1
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Souli MP, Nikitaki Z, Puchalska M, Brabcová KP, Spyratou E, Kote P, Efstathopoulos EP, Hada M, Georgakilas AG, Sihver L. Clustered DNA Damage Patterns after Proton Therapy Beam Irradiation Using Plasmid DNA. Int J Mol Sci 2022; 23:ijms232415606. [PMID: 36555249 PMCID: PMC9779025 DOI: 10.3390/ijms232415606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Modeling ionizing radiation interaction with biological matter is a major scientific challenge, especially for protons that are nowadays widely used in cancer treatment. That presupposes a sound understanding of the mechanisms that take place from the early events of the induction of DNA damage. Herein, we present results of irradiation-induced complex DNA damage measurements using plasmid pBR322 along a typical Proton Treatment Plan at the MedAustron proton and carbon beam therapy facility (energy 137-198 MeV and Linear Energy Transfer (LET) range 1-9 keV/μm), by means of Agarose Gel Electrophoresis and DNA fragmentation using Atomic Force Microscopy (AFM). The induction rate Mbp-1 Gy-1 for each type of damage, single strand breaks (SSBs), double-strand breaks (DSBs), base lesions and non-DSB clusters was measured after irradiations in solutions with varying scavenging capacity containing 2-amino-2-(hydroxymethyl)propane-1,3-diol (Tris) and coumarin-3-carboxylic acid (C3CA) as scavengers. Our combined results reveal the determining role of LET and Reactive Oxygen Species (ROS) in DNA fragmentation. Furthermore, AFM used to measure apparent DNA lengths provided us with insights into the role of increasing LET in the induction of highly complex DNA damage.
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Affiliation(s)
- Maria P Souli
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Zacharenia Nikitaki
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | | | | | - Ellas Spyratou
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11517 Athens, Greece
| | - Panagiotis Kote
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Efstathios P Efstathopoulos
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11517 Athens, Greece
| | - Megumi Hada
- Radiation Institute for Science & Engineering, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Lembit Sihver
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- Nuclear Physics Institute, Czech Academy of Sciences, Na Truhlářce 39/64, 180 86 Prague, Czech Republic
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2
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Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne JA, Schuemann J, Moreno-Barbosa E, Faddegon B. TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac79f9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Current Monte Carlo simulations of DNA damage have been reported only at ambient temperature. The aim of this work is to use TOPAS-nBio to simulate the yields of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) produced in plasmids under low-LET irradiation incorporating the effect of the temperature changes in the environment. A new feature was implemented in TOPAS-nBio to incorporate reaction rates used in the simulation of the chemical stage of water radiolysis as a function of temperature. The implemented feature was verified by simulating temperature-dependent G-values of chemical species in liquid water from 20 °C to 90 °C. For radiobiology applications, temperature dependent SSB and DSB yields were calculated from 0 °C to 42 °C, the range of available published measured data. For that, supercoiled DNA plasmids dissolved in aerated solutions containing EDTA irradiated by Cobalt-60 gamma-rays were simulated. TOPAS-nBio well reproduced published temperature-dependent G-values in liquid water and the yields of SSB and DSB for the temperature range considered. For strand break simulations, the model shows that the yield of SSB and DSB increased linearly with the temperature at a rate of (2.94 ± 0.17) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99) and (0.13 ± 0.01) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99), respectively. The extended capability of TOPAS-nBio is a complementary tool to simulate realistic conditions for a large range of environmental temperatures, allowing refined investigations of the biological effects of radiation.
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3
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D-Kondo N, Moreno-Barbosa E, Štěphán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J. DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions. Phys Med Biol 2021; 66. [PMID: 34787099 DOI: 10.1088/1361-6560/ac3a22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022]
Abstract
The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by60Co or137Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.
