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Rucinski A, Biernacka A, Schulte R. Applications of nanodosimetry in particle therapy planning and beyond. Phys Med Biol 2021; 66. [PMID: 34731854 DOI: 10.1088/1361-6560/ac35f1] [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: 06/22/2021] [Accepted: 11/03/2021] [Indexed: 12/28/2022]
Abstract
This topical review summarizes underlying concepts of nanodosimetry. It describes the development and current status of nanodosimetric detector technology. It also gives an overview of Monte Carlo track structure simulations that can provide nanodosimetric parameters for treatment planning of proton and ion therapy. Classical and modern radiobiological assays that can be used to demonstrate the relationship between the frequency and complexity of DNA lesion clusters and nanodosimetric parameters are reviewed. At the end of the review, existing approaches of treatment planning based on relative biological effectiveness (RBE) models or dose-averaged linear energy transfer are contrasted with an RBE-independent approach based on nandosimetric parameters. Beyond treatment planning, nanodosimetry is also expected to have applications and give new insights into radiation protection dosimetry.
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Affiliation(s)
| | - Anna Biernacka
- University of Gdansk, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdansk, 80-307 Gdansk, Poland
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2
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Grokhovsky SL. Use of β Radiation to Localize the Binding Sites of Mercury Ions and Platinum-Containing Ligand in DNA. Mol Biol 2018. [DOI: 10.1134/s0026893318050072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Ma J, Denisov SA, Marignier JL, Pernot P, Adhikary A, Seki S, Mostafavi M. Ultrafast Electron Attachment and Hole Transfer Following Ionizing Radiation of Aqueous Uridine Monophosphate. J Phys Chem Lett 2018; 9:5105-5109. [PMID: 30132673 PMCID: PMC6126959 DOI: 10.1021/acs.jpclett.8b02170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The primary localization process of radiation-induced charges (holes (cation radical sites) and excess electrons) remains poorly understood, even at the level of monomeric DNA/RNA models, in particular, in an aqueous environment. We report the first spectroscopic study of charge transfer occurring in radiolysis of aqueous uridine 5'-monophosphate (UMP) solutions and its components: uridine, uracil, ribose, and phosphate. Our results show that prehydrated electrons effectively attach to the base site of UMP; the holes in UMP formed by either direct ionization or reaction of UMP with the radiation-mediated water cation radical (H2O•+) facilely localize on the ribose site, despite the fact that a part of them were initially created on either the phosphate or uracil. The nature of phosphate-to-sugar hole transfer is characterized as a barrierless intramolecular electron transfer with a time constant of 2.5 ns, while the base-to-sugar hole transfer occurs much faster, within a 5 ps electron pulse.
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Affiliation(s)
- Jun Ma
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
- Corresponding Author:,
| | - Sergey A. Denisov
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
| | - Jean-Louis Marignier
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
| | - Pascal Pernot
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, 146 Library Drive, Oakland University, Rochester, Michigan 48309, USA
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510
| | - Mehran Mostafavi
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
- Corresponding Author:,
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4
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Sun H, Zheng L, Greenberg MM. Independent Generation of Reactive Intermediates Leads to an Alternative Mechanism for Strand Damage Induced by Hole Transfer in Poly(dA-T) Sequences. J Am Chem Soc 2018; 140:11308-11316. [PMID: 30169029 DOI: 10.1021/jacs.8b05484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Purine radical cations (dA•+ and dG•+) are the primary hole carriers of DNA hole migration due to their favorable oxidation potential. Much less is known about the reactivity of higher energy pyrimidine radical cations. The thymidine radical cation (T•+) was produced at a defined position in DNA from a photochemical precursor for the first time. T•+ initiates hole transfer to dGGG triplets in DNA. Hole localization in a dGGG sequence accounts for ∼26% of T•+ formed under aerobic conditions in 9. Reduction to yield thymidine is also quantified. 5-Formyl-2'-deoxyuridine is formed in low yield in DNA when T•+ is independently generated. This is inconsistent with mechanistic proposals concerning product formation from electron transfer in poly(dA-T) sequences, following hole injection by a photoexcited anthraquinone. Additional evidence that is inconsistent with the original mechanism was obtained using hole injection by a photoexcited anthraquinone in DNA. Instead of requiring the intermediacy of T•+, the strand damage patterns observed in those studies, in which thymidine is oxidized, are reproduced by independent generation of 2'-deoxyadenosin- N6-yl radical (dA•). Tandem lesion formation by dA• provides the basis for an alternative mechanism for thymidine oxidation ascribed to hole migration in poly(dA-T) sequences. Overall, these experiments indicate that the final products formed following DNA hole transfer in poly(dA-T) sequences do not result from deprotonation or hydration of T•+, but rather from deprotonation of the more stable dA•+, to form dA•, which produces tandem lesions in which 5'-flanking thymidines are oxidized.
