419 PMCID: PMC7084883 DOI: 10.3390/ijms21051701] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 01/04/2023] Open
Abstract
Complex DNA damage, defined as at least two vicinal lesions within 10-20 base pairs (bp), induced after exposure to ionizing radiation, is recognized as fatal damage to human tissue. Due to the difficulty of directly measuring the aggregation of DNA damage at the nano-meter scale, many cluster analyses of inelastic interactions based on Monte Carlo simulation for radiation track structure in liquid water have been conducted to evaluate DNA damage. Meanwhile, the experimental technique to detect complex DNA damage has evolved in recent decades, so both approaches with simulation and experiment get used for investigating complex DNA damage. During this study, we propose a simplified cluster analysis of ionization and electronic excitation events within 10 bp based on track structure for estimating complex DNA damage yields for electron and X-ray irradiations. We then compare the computational results with the experimental complex DNA damage coupled with base damage (BD) measured by enzymatic cleavage and atomic force microscopy (AFM). The computational results agree well with experimental fractions of complex damage yields, i.e., single and double strand breaks (SSBs, DSBs) and complex BD, when the yield ratio of BD/SSB is assumed to be 1.3. Considering the comparison of complex DSB yields, i.e., DSB + BD and DSB + 2BD, between simulation and experimental data, we find that the aggregation degree of the events along electron tracks reflects the complexity of induced DNA damage, showing 43.5% of DSB induced after 70 kVp X-ray irradiation can be classified as a complex form coupled with BD. The present simulation enables us to quantify the type of complex damage which cannot be measured through in vitro experiments and helps us to interpret the experimental detection efficiency for complex BD measured by AFM. This simple model for estimating complex DNA damage yields contributes to the precise understanding of the DNA damage complexity induced after X-ray and electron irradiations.
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Affiliation(s)
- Yusuke Matsuya
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
- Correspondence:
| | - Toshiaki Nakano
- Department of Quantum life Science, Quantum Beam Science Research Directorate, National Institutes of Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa-shi, Kyoto 619-0215, Japan
| | - Takeshi Kai
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Naoya Shikazono
- Department of Quantum life Science, Quantum Beam Science Research Directorate, National Institutes of Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa-shi, Kyoto 619-0215, Japan
| | - Ken Akamatsu
- Department of Quantum life Science, Quantum Beam Science Research Directorate, National Institutes of Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa-shi, Kyoto 619-0215, Japan
| | - Yuji Yoshii
- Central Institute of Isotope Science, Hokkaido University, Kita-15 Nishi-7, Kita-ku, Sapporo, Hokkaido 060-0815, Japan
| | - Tatsuhiko Sato
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
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Nickoloff JA, Sharma N, Taylor L. Clustered DNA Double-Strand Breaks: Biological Effects and Relevance to Cancer Radiotherapy. Genes (Basel) 2020; 11:E99. [PMID: 31952359 PMCID: PMC7017136 DOI: 10.3390/genes11010099] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 01/03/2023] Open
Abstract
Cells manage to survive, thrive, and divide with high accuracy despite the constant threat of DNA damage. Cells have evolved with several systems that efficiently repair spontaneous, isolated DNA lesions with a high degree of accuracy. Ionizing radiation and a few radiomimetic chemicals can produce clustered DNA damage comprising complex arrangements of single-strand damage and DNA double-strand breaks (DSBs). There is substantial evidence that clustered DNA damage is more mutagenic and cytotoxic than isolated damage. Radiation-induced clustered DNA damage has proven difficult to study because the spectrum of induced lesions is very complex, and lesions are randomly distributed throughout the genome. Nonetheless, it is fairly well-established that radiation-induced clustered DNA damage, including non-DSB and DSB clustered lesions, are poorly repaired or fail to repair, accounting for the greater mutagenic and cytotoxic effects of clustered lesions compared to isolated lesions. High linear energy transfer (LET) charged particle radiation is more cytotoxic per unit dose than low LET radiation because high LET radiation produces more clustered DNA damage. Studies with I-SceI nuclease demonstrate that nuclease-induced DSB clusters are also cytotoxic, indicating that this cytotoxicity is independent of radiogenic lesions, including single-strand lesions and chemically "dirty" DSB ends. The poor repair of clustered DSBs at least in part reflects inhibition of canonical NHEJ by short DNA fragments. This shifts repair toward HR and perhaps alternative NHEJ, and can result in chromothripsis-mediated genome instability or cell death. These principals are important for cancer treatment by low and high LET radiation.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; (N.S.); (L.T.)
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Abstract
The 30th summer school of the Research Community for Mechanisms of Mutations was held on September 2nd-3rd, 2017 at the Kyoto Prefecture Seminar House. The Community celebrated the 30th anniversary of the school this year. The Community has been organizing a meeting once a year since it was founded as the Society for Mechanisms of Anti-mutagenesis and Anti-carcinogenesis Studies in 1987. The Society was reorganized to the current Community in 2006, and since then has a summer school aimed at providing information on mutation research frontiers and exchanging scientific information among young scientists such as graduate students, post-doctoral fellows, and assistant professors. This year, three eminent scientists were invited to discuss radiation cluster damage, the evolution of snake venom, and colibactin and colorectal cancer, while 15 participants presented their own research. Fifty-six participants joined in enthusiastic discussions and acquired new scientific knowledge.
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