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Affiliation(s)
- N D-Kondo
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - E Moreno-Barbosa
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - V Štěphán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - S Incerti
- Univ. Bordeaux, CNRS/IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B De Celis Alonso
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - J Schuemann
- Department of Radiation Oncology, Massachusets General Hospital and Hardvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
| | - J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
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4
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Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štěpán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B. TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys Med Biol 2021; 66. [PMID: 34412044 DOI: 10.1088/1361-6560/ac1f39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022]
Abstract
The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for·OH, e-aq, and H2with published experimental data. For H2O2and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by137Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
| | - J A LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - N Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - J Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, United States of America
| | - V Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - W-G Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - S Incerti
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - A McNamara
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - H Paganetti
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - J Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA, United States of America
| | - J Schuemann
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
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5
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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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6
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Salado-Leza D, Traore A, Porcel E, Dragoe D, Muñoz A, Remita H, García G, Lacombe S. Radio-Enhancing Properties of Bimetallic Au:Pt Nanoparticles: Experimental and Theoretical Evidence. Int J Mol Sci 2019; 20:ijms20225648. [PMID: 31718091 PMCID: PMC6888691 DOI: 10.3390/ijms20225648] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/28/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022] Open
Abstract
The use of nanoparticles, in combination with ionizing radiation, is considered a promising method to improve the performance of radiation therapies. In this work, we engineered mono- and bimetallic core-shell gold–platinum nanoparticles (NPs) grafted with poly (ethylene glycol) (PEG). Their radio-enhancing properties were investigated using plasmids as bio-nanomolecular probes and gamma radiation. We found that the presence of bimetallic Au:Pt-PEG NPs increased by 90% the induction of double-strand breaks, the signature of nanosize biodamage, and the most difficult cell lesion to repair. The radio-enhancement of Au:Pt-PEG NPs were found three times higher than that of Au-PEG NPs. This effect was scavenged by 80% in the presence of dimethyl sulfoxide, demonstrating the major role of hydroxyl radicals in the damage induction. Geant4-DNA Monte Carlo simulations were used to elucidate the physical processes involved in the radio-enhancement. We predicted enhancement factors of 40% and 45% for the induction of nanosize damage, respectively, for mono- and bimetallic nanoparticles, which is attributed to secondary electron impact processes. This work contributed to a better understanding of the interplay between energy deposition and the induction of nanosize biomolecular damage, being Monte Carlo simulations a simple method to guide the synthesis of new radio-enhancing agents.
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Affiliation(s)
- Daniela Salado-Leza
- Institut des Sciences Moléculaires d’Orsay (UMR 8214) CNRS, Université Paris-Saclay, Université Paris Sud, 91405 Orsay, France; (D.S.-L.); (E.P.)
- Cátedras CONACyT, Universidad Autónoma de San Luis Potosí, Facultad de Ciencias Químicas, Av. Dr. Manuel Nava 6, Zona Universitaria, San Luis Potosí 78210, S.L.P., Mexico
| | - Ali Traore
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain; (A.T.); (G.G.)
| | - Erika Porcel
- Institut des Sciences Moléculaires d’Orsay (UMR 8214) CNRS, Université Paris-Saclay, Université Paris Sud, 91405 Orsay, France; (D.S.-L.); (E.P.)
| | - Diana Dragoe
- Institut de Chimie Moléculaire et des Matériaux d’Orsay (UMR 8182) CNRS, Université Paris Saclay, Université Paris Sud, 91405 Orsay, France;
| | - Antonio Muñoz
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avda. Complutense 22, 28040 Madrid, Spain;
| | - Hynd Remita
- Laboratoire de Chimie Physique (UMR 8000) CNRS, Université Paris Saclay, Université Paris Sud, 91405 Orsay, France;
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain; (A.T.); (G.G.)
| | - Sandrine Lacombe
- Institut des Sciences Moléculaires d’Orsay (UMR 8214) CNRS, Université Paris-Saclay, Université Paris Sud, 91405 Orsay, France; (D.S.-L.); (E.P.)