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Affiliation(s)
- Huabing Sun
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Liwei Zheng
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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5
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Kočišek J, Sedmidubská B, Indrajith S, Fárník M, Fedor J. Electron Attachment to Microhydrated Deoxycytidine Monophosphate. J Phys Chem B 2018; 122:5212-5217. [PMID: 29706064 DOI: 10.1021/acs.jpcb.8b03033] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA constituents are effectively decomposed via dissociative electron attachment (DEA). However, the DEA contribution to radiation damage in living tissues is a subject of ongoing discussion. We address an essential question, how aqueous environment influences the DEA to DNA. In particular, we report experimental fragmentation patterns for DEA to microhydrated 2-deoxycytidine 5-monophosphate (dCMP). Isolated dCMP was previously set as a model to describe mechanisms of DNA-strand breaks induced by secondary electrons and decomposes primarily by dissociation of the C-O phosphoester bond. We show that hydrated molecules decompose via dissociation of the C-N glycosidic bond followed by dissociation of the P-O bond. This significant change of the proposed mechanism can be interpreted by a reactive role of water in the postattachment dynamics. Comparison of the fragmentation with previous macroscopic irradiation studies suggests that the actual contribution of DEA to DNA radiation damage in living tissue is rather small.
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Affiliation(s)
- Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic
| | - Barbora Sedmidubská
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic.,Deptartment of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering , Czech Technical University in Prague , Brehová 7 , 115 19 Prague , Czech Republic
| | | | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic
| | - Juraj Fedor
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic
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6
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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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7
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Fujii K, Izumi Y, Narita A, Ghose KK, López-Tarifa P, Touati A, Spezia R, Vuilleumier R, Gaigeot MP, Politis MF, Du Penhoat MAH, Yokoya A. Roles of Hydration for Inducing Decomposition of 2-Deoxy-d-ribose by Ionization of Oxygen K-Shell Electrons. Radiat Res 2018; 189:264-272. [DOI: 10.1667/rr14225.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kentaro Fujii
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Japan
| | - Yudai Izumi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Ayumi Narita
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Krishna Kamol Ghose
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | - Pablo López-Tarifa
- École Polytechnique Fédérale de Lausanne, EPFL SB-ISIC-LCBC-BCH, 1015, Lausanne, Switzerland
| | - Alain Touati
- IMPMC, Sorbonne Universités - UPMC Univ Paris 06, UMR CNRS 7590, MNHN, IRD UMR 206, Paris, France
| | - Riccardo Spezia
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Paris 75005, France
| | - Marie-Pierre Gaigeot
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | - Marie-Françoise Politis
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | | | - Akinari Yokoya
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Japan
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8
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Han Y, Chen W, Kuang Y, Sun H, Wang Z, Peng X. UV-Induced DNA Interstrand Cross-Linking and Direct Strand Breaks from a New Type of Binitroimidazole Analogue. Chem Res Toxicol 2015; 28:919-26. [PMID: 25844639 DOI: 10.1021/tx500522r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Four novel photoactivated binitroimidazole prodrugs were synthesized. These agents produced DNA interstrand cross-links (ICLs) and direct strand breaks (DSB) upon UV irradiation, whereas no or very few DNA ICLs and DSBs were observed without UV treatment. Although these four molecules (1-4) contain the same binitroimidazole moiety, they bear four different leaving groups, which resulted in their producing different yields of DNA damage. Compound 4, with nitrogen mustard as a leaving group, showed the highest ICL yield. Surprisingly, compounds 1-3, without any alkylating functional group, also induced DNA ICL formation, although they did so with lower yields, which suggested that the binitroimidazole moiety released from UV irradiation of 1-3 is capable of cross-linking DNA. The DNA cross-linked products induced by these compounds were completely destroyed upon 1.0 M piperidine treatment at 90 °C (leading to cleavage at dG sites), which revealed that DNA cross-linking mainly occurred via alkylation of dGs. We proposed a possible mechanism by which alkylating agents were released from these compounds. HRMS and NMR analysis confirmed that free nitrogen mustards were generated by UV irradiation of 4. Suppression of DNA ICL and DSB formation by a radical trap, TEMPO, indicated the involvement of free radicals in the photo reactions of 3 and 4 with DNA. On the basis of these data, we propose that UV irradiation of compounds 1-4 generated a binitroimidazole intermediate that cross-links DNA. The higher ICL yield observed with 4 resulted from the amine effector nitrogen mustard released from UV irradiation.
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Affiliation(s)
- Yanyan Han
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Wenbing Chen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Yunyan Kuang
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Huabing Sun
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Zhiqiang Wang
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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9
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Ma J, Schmidhammer U, Mostafavi M. Picosecond Pulse Radiolysis of Highly Concentrated Sulfuric Acid Solutions: Evidence for the Oxidation Reactivity of Radical Cation H2O•+. J Phys Chem A 2014; 118:4030-7. [DOI: 10.1021/jp503861h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jun Ma
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bât.
349, 91405 Orsay, France
| | - Uli Schmidhammer
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bât.
349, 91405 Orsay, France
| | - Mehran Mostafavi
- Laboratoire
de Chimie Physique, CNRS/Université Paris-Sud, Bât.
349, 91405 Orsay, France
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10
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Ma J, Schmidhammer U, Pernot P, Mostafavi M. Reactivity of the Strongest Oxidizing Species in Aqueous Solutions: The Short-Lived Radical Cation H2O(•.). J Phys Chem Lett 2014; 5:258-261. [PMID: 26276210 DOI: 10.1021/jz402411x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The radical cation H2O(•+) formed under irradiation of liquid water undergoes an ultrafast proton transfer reaction and consequently exhibits an extremely short lifetime. The proton transfer yields an oxidizing OH(•) radical whose reactivity has been extensively studied. By contrast, H2O(•+) reactivity with molecules other than water has not been established experimentally and was subject to controversy. The direct oxidation by H2O(•+) can take place in various situations. In highly concentrated solutions, the radical cation H2O(•+) may also be involved in ultrafast electron transfer reactions. We have applied picosecond pulse radiolysis conducted at the electron accelerator ELYSE on solutions with various H2SO4 concentrations to determine the scavenging yield of H2O(•+). The yield of H2O(•+) at a few tens of femtoseconds is estimated to be around 5.3 × 10(-7) mol J(-1), and its reactivity is quantitatively determined. Moreover, a simple estimation of the reduction potential of this short-lived radical cation shows that it is the most powerful oxidizing species.
