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Brabcová KP, Jamborová Z, Michaelidesová A, Davídková M, Kodaira S, Šefl M, Štěpán V. RADIATION-INDUCED PLASMID DNA DAMAGE: EFFECT OF CONCENTRATION AND LENGTH. RADIATION PROTECTION DOSIMETRY 2019; 186:168-171. [PMID: 31803909 DOI: 10.1093/rpd/ncz196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Plasmid DNA is commonly used as a simpler substitute for a cell in studies of early effects of ionizing radiation because it allows to determine yields of primary DNA lesions. Experimental studies often employ plasmids of different lengths, in different concentrations in the aqueous solution. Influence of these parameters on the heavy-ion induced yields of primary DNA damage has been studied, using plasmids pUC19 (2686 bp), pBR322 (4361 bp) and pKLAC2 (9107 bp) in 10 and 50 ng/μl concentration. Results demonstrate the impact of plasmid length, while no significant difference was observed between the two concentrations. The uncertainty of the results is discussed.
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Affiliation(s)
- Kateřina Pachnerová Brabcová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, 180 00 Praha, Czech Republic
| | - Zuzana Jamborová
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 110 00 Praha, Czech Republic
| | - Anna Michaelidesová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, 180 00 Praha, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 110 00 Praha, Czech Republic
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, 180 00 Praha, Czech Republic
| | - Satoshi Kodaira
- National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage, 263-8555 Chiba, Japan
| | - Martin Šefl
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, 180 00 Praha, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 110 00 Praha, Czech Republic
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, 180 00 Praha, Czech Republic
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2
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Yan J, Xie Y, Zhang Q, Gan L, Wang F, Li H, Si J, Zhang H. Dynamic recognition and repair of DNA complex damage. J Cell Physiol 2018; 234:13014-13020. [PMID: 30537094 DOI: 10.1002/jcp.27971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/19/2018] [Indexed: 11/11/2022]
Abstract
Irradiation (IR) can be used to treat cancer by inducing complex and irreparable DNA damage in the cancer cells, which may lead to their apoptotic death. However, little is known about the molecular mechanism of this DNA damage. Here, the non-small-cell lung cancer cell line A549 was treated with either X-ray or carbon ion combined with bleomycin (BLM). The cell survival rate, frequency of double-strand breaks (DSBs), dynamic changes in γH2AX, and p53 binding protein 1 (53BP1), and protein expression of Ku70, Rad51, and XRCC1 were determined by the clone formation assay, agarose gel electrophoresis, immunofluorescence, and western blot analysis. The results showed that the most obvious complex DSBs occurred in the carbon IR + BLM group. The number of γH2AX and 53BP1 foci in the 0.5 hr X-ray IR + BLM group was the highest (p < 0.001) among all the groups. γH2AX foci were detected in the nucleus at 0.5, 1, 2, and 4 hr, but were distributed throughout the cell at 6 hr after IR in the carbon ion IR + BLM group. The expression of Ku70 increased and XRCC1 decreased at 2 and 6 hr after IR. Our data indicate that a DNA damage frequency of 13.4/Mbp is caused by clustered DNA damage and further show a correlation between γH2AX, 53BP1, and XRCC1 levels and the extent of DNA damage. The results of this study provide insights into DNA damage recognition and a rationale for the clinical use of radiotherapy.
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Affiliation(s)
- Junfang Yan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Qianjing Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Fang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.,Graduate School of University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
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3
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Neužilová B, Ondrák L, Čuba V, Múčka V. Influence of the dose rate of gamma irradiation and some other conditions on the radiation protection of microbial cells by scavenging of OH radicals. J Radioanal Nucl Chem 2018. [DOI: 10.1007/s10967-018-6185-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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4
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Šefl M, Pachnerová Brabcová K, Štěpán V. Dosimetry as a Catch in Radiobiology Experiments. Radiat Res 2018; 190:404-411. [PMID: 30016217 DOI: 10.1667/rr15020.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Experimental radiobiological studies in which the effects of ionizing radiation on a biological model are examined often highlight the biological aspects while missing detailed descriptions of the geometry, sample and dosimetric methods used. Such omissions can hinder the reproducibility and comparability of the experimental data. An application based on the Geant4 simulation toolkit was developed to design experiments using a biological solution placed in a microtube. The application was used to demonstrate the influence of the type of microtube, sample volume and energy of a proton source on the dose distribution across the sample, and on the mean dose in the whole sample. The results shown here are for samples represented by liquid water in the 0.4-, 1.5- and 2.0-ml microtubes irradiated with 20, 30 and 100 MeV proton beams. The results of this work demonstrate that the mean dose and homogeneity of the dose distribution within the sample strongly depend on all three parameters. Furthermore, this work shows how the dose uncertainty propagates into the scored primary DNA damages in plasmid DNA studies using agarose gel electrophoresis. This application is provided freely to assist users in verifying their experimental setup prior to the experiment.