- Correspondence: ; Tel.: +33-(1)-6915-8263
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7
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Liu R, Zhao T, Swat MH, Reynoso FJ, Higley KA. Development of computational model for cell dose and DNA damage quantification of multicellular system. Int J Radiat Biol 2019; 95:1484-1497. [DOI: 10.1080/09553002.2019.1642537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ruirui Liu
- School of Nuclear Science and Engineering, Oregon State University, Corvallis, OR, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tianyu Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maciej H. Swat
- Biocomplexity Institute, Indiana University, Bloomington, IN, USA
| | - Francisco J. Reynoso
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathryn A. Higley
- School of Nuclear Science and Engineering, Oregon State University, Corvallis, OR, USA
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8
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Souici M, Khalil TT, Boulanouar O, Belafrites A, Mavon C, Fromm M. DNA strand break dependence on Tris and arginine scavenger concentrations under ultra-soft X-ray irradiation: the contribution of secondary arginine radicals. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2016; 55:215-228. [PMID: 26994994 DOI: 10.1007/s00411-016-0642-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
In this study, we used a bench-top cold-cathode ultra-soft X-ray (USX) generator to expose aqueous DNA plasmid solutions to low-LET radiation under various scavenging conditions. Single- and double-strand breaks were assessed using classic gel electrophoresis quantification of linear, circular and supercoiled plasmid DNA topologies. With their very low penetration range in water, USX can only interact with matter up to short distances, of the order of 50 μm. We validated a stirring procedure which makes it possible to expose 100 µL of aqueous samples (2 mm thick). The scavenging of OH radicals by Tris buffer was studied at ambient temperature under aerobic conditions and compared to data gathered in the literature. A very good agreement was found with the rare data dealing with DNA plasmid exposed to Al Kα photons at low temperature (T ≤ 277 K), which therefore validated the experimental procedure. The yields for DNA single-strand breaks determined during this study enabled the ratio of indirect to direct effects to be determined at 96.2%, in good agreement with the value of 97.7% stemming from a study based on γ-ray irradiation of frozen solutions of plasmid DNA. Then, arginine was used both to create a "biological-like" chemical environment around the DNA plasmids and as an OH radical scavenger, in vitro. Although arginine has a greater scavenging (protecting) power than Tris, surprisingly, it led to higher rates of strand breakage. Based on the specific binding modes of arginine to DNA, we suggest that the side effects observed are due to the presence of arginine near to, but also inside, the DNA double helix.
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Affiliation(s)
- Mounir Souici
- UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France
- Laboratoire de Physique des Rayonnements et Applications, Université de Jijel, B.P. 98, 18000, Ouled Aissa, Jijel, Algeria
| | - Talat Tariq Khalil
- UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France
| | - Omar Boulanouar
- UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France
| | - Abdelfettah Belafrites
- Laboratoire de Physique des Rayonnements et Applications, Université de Jijel, B.P. 98, 18000, Ouled Aissa, Jijel, Algeria
| | - Christophe Mavon
- UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France
| | - Michel Fromm
- UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France.
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9
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Semsarha F, Raisali G, Goliaei B, Khalafi H. Microdosimetry of DNA conformations: relation between direct effect of (60)Co gamma rays and topology of DNA geometrical models in the calculation of A-, B- and Z-DNA radiation-induced damage yields. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2016; 55:243-254. [PMID: 26984469 DOI: 10.1007/s00411-016-0644-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
In order to obtain the energy deposition pattern of ionizing radiation in the nanometric scale of genetic material and to investigate the different sensitivities of the DNA conformations, direct effects of (60)Co gamma rays on the three A, B and Z conformations of DNA have been studied. For this purpose, single-strand breaks (SSB), double-strand breaks (DSB), base damage (BD), hit probabilities and three microdosimetry quantities (imparted energy, mean chord length and lineal energy) in the mentioned DNA conformations have been calculated and compared by using GEometry ANd Tracking 4 (Geant4) toolkit. The results show that A-, B- and Z-DNA conformations have the highest yields of DSB (1.2 Gy(-1) Gbp(-1)), SSB (25.2 Gy(-1) Gbp(-1)) and BD (4.81 Gy(-1) Gbp(-1)), respectively. Based on the investigation of direct effects of radiation, it can be concluded that the DSB yield is largely correlated to the topological characteristics of DNA models, although the SSB yield is not. Moreover, according to the comparative results of the present study, a reliable candidate parameter for describing the relationship between DNA damage yields and geometry of DNA models in the theoretical radiation biology research studies would be the mean chord length (4 V/S) of the models.
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Affiliation(s)
- Farid Semsarha
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box: 11365-3486, Tehran, Iran
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, P.O. Box: 13145-1384, Tehran, Iran
| | - Gholamreza Raisali
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box: 11365-3486, Tehran, Iran.