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Affiliation(s)
- Jun Ma
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
| | - Uli Schmidhammer
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
| | - Pascal Pernot
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
| | - Mehran Mostafavi
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
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11
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Close DM, Nelson WH, Bernhard WA. DNA damage by the direct effect of ionizing radiation: products produced by two sequential one-electron oxidations. J Phys Chem A 2013; 117:12608-15. [PMID: 24131335 DOI: 10.1021/jp4084844] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It has long been assumed that the population of radicals trapped in irradiated DNA (that is, the radicals escaping recombination) would quantitatively account for the lesions observed in DNA. Recent results indicate that this is not the case. The yield of DNA lesions exceed the yield of trappable radicals. To account for a portion of this shortfall, it is thought that some of the initially formed 2'-deoxyribose radicals undergo a second oxidation by nearby base cation radicals to form 2'-carbocations. The carbocations react to give strand breaks and free base release. Schemes are presented to account for the major oxidation products observed including 8-oxoGua, 8-oxoAde, 5-OHMeUra, and free base release. Theoretical calculations were performed to ascertain the likelihood of the second oxidation step in these reaction pathways actually occurring, and to account for base sequence dependence and various levels of hydration.
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Affiliation(s)
- David M Close
- Department of Physics, East Tennessee State University , Johnson City, Tennessee 37614, United States
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12
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Peoples AR, Lee J, Weinfeld M, Milligan JR, Bernhard WA. Yields of damage to C4' deoxyribose and to pyrimidines in pUC18 by the direct effect of ionizing radiation. Nucleic Acids Res 2012; 40:6060-9. [PMID: 22467205 PMCID: PMC3401456 DOI: 10.1093/nar/gks271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Our mechanistic understanding of damage formation in DNA by the direct effect relies heavily on what is known of free radical intermediates studied by EPR spectroscopy. Bridging this information to stable product formation requires methods with comparable sensitivities, a criterion met by the 32P-post-labeling assay developed by Weinfeld and Soderlind, [Weinfeld,M. and Soderlind,K.-J.M. (1991) 32P-Postlabeling detection of radiation-induced DNA damage: identification and estimation of thymine glycols and phosphoglycolate termini. Biochemistry, 30, 1091–1097] which when applied to the indirect effect, detected phosphoglycolate (pg) and thymine glycol (Tg). Here we applied this assay to the direct effect, measuring product yields in pUC18 films with hydration levels (Γ) of 2.5, 16 or 23 waters per nucleotide and X-irradiated at either 4 K or room temperature (RT). The yields of pg [G(pg)] for Γ ∼ 2.5 were 2.8 ± 0.2 nmol/J (RT) and 0.2 ± 0.3 nmol/J (4 K), which is evidence that the C4′ radical contributes little to the total deoxyribose damage via the direct effect. The yield of detectable base damage [G(B*)] at Γ ∼ 2.5 was found to be 30.2 ± 1.0 nmol/J (RT) and 12.9 ± 0.7 nmol/J (4 K). While the base damage called B*, could be due to either oxidation or reduction, we argue that two reduction products, 5,6-dihydrouracil and 5,6-dihydrothymine, are the most likely candidates.
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Affiliation(s)
- Anita R Peoples
- Department of Biochemistry and Biophysics, University of Rochester, Medical Center, Rochester, NY 14642, USA
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13
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McMahon SJ, Currell FJ. A Robust Curve-Fitting Procedure for the Analysis of Plasmid DNA Strand Break Data from Gel Electrophoresis. Radiat Res 2011; 175:797-805. [DOI: 10.1667/rr2514.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Stoychev SD, Kuleff AI, Cederbaum LS. Intermolecular Coulombic Decay in Small Biochemically Relevant Hydrogen-Bonded Systems. J Am Chem Soc 2011; 133:6817-24. [DOI: 10.1021/ja200963y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Spas D. Stoychev
- Theoretische Chemie, PCI, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Alexander I. Kuleff
- Theoretische Chemie, PCI, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Lorenz S. Cederbaum
- Theoretische Chemie, PCI, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
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15
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Sharma KKK, Swarts SG, Bernhard WA. Mechanisms of direct radiation damage to DNA: the effect of base sequence on base end products. J Phys Chem B 2011; 115:4843-55. [PMID: 21473599 DOI: 10.1021/jp200902h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
It has been generally assumed that product formation in DNA damaged by ionizing radiation is relatively independent of base sequence, i.e., that the yield of a given product depends primarily on the chemical properties of each DNA constituent and not on its base sequence context. We examined this assumption by comparing direct-type end products produced in films of d(CTCTCGAGAG)(2) with those produced in films of d(GCACGCGTGC)(2). Here we report the product yields in d(CTCTCGAGAG)(2) hydrated to Γ = 2.5 and 15, where Γ is the hydration level given in moles of H(2)O/mole of nucleotide. Of the 17 products monitored by GC/MS, seven exhibited statistically significant yields: 8-oxoGua, 8-oxoAde, 5-OHMeUra, 5,6-diHUra, 5,6-diHThy, 5-OHCyt, and 5-OHUra. These yields at Γ = 2.5 are compared with the yields from our previously reported study of d(GCACGCGTGC)(2) (after projecting the yields to a CG/AT ratio of 1). The ratio of projected yields, d(CTCTCGAGAG)(2) divided by d(GCACGCGTGC)(2), are 1.3 ± 0.9, 1.8 ± 0.3, 1.6 ± 0.6, 11.4 ± 4.7, 0.2 ± 0.1, >28, and 0.8 ± 1.1, respectively. Considering just d(CTCTCGAGAG)(2), the ratios of yields at Γ = 2.5 divided by yields at Γ = 15 are 0.7 ± 0.2, 0.5 ± 0.1, 2.3 ± 4.0, 3.4 ± 1.2, 3.5 ± 3.3, 1.2 ± 0.2, and 0.4 ± 0.2, respectively. The effects of sequence and hydration on base product yields are explained by a working model emphasizing the difference between two distinctly different types of reaction: (i) radical reactions that progress to nonradical intermediates and product prior to dissolution and (ii) reactions that stem from radicals trapped in the solid state at room temperature that go on to yield nonradical product after sample dissolution. Based on these findings, insights into rates of hole and excess electron-transfer relative to rates of proton transfer are discussed.