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Affiliation(s)
- Martin Šefl
- a Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic.,b Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | | | - Václav Štěpán
- a Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
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Liu W, Tan Z, Zhang L, Champion C. Investigation on the correlation between energy deposition and clustered DNA damage induced by low-energy electrons. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2018; 57:179-187. [PMID: 29335772 DOI: 10.1007/s00411-018-0730-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 01/10/2018] [Indexed: 06/07/2023]
Abstract
This study presents the correlation between energy deposition and clustered DNA damage, based on a Monte Carlo simulation of the spectrum of direct DNA damage induced by low-energy electrons including the dissociative electron attachment. Clustered DNA damage is classified as simple and complex in terms of the combination of single-strand breaks (SSBs) or double-strand breaks (DSBs) and adjacent base damage (BD). The results show that the energy depositions associated with about 90% of total clustered DNA damage are below 150 eV. The simple clustered DNA damage, which is constituted of the combination of SSBs and adjacent BD, is dominant, accounting for 90% of all clustered DNA damage, and the spectra of the energy depositions correlating with them are similar for different primary energies. One type of simple clustered DNA damage is the combination of a SSB and 1-5 BD, which is denoted as SSB + BD. The average contribution of SSB + BD to total simple clustered DNA damage reaches up to about 84% for the considered primary energies. In all forms of SSB + BD, the SSB + BD including only one base damage is dominant (above 80%). In addition, for the considered primary energies, there is no obvious difference between the average energy depositions for a fixed complexity of SSB + BD determined by the number of base damage, but average energy depositions increase with the complexity of SSB + BD. In the complex clustered DNA damage constituted by the combination of DSBs and BD around them, a relatively simple type is a DSB combining adjacent BD, marked as DSB + BD, and it is of substantial contribution (on average up to about 82%). The spectrum of DSB + BD is given mainly by the DSB in combination with different numbers of base damage, from 1 to 5. For the considered primary energies, the DSB combined with only one base damage contributes about 83% of total DSB + BD, and the average energy deposition is about 106 eV. However, the energy deposition increases with the complexity of clustered DNA damage, and therefore, the clustered DNA damage with high complexity still needs to be considered in the study of radiation biological effects, in spite of their small contributions to all clustered DNA damage.
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Affiliation(s)
- Wei Liu
- School of Electrical Engineering, Shandong University, Jinan, 250061, Shandong, People's Republic of China
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan, 250357, People's Republic of China
| | - Zhenyu Tan
- School of Electrical Engineering, Shandong University, Jinan, 250061, Shandong, People's Republic of China.
| | - Liming Zhang
- Electric Power Research Institute of Tianjin Electric Power Corporation, Tianjin, 300384, People's Republic of China
| | - Christophe Champion
- Centre d'Etudes Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, BP 120, 33175, Gradignan, France
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Vyšín L, Burian T, Ukraintsev E, Davídková M, Grisham ME, Heinbuch S, Rocca JJ, Juha L. Dose-Rate Effects in Breaking DNA Strands by Short Pulses of Extreme Ultraviolet Radiation. Radiat Res 2018; 189:466-476. [PMID: 29505347 DOI: 10.1667/rr14825.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, we examined dose-rate effects on strand break formation in plasmid DNA induced by pulsed extreme ultraviolet (XUV) radiation. Dose delivered to the target molecule was controlled by attenuating the incident photon flux using aluminum filters as well as by changing the DNA/buffer-salt ratio in the irradiated sample. Irradiated samples were examined using agarose gel electrophoresis. Yields of single- and double-strand breaks (SSBs and DSBs) were determined as a function of the incident photon fluence. In addition, electrophoresis also revealed DNA cross-linking. Damaged DNA was inspected by means of atomic force microscopy (AFM). Both SSB and DSB yields decreased with dose rate increase. Quantum yields of SSBs at the highest photon fluence were comparable to yields of DSBs found after synchrotron irradiation. The average SSB/DSB ratio decreased only slightly at elevated dose rates. In conclusion, complex and/or clustered damages other than cross-links do not appear to be induced under the radiation conditions applied in this study.