| | - Bahram Goliaei
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, P.O. Box: 13145-1384, Tehran, Iran
| | - Hossein Khalafi
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box: 11365-3486, Tehran, Iran
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10
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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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Pachnerová Brabcová K, Sihver L, Yasuda N, Matuo Y, Stěpán V, Davídková M. Clustered DNA damage on subcellular level: effect of scavengers. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2014; 53:705-712. [PMID: 25034012 DOI: 10.1007/s00411-014-0557-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/08/2014] [Indexed: 06/03/2023]
Abstract
Clustered DNA damages are induced by ionizing radiation, particularly of high linear energy transfer (LET). Compared to isolated DNA damage sites, their biological effects can be more severe. We investigated a clustered DNA damage induced by high LET radiation (C 290 MeV u(-1) and Fe 500 MeV u(-1)) in pBR322 plasmid DNA. The plasmid is dissolved in pure water or in aqueous solution of one of the three scavengers (coumarin-3-carboxylic acid, dimethylsulfoxide, and glycylglycine). The yield of double strand breaks (DSB) induced in the DNA plasmid-scavenger system by heavy ion radiation was found to decrease with increasing scavenging capacity due to reaction with hydroxyl radical, linearly with high correlation coefficients. The yield of non-DSB clusters was found to occur twice as much as the DSB. Their decrease with increasing scavenging capacity had lower linear correlation coefficients. This indicates that the yield of non-DSB clusters depends on more factors, which are likely connected to the chemical properties of individual scavengers.
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Saloua KS, Sonia G, Pierre C, Léon S, Darel HJ. The relative contributions of DNA strand breaks, base damage and clustered lesions to the loss of DNA functionality induced by ionizing radiation. Radiat Res 2014; 181:99-110. [PMID: 24397439 DOI: 10.1667/rr13450.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The majority of studies on lethal radiobiological damage have focused on double-strand breaks (DSBs), a type of clustered DNA damage and the evaluation of their toxicity, while other types of clustered DNA damage have received much less attention. The main purpose of this study is to evaluate the contribution of different lesions induced by ionizing radiation to the loss of plasmid DNA functionality. We employed a simple model system comprising E. coli transformed with an irradiated plasmid [pGEM-3Zf (-)] to determine the effect of DSBs and other lesions including base damage and clustered lesions on the functionality ("viability") of the plasmid. The yields of γ-radiation-induced single-strand breaks (SSBs) and DSBs were measured by gel electrophoresis. We found that the transformation efficiency decreases with radiation dose, but this decrease cannot be explained by the formation of DSBs. For example, at doses of 500 and 700 Gy, the relative transformation efficiency falls from 100% to 53% and 26%, respectively, while only 5.7% and 9.1% of the plasmids contain a DSB. In addition, it is also unlikely that randomly distributed base lesions could explain the loss of functionality of the plasmid, since cells can repair them efficiently. However, clustered lesions other than DSBs, which are difficult to repair and result in the loss of information on both DNA strands, have the potential to induce the loss of plasmid functionality. We therefore measured the yields of γ-radiation-induced base lesions and cluster damage, which are respectively converted into SSBs and DSBs by the base excision repair enzymes endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg). Our data demonstrate that the yield of cluster damage (i.e., lesions that yield DSBs following digestion) is 31 times higher than that of frank DSBs. This finding suggests that frank DSBs make a relatively minor contribution to the loss of DNA functionality induced by ionizing radiation, while other toxic lesions formed at a much higher frequencies than DSBs must be responsible for the loss of plasmid functionality. These lesions may be clustered lesions/locally multiply damaged sites (LMDS), including base damage, SSBs and/or intrastrand and interstrand crosslinks, leading to the loss of vital information in the DNA. Using a mathematical model, we estimate that at least three toxic lesions are required for the inactivation of plasmid functionality, in part because even these complex lesions can be repaired.
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Affiliation(s)
- Kouass Sahbani Saloua
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
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Grygoryev D, Moskalenko O, Zimbrick JD. Effect of sodium and acetate ions on 8-hydroxyguanine formation in irradiated aqueous solutions of DNA and 2'-deoxyguanosine 5'-monophosphate. Int J Radiat Biol 2011; 87:974-83. [PMID: 21749183 DOI: 10.3109/09553002.2011.584940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
PURPOSE The aim of this work was to study the combined effect of sodium and acetate ions on the radiation yield of 8-hydroxyguanine (8-OHG), one of the major DNA base lesions induced by free radicals. MATERIALS AND METHODS Aqueous solutions of DNA and 2'-deoxyguanosine 5'-monophosphate (dGMP) with various concentrations of sodium acetate and sodium perchlorate were γ-irradiated, enzymatically digested and analyzed by high-performance liquid chromatography (HPLC) methods. RESULTS It was found that both salts decrease the 8-OHG radiation yield in the concentration range studied for both DNA and dGMP, except in the case of dGMP wherein an increase in yield occurs in the concentration range from 0.1-1 mM. The dependence of the 8-hydroxy-2'-deoxyguanosine radiation yield on the concentration of both sodium acetate and sodium perchlorate have different shapes and have steeper slopes for the DNA compared with the dGMP solutions. CONCLUSIONS The observed decrease in the radiation yield of 8-OHG with increasing concentrations of sodium acetate is consistent with the hypothesis that sodium acetate produces two concentration-dependent effects in the DNA solutions: (1) A conformational change in the DNA caused by Na(+) counterions; and (2) free radical reactions related to the radiolysis of acetate ion.