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Affiliation(s)
- Kiran K K Sharma
- School of Chemical Sciences, North Maharashtra University, Jalgaon, Maharashtra, India
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16
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Gual MR, Milian FM, Deppman A, Coelho PRP. Study of DNA damage with a new system for irradiation of samples in a nuclear reactor. Appl Radiat Isot 2011; 69:373-6. [PMID: 21075641 DOI: 10.1016/j.apradiso.2010.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 10/25/2010] [Accepted: 10/25/2010] [Indexed: 11/29/2022]
Abstract
In this paper, we report results of a quantitative analysis of the effects of neutrons on DNA, and, specifically, the production of simple and double breaks of plasmid DNA in aqueous solutions with different concentrations of free-radical scavengers. The radiation damage to DNA was evaluated by electrophoresis through agarose gels. The neutron and gamma doses were measured separately with thermoluminescent detectors. In this work, we have also demonstrated usefulness of a new system for positioning and removing samples in channel BH#3 of the IEA-R1 reactor at the Instituto de Pesquisas Energéticas e Nucleares (Brazil) without necessity of interrupting the reactor operation.
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Affiliation(s)
- Maritza R Gual
- Instituto Superior de Tecnologías y Ciencias Aplicadas, InSTEC; Avenida Salvador Allende y Luaces, Quinta de Los Molinos, Plaza de la Revolución, Havana, AP 6163, Cuba.
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17
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Vendrell O, Stoychev SD, Cederbaum LS. Generation of Highly Damaging H2O+ Radicals by Inner Valence Shell Ionization of Water. Chemphyschem 2010; 11:1006-9. [DOI: 10.1002/cphc.201000034] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sharma KK, Razskazovskiy Y, Purkayastha S, Bernhard WA. Mechanisms of strand break formation in DNA due to the direct effect of ionizing radiation: the dependency of free base release on the length of alternating CG oligodeoxynucleotides. J Phys Chem B 2009; 113:8183-91. [PMID: 19492855 DOI: 10.1021/jp900803b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The question of how NA base sequence influences the yield of DNA strand breaks produced by the direct effect of ionizing radiation was investigated in a series of oligodeoxynucleotides of the form (d(CG)(n))(2) and (d(GC)(n))(2). The yields of free base release from X-irradiated DNA films containing 2.5 waters/nucleotide were measured by HPLC as a function of oligomer length. For (d(CG)(n))(2), the ratio of the Gua yield to Cyt yield, R, was relatively constant at 2.4-2.5 for n = 2-4 and it decreased to 1.2 as n increased from 5 to 10. When Gua was moved to the 5' end, for example going from d(CG)(5) to d(GC)(5), R dropped from 1.9 +/- 0.1 to 1.1 +/- 0.1. These effects are poorly described if the chemistry at the oligomer ends is assumed to be independent of the remainder of the oligomer. A mathematical model incorporating charge transfer through the base stack was derived to explain these effects. In addition, EPR was used to measure the yield of trapped-deoxyribose radicals at 4 K following X-irradiation at 4 K. The yield of free base release was substantially greater, by 50-100 nmol/J, than the yield of trapped-deoxyribose radicals. Therefore, a large fraction of free base release stems from a nonradical intermediate. For this intermediate, a deoxyribose carbocation formed by two one-electron oxidations is proposed. This reaction pathway requires that the hole (electron loss site) transfers through the base stack and, upon encountering a deoxyribose hole, oxidizes that site to form a deoxyribose carbocation. This reaction mechanism provides a consistent way of explaining both the absence of trapped radical intermediates and the unusual dependence of free base release on oligomer length.