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Affiliation(s)
- Luděk Vyšín
- a Institute of Physics.,e Department of Nuclear Chemistry, Czech Technical University in Prague, Prague, Czech Republic
| | - Tomáš Burian
- a Institute of Physics.,c Institute of Plasma Physics.,d J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | | | | | - Michael E Grisham
- f Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado
| | - Scott Heinbuch
- f Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado
| | - Jorge J Rocca
- f Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado
| | - Libor Juha
- a Institute of Physics.,c Institute of Plasma Physics
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Ribar A, Huber SE, Smiałek MA, Tanzer K, Neustetter M, Schürmann R, Bald I, Denifl S. Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment. Phys Chem Chem Phys 2018; 20:5578-5585. [PMID: 29410988 DOI: 10.1039/c7cp07697e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
2-Amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) and ethylenediaminetetraacetic acid (EDTA) are key components of biological buffers and are frequently used as DNA stabilizers in irradiation studies. Such surface or liquid phase studies are done with the aim to understand the fundamental mechanisms of DNA radiation damage and to improve cancer radiotherapy. When ionizing radiation is used, abundant secondary electrons are formed during the irradiation process, which are able to attach to the molecular compounds present on the surface. In the present study we experimentally investigate low energy electron attachment to TRIS and methyliminodiacetic acid (MIDA), an analogue of EDTA, supported by quantum chemical calculations. The most prominent dissociation channel for TRIS is through hydroperoxyl radical formation, whereas the dissociation of MIDA results in the formation of formic and acetic acid. These compounds are well-known to cause DNA modifications, like strand breaks. The present results indicate that buffer compounds may not have an exclusive protecting effect on DNA as suggested previously.
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Affiliation(s)
- Anita Ribar
- Institute for Ion Physics and Applied Physics and Center of Molecular Biosciences Innsbruck, Leopold Franzens University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
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8
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Vyšín L, Tomanová K, Pavelková T, Wagner R, Davídková M, Múčka V, Čuba V, Juha L. Degradation of phospholipids under different types of irradiation and varying oxygen saturation. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2017; 56:241-247. [PMID: 28500389 DOI: 10.1007/s00411-017-0693-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
The effects of different types of radiation on the formation of peroxide forms of 2-dioleoyl-sn-glycero-3-phosphocholine were studied under various conditions. For the irradiation, an aqueous solution of small unilamellar vesicles was prepared. Variations in parameters such as the dose rate and molecular oxygen saturation levels were evaluated. Our study suggests that the mechanism of the peroxides formation process remains unchanged under irradiation by accelerated electrons, gamma and accelerated protons. The values of radiation chemical yields of the peroxidic form depend on the type of radiation, dose rate, and the saturation of molecular oxygen. The level of oxygen saturation strongly affects the values of radiation chemical yields as well, as the dissolved oxygen is an important agent participating in peroxidation and it is a source of free radicals during the radiolysis. The values of radiation chemical yields strongly suggest that the mechanism of radiation-induced peroxidation of phosphatidylcholines does not proceed via chain reaction.
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Affiliation(s)
- Luděk Vyšín
- Institute of Physics of the CAS, Na Slovance 1999/2, 182 21, Prague, Czech Republic.