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Affiliation(s)
- Dmytro Grygoryev
- Center for Research on Occupational and Environmental Toxicology, Oregon Health & Science University, Portland, OR, USA
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15
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Mutation breeding for productive yeast strains through a novel method: High-energy-pulse-electron-beam. ANN MICROBIOL 2008. [DOI: 10.1007/bf03175556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Milian FM, Gouveia AN, Gual MR, Echeimberg JO, Arruda-Neto JDT, Garcia F, Schenberg ACG, Vicente EJ, Rodriguez O, Guzman F, Deppman A. In vitro effects of gamma radiation from 60Co and 137Cs on plasmid DNA. J Biol Phys 2008; 33:155-60. [PMID: 19669547 DOI: 10.1007/s10867-007-9050-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 12/08/2007] [Indexed: 11/27/2022] Open
Abstract
The effects of gamma radiation from (60)Co and (137)Cs on DNA in aqueous solution are studied experimentally. Using an improved plasmid purification protocol and improved electrophoretic gel analysis techniques provided results with relatively small uncertainties. The results are compared with both theoretical and experimental results. In particular, the results obtained here are discussed in the light of recent discussion on supposed differences of the effects induced by gamma radiation from (60)Co and (137)Cs. We find that the effects of both types of gamma radiation are similar.
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Affiliation(s)
- F M Milian
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil.
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Zhu H, Xu J, Li S, Sun X, Yao S, Wang S. Effects of high-energy-pulse-electron beam radiation on biomacromolecules. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11426-008-0017-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Conformation changes in the DNA molecule caused by γ-irradiation of its water ethanol solutions of great ionic strength. J STRUCT CHEM+ 2007. [DOI: 10.1007/s10947-007-0112-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Elsässer T, Scholz M. Cluster Effects within the Local Effect Model. Radiat Res 2007; 167:319-29. [PMID: 17316069 DOI: 10.1667/rr0467.1] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 10/02/2006] [Indexed: 11/03/2022]
Abstract
The local effect model predicts the relative biological effectiveness (RBE) for different ions and cell lines starting from the corresponding experimental photon data and an amorphous track structure model. Here we present an extension of the model that takes cluster effects of single-strand breaks (SSBs) at the nanometer scale into account. In line with the main idea of the local effect model, we take the yields of SSBs and double-strand breaks (DSBs) from experimental photon data and use a Monte Carlo method to distribute them onto the DNA. We score clusters of SSBs where individual SSBs are separated by less than 25 bp as additional DSBs. Assuming that the number of DSBs is a measure of cell lethality, we derive a modified cell survival curve for photons that takes these cluster effects into account. In combination with an improved radial dose distribution, we find that the extended local effect model including cluster effects reproduces most experimental data better than the original local effect model and thus enhances the accuracy of the local effect model.
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Affiliation(s)
- Thilo Elsässer
- Gesellschaft für Schwerionenforschung (GSI), Biophysics, 64291 Darmstadt, Germany.
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Yokoya A, Cunniffe SMT, O'Neill P. Effect of hydration on the induction of strand breaks and base lesions in plasmid DNA films by gamma-radiation. J Am Chem Soc 2002; 124:8859-66. [PMID: 12137539 DOI: 10.1021/ja025744m] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The yields of gamma-radiation-induced single- and double-strand breaks (ssb's and dsb's) as well as base lesions, which are converted into detectable ssb by the base excision repair enzymes endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg), at 278 K have been measured as a function of the level of hydration of closed-circular plasmid DNA (pUC18) films. The yields of ssb and dsb increase slightly on increasing the level of hydration (Gamma) from vacuum-dried DNA up to DNA containing 15 mol of water per mole of nucleotide. At higher levels of hydration (15 < Gamma < 35), the yields are constant, indicating that H2O*+ or diffusible hydroxyl radicals, if produced in the hydrated layer, do not contribute significantly to the induction of strand breaks. In contrast, the yields of base lesions, recognized by Nth and Fpg, increase with increasing hydration of the DNA over the range studied. The maximum ratios of the yields of base lesions to that of ssb are 1.7:1 and 1.4:1 for Nth- and Fpg-sensitive sites, respectively. The yields of additional dsb, revealed after enzymatic treatment, increase with increasing level of hydration of DNA. The maximum yield of these enzymatically induced dsb is almost the same as that for prompt, radiation-induced dsb's, indicating that certain types of enzymatically revealed, clustered DNA damage, e.g., two or more lesions closely located, one on each DNA strand, are induced in hydrated DNA by radiation. It is proposed that direct energy deposition in the hydration layer of DNA produces H2O*+ and an electron, which react with DNA to produce mainly base lesions but not ssb. The nucleobases are oxidized by H2O*+ in competition with its conversion to hydroxyl radicals, which if formed do not produce ssb's, presumably due to their scavenging by Tris present in the samples. This pathway plays an important role in the induction of base lesions and clustered DNA damage by direct energy deposition in hydrated DNA and is important in understanding the processes that lead to radiation degradation of DNA in cells or biological samples.