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Affiliation(s)
- Kiran K Sharma
- Department of Biochemistry, University of Rochester Medical Center, Rochester, New York 14642, USA
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Gomez-Mejiba SE, Zhai Z, Akram H, Deterding LJ, Hensley K, Smith N, Towner RA, Tomer KB, Mason RP, Ramirez DC. Immuno-spin trapping of protein and DNA radicals: "tagging" free radicals to locate and understand the redox process. Free Radic Biol Med 2009; 46:853-65. [PMID: 19159679 PMCID: PMC2692890 DOI: 10.1016/j.freeradbiomed.2008.12.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Revised: 12/17/2008] [Accepted: 12/19/2008] [Indexed: 12/31/2022]
Abstract
Biomolecule-centered radicals are intermediate species produced during both reversible (redox modulation) and irreversible (oxidative stress) oxidative modification of biomolecules. These oxidative processes must be studied in situ and in real time to understand the molecular mechanism of cell adaptation or death in response to changes in the extracellular environment. In this regard, we have developed and validated immuno-spin trapping to tag the redox process, tracing the oxidatively generated modification of biomolecules, in situ and in real time, by detecting protein- and DNA-centered radicals. The purpose of this methods article is to introduce and update the basic methods and applications of immuno-spin trapping for the study of redox biochemistry in oxidative stress and redox regulation. We describe in detail the production, detection, and location of protein and DNA radicals in biochemical systems, cells, and tissues, and in the whole animal as well, by using immuno-spin trapping with the nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide.
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Affiliation(s)
- Sandra E. Gomez-Mejiba
- Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Zili Zhai
- Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Hammad Akram
- Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Leesa J. Deterding
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Kenneth Hensley
- Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Nataliya Smith
- Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Rheal A. Towner
- Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Kenneth B. Tomer
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Ronald P. Mason
- Laboratory of Pharmacology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Dario C. Ramirez
- Free Radical Biology and Aging Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
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20
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Anchordoquy TJ, Molina MDC, Kempner ES. A radiation target method for size determination of supercoiled plasmid DNA. Anal Biochem 2009; 385:229-33. [PMID: 19028447 PMCID: PMC3085921 DOI: 10.1016/j.ab.2008.10.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 10/14/2008] [Accepted: 10/30/2008] [Indexed: 11/25/2022]
Abstract
Supercoiled DNA plasmids were exposed in the frozen state to high-energy electrons. Surviving supercoiled molecules were separated from their degradation products (e.g., open circle and linear forms) by agarose gel electrophoresis and subsequently quantified by staining and image analysis. Complex survival curves were analyzed using radiation target theory, yielding the radiation-sensitive mass of each form. One of the irradiated plasmids was transfected into cells, permitting radiation analysis of gene expression. Loss of this function was associated with a mass much smaller than the entire plasmid molecule, indicating a lack of energy transfer in amounts sufficient to cause structural damage along the DNA polynucleotide. The method of radiation target analysis can be applied to study both structure and function of DNA.
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Affiliation(s)
- T J Anchordoquy
- School of Pharmacy, University of Colorado Health Sciences Center, Denver, CO 80262, USA
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Sharma KKK, Milligan JR, Bernhard WA. Multiplicity of DNA single-strand breaks produced in pUC18 exposed to the direct effects of ionizing radiation. Radiat Res 2008; 170:156-62. [PMID: 18666814 DOI: 10.1667/rr1277.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 04/30/2008] [Indexed: 11/03/2022]
Abstract
The transition of plasmid DNA from a supercoiled to an open circle conformation, as detected by gel electrophoresis, affords an extraordinarily sensitive method for detecting single-strand breaks (SSBs), one measure of deoxyribose damage. To determine the yield of SSBs, G(ssb), by this method, it is commonly assumed that Poisson statistics apply such that, on average, one SSB occurs per supercoiled plasmid lost. For the direct effect, at a large enough plasmid size, this assumption may be invalid. In this report, the assumption that one SSB occurs per pUC18 plasmid (2686 bp) is tested by measuring free base release (fbr), which is also a measure of deoxyribose damage in films prepared under controlled relative humidity so as to produce known levels of DNA hydration. The level of DNA hydration, Gamma, is expressed in mol water/mol nucleotide. The yield of free base release, G(fbr), was measured by HPLC after exposure of the films to 70 kV X rays and subsequent dissolution in water. It is well known that damage in deoxyribose leads to SSBs and free base release. Based on known mechanisms, there exists a close correspondence between free base release and SSBs, i.e., G(fbr) congruent with G(ssb). Following this assumption, the SSB multiplicity, m(ssb), was determined, where m(ssb) was defined as the mean number of SSBs per supercoiled plasmid lost. The yield of lost supercoil was determined previously (S. Purkayastha et al., J. Phys. Chem. B 110, 26286-26291, 2006). We found that m(ssb) = 1.4 +/- 0.2 at Gamma = 2.5 and m(ssb) = 2.8 +/- 0.5 to 3.1 +/- 0.5 at Gamma = 22.5, indicating that the assumption of one SSB per lost supercoil is not likely to hold for a 2686-bp plasmid exposed to the direct effect. In addition, an increase in G(fbr), upon stepping from Gamma = 2.5 to Gamma = 22.5, was paralleled by an increase in the yield of trapped deoxyribose radicals, G(dRib)(fr), also measured previously. As a consequence, the shortfall between SSBs and trapped radicals, G(diff) = G(ssb) - G(dRib)(fr), remained relatively constant at 90-110 nmol/J. The lack of change between the two extremes of hydration is in keeping with the suggestion that non-radical species, such as doubly oxidized deoxyribose, are responsible for the shortfall.