- FNSPE, Czech Technical University in Prague, Břehová 7, 115 19, Prague, Czech Republic.
| | - Kateřina Tomanová
- FNSPE, Czech Technical University in Prague, Břehová 7, 115 19, Prague, Czech Republic
| | - Tereza Pavelková
- FNSPE, Czech Technical University in Prague, Břehová 7, 115 19, Prague, Czech Republic
| | - Richard Wagner
- Nuclear Physics Institute of the CAS, Husinec-Řež 130, 250 68, Řež, Czech Republic
| | - Marie Davídková
- Nuclear Physics Institute of the CAS, Husinec-Řež 130, 250 68, Řež, Czech Republic
| | - Viliam Múčka
- FNSPE, Czech Technical University in Prague, Břehová 7, 115 19, Prague, Czech Republic
| | - Václav Čuba
- FNSPE, Czech Technical University in Prague, Břehová 7, 115 19, Prague, Czech Republic
| | - Libor Juha
- Institute of Physics of the CAS, Na Slovance 1999/2, 182 21, Prague, Czech Republic
- Institute of Plasma Physics of the CAS, Za Slovankou 3, 182 00, Prague, Czech Republic
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9
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Vyšín L, Pachnerová Brabcová K, Štěpán V, Moretto-Capelle P, Bugler B, Legube G, Cafarelli P, Casta R, Champeaux JP, Sence M, Vlk M, Wagner R, Štursa J, Zach V, Incerti S, Juha L, Davídková M. Proton-induced direct and indirect damage of plasmid DNA. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2015; 54:343-352. [PMID: 26007308 DOI: 10.1007/s00411-015-0605-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
Clustered DNA damage induced by 10, 20 and 30 MeV protons in pBR322 plasmid DNA was investigated. Besides determination of strand breaks, additional lesions were detected using base excision repair enzymes. The plasmid was irradiated in dry form, where indirect radiation effects were almost fully suppressed, and in water solution containing only minimal residual radical scavenger. Simultaneous irradiation of the plasmid DNA in the dry form and in the solution demonstrated the contribution of the indirect effect as prevalent. The damage composition slightly differed when comparing the results for liquid and dry samples. The obtained data were also subjected to analysis concerning different methodological approaches, particularly the influence of irradiation geometry, models used for calculation of strand break yields and interpretation of the strand breaks detected with the enzymes. It was shown that these parameters strongly affect the results.
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Affiliation(s)
- Luděk Vyšín
- Institute of Physics CAS, Na Slovance 1999/2, 182 21, Prague, Czech Republic
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Nikitaki Z, Hellweg CE, Georgakilas AG, Ravanat JL. Stress-induced DNA damage biomarkers: applications and limitations. Front Chem 2015; 3:35. [PMID: 26082923 PMCID: PMC4451417 DOI: 10.3389/fchem.2015.00035] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/07/2015] [Indexed: 11/13/2022] Open
Abstract
A variety of environmental stresses like chemicals, UV and ionizing radiation and organism's endogenous processes such as replication stress and metabolism can lead to the generation of reactive oxygen and nitrogen species (ROS/RNS) that can attack cellular vital components like DNA, proteins and lipid membranes. Among them, much attention has been focused on DNA since DNA damage plays a role in several biological disorders and aging processes. Thus, DNA damage can be used as a biomarker in a reliable and accurate way to quantify for example radiation exposure and can indicate its possible long term effects and cancer risk. Based on the type of DNA lesions detected one can hypothesize on the most probable mechanisms involved in the formation of these lesions for example in the case of UV and ionizing radiation (e.g., X- or α-, γ-rays, energetic ions, neutrons). In this review we describe the most accepted chemical pathways for DNA damage induction and the different types of DNA lesions, i.e., single, complex DNA lesions etc. that can be used as DNA damage biomarkers. We critically compare DNA damage detection methods and their limitations. In addition, we suggest the use of DNA repair gene products as biomarkes for identification of different types of stresses i.e., radiation, oxidative, or replication stress, based on bioinformatic approaches and meta-analysis of literature data.
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Affiliation(s)
- Zacharenia Nikitaki
- DNA Damage and Repair Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens Athens, Greece
| | - Christine E Hellweg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine Köln, Germany
| | - Alexandros G Georgakilas
- DNA Damage and Repair Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens Athens, Greece
| | - Jean-Luc Ravanat
- Laboratoire des Lésions des Acides Nucléiques, Institut des Nanosciences et Cryogénie, Service de Chimie Inorgranique et Biologique, Université Grenoble Alpes Grenoble, France ; CEA, Institut des Nanosciences et Cryogénie, Service de Chimie Inorgranique et Biologique Grenoble, France
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