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Affiliation(s)
- Akinari Yokoya
- SPring-8, Japan Atomic Energy Research Institute, Hyogo 679-5148, Japan
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Shao C, Saito M, Yu Z. Radiation induced DNA strand breaks measured by a modified method of gel scanning. Radiat Phys Chem Oxf Engl 1993 1999. [DOI: 10.1016/s0969-806x(99)00296-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Stankus AA, Xapsos MA, Kolanko CJ, Gerstenberg HM, Blakely WF. Energy deposition events produced by fission neutrons in aqueous solutions of plasmid DNA. Int J Radiat Biol 1995; 68:1-9. [PMID: 7629431 DOI: 10.1080/09553009514550851] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using an agarose gel electrophoresis assay, single-strand breaks (ssb) induced by fission neutrons and 60Co gamma-rays in aerobic aqueous solutions of pBR322 plasmid DNA were studied. The energy-deposition events of the two radiations were characterized using a Rossi-type proportional counter to measure lineal-energy spectra. For neutrons, the dose-weighted lineal-energy mean, yD, is 63 keV micron-1--about 30 times that for gamma-rays. With increasing yD, hydroxyl radicals produced within spurs or tracks are less likely to survive due to recombination effects, resulting in decreased ssb yields. In TE buffer solution, the ssb yield induced by gamma-rays is 3.2 +/- 0.66 times that induced by neutrons at the same dose. Since the direct radiation effect is small under these conditions, we can estimate that the previously unknown G for hydroxyl radical production by fission neutrons is 0.088 mumol J-1. For glycerol concentrations that give the solution a hydroxyl radical scavenging capacity similar to that of cellular environments, the ssb yield induced by gamma-rays is about 2.0 +/- 0.24 times that induced by neutrons. Analysis shows that this trend with added scavenger is caused primarily by hydroxyl radical yields.
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Affiliation(s)
- A A Stankus
- Naval Research Laboratory, Washington, DC 20375-5345, USA
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Görner H. Photochemistry of DNA and related biomolecules: quantum yields and consequences of photoionization. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1994; 26:117-39. [PMID: 7815187 DOI: 10.1016/1011-1344(94)07068-7] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The reactions of nucleic acids and constituents, which can be induced by laser UV irradiation, are described. Emphasis is placed on the quantum yields of various stable photoproducts of DNA and model compounds upon irradiation at 193, 248, 254 or 266 nm. In particular, those quantum yields and processes are discussed which involve photoionization as the initial step and occur in aqueous solution under well defined conditions, e.g. type of atmosphere. The efficiencies of some photoproducts, with respect to photoionization using irradiation at 193 or 248 nm, are presented. Radical cations of nucleobases are important sources of damage of biological substrates since they can cause lesions other than dimers and adducts, e.g. strand breakage, abasic sites, crosslinks or inactivation of plasmid and chromosomal DNA. While competing photoreactions, such as hydration, dimerization or adduct formation, diminish the selectivity of the photoionization method, a combination with model studies on pyrimidine- and purine-containing constituents of DNA has brought about an enhanced insight into the reaction mechanisms. The knowledge concerning the lethal events in plasmid and cellular DNA has been greatly improved by correlation with the chemical effects obtained by gamma-radiolysis, vacuum-UV (< 190 nm) and low-intensity irradiation at 254 nm.
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Affiliation(s)
- H Görner
- Max-Planck-Institut für Strahlenchemie, Germany
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