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Affiliation(s)
- Kiran Kumar K Sharma
- Department of Biochemistry and Biophysics, University of Rochester, 575 Elmwood Avenue, Rochester, NY 14642, USA
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Butterworth KT, Wyer JA, Brennan-Fournet M, Latimer CJ, Shah MB, Currell FJ, Hirst DG. Variation of strand break yield for plasmid DNA irradiated with high-Z metal nanoparticles. Radiat Res 2008; 170:381-7. [PMID: 18763863 DOI: 10.1667/rr1320.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 04/29/2008] [Indexed: 04/11/2024]
Abstract
Using agarose gel electrophoresis, we measured the effectiveness of high-Z metal particles of different sizes on SSB and DSB yields for plasmid DNA irradiated with 160 kVp X rays. For plasmid samples prepared in Tris-EDTA buffer, gold nanoparticles were shown to increase G'(SSB) typically by a factor of greater than 2 while G'(DSB) increased by a factor of less than 2. Similar dose-modifying effects were also observed using gold microspheres. Addition of 10(-1) M DMSO typically decreased damage yields by a factor of less than 0.5. Plasmid samples prepared in PBS showed significantly different damage yields compared to those prepared in Tris-EDTA (P < 0.001) with G'(SSB) and G'(DSB) increasing by factors of 100 and 48, respectively. Furthermore, addition of gold nanoparticles to samples prepared in PBS decreased G'(SSB) and G'(DSB) by factors of 0.2 and 0.3, respectively. The results show plasmid damage yields to be highly dependent on differences in particle size between the micro- and nanometer scale, atomic number (Z) of the particle, and scavenging capacity of preparation buffers. This study provides further evidence using a plasmid DNA model system for the potential of high-Z metal nanoparticles as local dose-modifying agents.
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Affiliation(s)
- K T Butterworth
- Experimental Therapeutics Research Group, School of Pharmacy Queen's University Belfast Northern Ireland, BT9 7BL.
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Urushibara A, Shikazono N, O'Neill P, Fujii K, Wada S, Yokoya A. LET dependence of the yield of single-, double-strand breaks and base lesions in fully hydrated plasmid DNA films by 4He(2+) ion irradiation. Int J Radiat Biol 2008; 84:23-33. [PMID: 17852554 DOI: 10.1080/09553000701616072] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE To characterize the complexity of DNA damage through determination of the yields of single (SSB) and double strand breaks (DSB), base lesions and clustered damage sites induced in fully hydrated plasmid DNA by direct radiation effects as a function of the ionizing density of the radiation using 4He(2+) ion irradiation with linear energy-transfer (LET) values in the range 19 to 148 keV/microm. MATERIALS AND METHODS Hydrated plasmid DNA (pUC18) containing 34.5 water molecules/nucleotide was irradiated with He(2+) ions with LET values of 19, 63, 95, 121 and 148 keV/microm. From quantification of the conformational changes of the irradiated samples (closed circular, open or linear forms) analyzed by agarose gel electrophoresis, the yields of SSB and DSB were obtained. Base lesions were visualized as additional strand breaks by treatment with base excision repair enzymes (endonuclease III (Nth) and formamidpyrimidine DNA glycosylase (Fpg)). RESULTS The yield of prompt SSB does not depend significantly on LET of the 4He(2+) ions, whereas the yield of prompt DSB increases with increasing LET. The yields of isolated base lesions, revealed by Nth and Fpg as additional SSB, decrease drastically with increasing LET. The sum of the yields of DSB and additional DSB revealed by Nth and Fpg increase with increasing LET of the 4He(2+) ions except at the highest LET investigated. CONCLUSION The yields of clustered damage, revealed as DSB and non-DSB clustered damage sites, but not isolated lesions, namely SSB, increase with increasing ionization density of the 4He(2+) ions except at the highest LET investigated.
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Affiliation(s)
- Ayumi Urushibara
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
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Purkayastha S, Milligan JR, Bernhard WA. On the chemical yield of base lesions, strand breaks, and clustered damage generated in plasmid DNA by the direct effect of X rays. Radiat Res 2007; 168:357-66. [PMID: 17705639 PMCID: PMC2631664 DOI: 10.1667/rr0964.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 05/08/2007] [Indexed: 11/03/2022]
Abstract
The purpose of this study was to determine the yield of DNA base damages, deoxyribose damage, and clustered lesions due to the direct effects of ionizing radiation and to compare these with the yield of DNA trapped radicals measured previously in the same pUC18 plasmid. The plasmids were prepared as films hydrated in the range 2.5 < Gamma < 22.5 mol water/mol nucleotide. Single-strand breaks (SSBs) and double-strand breaks (DSBs) were detected by agarose gel electrophoresis. Specific types of base lesions were converted into SSBs and DSBs using the base-excision repair enzymes endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg). The yield of base damage detected by this method displayed a strikingly different dependence on the level of hydration (Gamma) compared with that for the yield of DNA trapped radicals; the former decreased by 3.2 times as Gamma was varied from 2.5 to 22.5 and the later increased by 2.4 times over the same range. To explain this divergence, we propose that SSB yields produced in plasmid DNA by the direct effect cannot be analyzed properly with a Poisson process that assumes an average of one strand break per plasmid and neglects the possibility of a single track producing multiple SSBs within a plasmid. The yields of DSBs, on the other hand, are consistent with changes in free radical trapping as a function of hydration. Consequently, the composition of these clusters could be quantified. Deoxyribose damage on each of the two opposing strands occurs with a yield of 3.5 +/- 0.5 nmol/J for fully hydrated pUC18, comparable to the yield of 4.1 +/- 0.9 nmol/J for DSBs derived from opposed damages in which at least one of the sites is a damaged base.
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Affiliation(s)
- Shubhadeep Purkayastha
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
| | - Jamie R. Milligan
- Department of Radiology, University of California at San Diego, La Jolla, California 92093-0610
| | - William A. Bernhard
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- Address for correspondence: Department of Biochemistry & Biophysics, 575 Elmwood Avenue, Rochester, NY 14642; e-mail:
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Swarts SG, Gilbert DC, Sharma KK, Razskazovskiy Y, Purkayastha S, Naumenko KA, Bernhard WA. Mechanisms of direct radiation damage in DNA, based on a study of the yields of base damage, deoxyribose damage, and trapped radicals in d(GCACGCGTGC)(2). Radiat Res 2007; 168:367-81. [PMID: 17705640 PMCID: PMC2791345 DOI: 10.1667/rr1058.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 05/17/2007] [Indexed: 11/03/2022]
Abstract
Dose-response curves were measured for the formation of direct-type DNA products in X-irradiated d(GCACGCGTGC)(2)prepared as dry films and as crystalline powders. Damage to deoxyribose (dRib) was assessed by HPLC measurements of strand break products containing 3' or 5' terminal phosphate and free base release. Base damage was measured using GC/ MS after acid hydrolysis and trimethylsilylation. The yield of trappable radicals was measured at 4 K by EPR of films X-irradiated at 4 K. With exception of those used for EPR, all samples were X-irradiated at room temperature. There was no measurable difference between working under oxygen or under nitrogen. The chemical yields (in units of nmol/J) for trapped radicals, free base release, 8-oxoGua, 8-oxoAde, diHUra and diHThy were G(total)(fr) = 618 +/- 60, G(fbr) = 93 +/- 8, G(8-oxoGua) = 111 +/- 62, G(8-oxoAde) = 4 +/- 3, G(diHUra) = 127 +/- 160, and G(diHThy) = 39 +/- 60, respectively. The yields were determined and the dose-response curves explained by a mechanistic model consisting of three reaction pathways: (1) trappable-radical single-track, (2) trappable-radical multiple-track, and (3) molecular. If the base content is projected from the decamer's GC:AT ratio of 4:1 to a ratio of 1:1, the percentage of the total measured damage (349 nmol/J) would partition as follows: 20 +/- 16% 8-oxoGua, 3 +/- 3% 8-oxoAde, 28 +/- 46% diHThy, 23 +/- 32% diHUra, and 27 +/- 17% dRib damage. With a cautionary note regarding large standard deviations, the projected yield of total damage is higher in CG-rich DNA because C combined with G is more prone to damage than A combined with T, the ratio of base damage to deoxyribose damage is approximately 3:1, the yield of diHUra is comparable to the yield of diHThy, and the yield of 8-oxoAde is not negligible. While the quantity and quality of the data fall short of proving the hypothesized model, the model provides an explanation for the dose-response curves of the more prevalent end products and provides a means of measuring their chemical yields, i.e., their rate of formation at zero dose. Therefore, we believe that this comprehensive analytical approach, combined with the mechanistic model, will prove important in predicting risk due to exposure to low doses and low dose rates of ionizing radiation.
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Affiliation(s)
| | | | | | | | | | | | - William A. Bernhard
- Address for correspondence: Dept. of Biochemistry & Biophysics, 575 Elmwood Ave., Rochester, NY 14642;
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Sharma KK, Purkayastha S, Bernhard WA. Unaltered free base release from d(CGCGCG)2 produced by the direct effect of ionizing radiation at 4 K and room temperature. Radiat Res 2007; 167:501-7. [PMID: 17474798 PMCID: PMC2603164 DOI: 10.1667/rr0847.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 12/15/2006] [Indexed: 11/03/2022]
Abstract
Unaltered free base release in d(CGCGCG)2 exposed to X rays at 4 K or room temperature was measured by HPLC. Samples were prepared either as films hydrated to a level of Gamma = 2.5 mol water/mol nucleotide or as polycrystalline with Gamma approximately 7.5 mol water/mol nucleotide. X irradiation of films at 4 K, followed by annealing to room temperature, resulted in yields for cytosine and guanine of G(Cyt) = 0.036 +/- 0.001 micromol/J and G(Gua) = 0.090 +/- 0.002 micromol/J. Irradiation of films at room temperature gave similar yields. The yields for polycrystalline d(CGCGCG)2 X-irradiated at room temperature were G(Cyt) = 0.035 +/- 0.005 micromol/J and G(Gua) = 0.077 +/- 0.023 micromol/J. The total free base release yield, G(fbr), was 0.124 +/- 0.008 micromol/J for films and 0.112 +/- 0.028 micromol/J for polycrystalline samples. G(fbr) is believed to be a good estimate of total strand break yield. The yields of total free radicals trapped [G(Sigmafr)] by the d(CGCGCG)2 films at 4 K were measured by EPR. The measured value, G(Sigmafr) = 0.450 +/- 0.005 micromol/J, was used to calculate the yield of trappable sugar radicals, giving G(sugar)(fr) = 0.04-0.07 micromol/J. We found that (1) guanine release exceeded cytosine release by more than twofold, (2) G(sugar)(fr) cannot account for more than half of the free base release, and (3) G(fbr), G(Cyt) and G(Gua) were independent of the sample temperature during irradiation. Finding (1) suggests that base and or sequence influences sugar damage, and finding (2) is consistent with our working hypothesis that an important pathway to strand break formation entails two one-electron oxidations at the same sugar site.
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Affiliation(s)
- Kiran K Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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Purkayastha S, Milligan JR, Bernhard WA. An investigation into the mechanisms of DNA strand breakage by direct ionization of variably hydrated plasmid DNA. J Phys Chem B 2007; 110:26286-91. [PMID: 17181287 PMCID: PMC1817901 DOI: 10.1021/jp065489i] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms by which ionizing radiation directly causes strand breaks in DNA were investigated by comparing the chemical yield of DNA-trapped free radicals to the chemical yield of DNA single strand break (ssb) and double strand break (dsb), as a function of hydration (Gamma). Solid-state films of plasmid pUC18, hydrated to 2.5 < Gamma < 22.5 mol, were X-irradiated at 4 K, warmed to room temperature, and dissolved in water. Free radical yields were determined by EPR at 4 K. With use of the same samples, Gel electrophoresis was used to measure the chemical yield of total strand breaks, which includes prompt plus heat labile ssb; G'total(ssb) decreased from 0.092 +/- 0.016 micromol/J at Gamma= 2.5 to 0.066 +/- 0.008 micromol/J at Gamma= 22.5. Most provocative is that at Gamma= 2.5 the yield of total ssb exceeds the yield of trapped deoxyribose radicals: G'total(ssb) - G'sugar(fr) = 0.06 +/- 0.02 micromol/J. Nearly 2/3 of the strand breaks are derived from precursors other than radicals trapped on the deoxyribose moiety. To account for these nonradical precursors, we hypothesize that strand breaks are produced by two one-electron oxidations at a single deoxyribose residue within an ionization cluster.
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Affiliation(s)
| | | | - William A. Bernhard
- * To whom correspondence should be addressed. E-mail: . Fax: (585) 275-6007. Phone: (585) 275-3730
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Abstract
Immuno-spin trapping is a highly sensitive method for detecting DNA radicals in biological systems. This technique involves three main steps: (i) in situ and real-time trapping of DNA radicals with the nitrone spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), thus forming DMPO-DNA nitrone adducts (referred to here as nitrone adducts); (ii) purification of nitrone adducts; and (iii) analysis of nitrone adducts by heterogeneous immunoassays using Abs against DMPO. In experiments, DMPO is added prior to the formation of free radicals. It diffuses easily through all cell compartments and is present when DNA free radicals are formed as a result of oxidative damage. Due to its low toxicity, DMPO can be used in cells at high enough concentrations to out-compete the normal reactions of DNA radicals, thus ensuring a high yield of DNA nitrone adducts. Because both protein and DNA nitrone adducts are formed, it is important that the DNA be pure in order to avoid misinterpretations. Depending on the model under study, this protocol can be completed in as few as 6 h.
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Affiliation(s)
- Dario C Ramirez
- Laboratory of Pharmacology and Chemistry, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Drive, Building 101, MD F0-02, Research Triangle Park, North Carolina 27709, USA.
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Zhang JD, Schaefer HF. Molecular Structures and Energetics Associated with Hydrogen Atom Addition to the Guanine−Cytosine Base Pair. J Chem Theory Comput 2006; 3:115-26. [DOI: 10.1021/ct600262p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jun D. Zhang
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2525
| | - Henry F. Schaefer
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2525
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31
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Purkayastha S, Milligan JR, Bernhard WA. The role of hydration in the distribution of free radical trapping in directly ionized DNA. Radiat Res 2006; 166:1-8. [PMID: 16808596 PMCID: PMC1847792 DOI: 10.1667/rr3585.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The purpose of this study was to elucidate the role of hydration (Gamma) in the distribution of free radical trapping in directly ionized DNA. Solid-state films of pUC18 (2686 bp) plasmids were hydrated to Gamma in the range 2.5 < or = Gamma < or = 22.5 mol water/mol nucleotide. Free radical yields, G(Sigmafr), measured by EPR at 4 K are seen to increase from 0.28 +/- 0.01 micromol/J at Gamma = 2.5 to 0.63 +/- 0.01 micromol/J at Gamma= 22.5, respectively. Based on a semi-empirical model of the free radical trapping events that follow the initial ionizations of the DNA components, we conclude that two-thirds of the holes formed on the inner solvation shell (Gamma < 10) transfer to the sugar-phosphate backbone. Likewise, of the holes produced by direct ionization of the sugar-phosphate, about one-third are trapped by deprotonation as neutral sugar-phosphate radical species, while the remaining two-thirds are found to transfer to the bases. This analysis provides the best measure to date for the probability of hole transfer (approximately 67%) into the base stack. It can thus be predicted that the distribution of holes formed in fully hydrated DNA at 4 K will be 78% on the bases and 22% on the sugar-phosphate. Adding the radicals due to electron attachment (confined to the pyrimidine bases), the distribution of all trapped radicals will be 89% on the bases and 11% on the sugar-phosphate backbone. This prediction is supported by partitioning results obtained from the high dose-response curves fitted to the two-component model. These results not only add to our understanding of how the holes redistribute after ionization but are also central to predicting the yield and location of strand breaks in DNA exposed to the direct effects of ionizing radiation.
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Affiliation(s)
- Shubhadeep Purkayastha
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York, 14642
| | - Jamie R. Milligan
- Department of Radiology, University of California at San Diego, La Jolla, California 92093-0610
| | - William A. Bernhard
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York, 14642
- Address for correspondence: Department of Biochemistry & Biophysics, 575 Elmwood Ave., Rochester, NY 14642; e-mail:
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