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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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Hervé du Penhoat MA, Kamol Ghose K, Gaigeot MP, Vuilleumier R, Fujii K, Yokoya A, Politis MF. Investigation of the fragmentation of core-ionised deoxyribose: a study as a function of the tautomeric form. Phys Chem Chem Phys 2015; 17:32375-83. [DOI: 10.1039/c5cp05196g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fragmentation dynamics following the core ionisation of isolated 2-deoxy-d-ribose by DFT-MD simulations.
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Affiliation(s)
| | | | | | - Rodolphe Vuilleumier
- Ecole Normale Supérieure
- Département de Chimie
- UMR 8640 CNRS-ENS-UPMC
- 75005 Paris
- France
| | - Kentaro Fujii
- Advance Science Research Center
- Japan Atomic Energy Agency
- Tokai
- Japan
| | - Akinari Yokoya
- Advance Science Research Center
- Japan Atomic Energy Agency
- Tokai
- Japan
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Fujii K, Fukuda Y, Yokoya A. Observation of cleavage in DNA and nucleotides following oxygen K-shell ionization by measuring X-ray absorption near edge structure. Int J Radiat Biol 2012; 88:888-94. [PMID: 22702534 DOI: 10.3109/09553002.2012.703363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To investigate which type of bond is more likely to be cleaved in functional groups in DNA including the nucleobases by the K-shell ionization of oxygen of DNA, and to determine whether the production of propenal is specific to the oxygen resonant excitation. To investigate the degradation pattern which depends on the type of nucleobase in the DNA monomer. MATERIALS AND METHODS Calf thymus DNA film and four nucleotides (dAMP, TMP, dGMP, and dCMP) films were used as samples. Soft X-rays with energy of 560 eV were used to irradiate the samples, and the changes in the X-ray absorption near edge structure (XANES) spectra during the irradiation were measured. The XANES measurements were performed by using a 0.02 eV scanning photon energy step. RESULTS The difference spectra for DNA and nucleotides were similar to those for pyridine deprotonation. The oxygen K-edge regions in the difference spectra were all similar apart from the spectrum obtained at the resonant excitation energy of oxygen in DNA. The spectral change did not depend on the type of nucleotide. CONCLUSION (1) Deprotonation of the nucleobase -NH is usually induced by core ionization of carbon, nitrogen, and oxygen; (2) propenal production is specific to the oxygen K-shell resonant excitation; and (3) the pattern of XANES spectral changes does not significantly depend on the type of nucleobase.
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Affiliation(s)
- Kentaro Fujii
- Advanced Science Research Center, Japan Atomic Energy Agency, Tokai, Naka, Ibaraki, Japan.
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Fujii K, Yokoya A. Spectral change in X-ray absorption near edge structure of DNA thin films irradiated with monochromatic soft X-rays. Radiat Phys Chem Oxf Engl 1993 2009. [DOI: 10.1016/j.radphyschem.2009.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yokoya A, Fuji K, Shikazono N, Akamatsu K, Urushibara A, Watanabe R. Studies of soft X-ray-induced Auger effect on the induction of DNA damage. Int J Radiat Biol 2009; 84:1069-81. [DOI: 10.1080/09553000802534950] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Fujii K, Yokoya A, Shikazono N. Induction of single strand breaks, and base lesions in plasmid DNA films induced by carbon, nitrogen, and oxygenKLLAuger process. Int J Radiat Biol 2009; 84:1104-11. [DOI: 10.1080/09553000802482564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Fujii K, Akamatsu K, Yokoya A. Decomposition of 2‐deoxy‐D‐ribose by irradiation with 0.6 keV electrons and by 0.5 keV ultrasoft X‐rays. Int J Radiat Biol 2009; 80:909-14. [PMID: 15764401 DOI: 10.1080/09553000400017721] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE To compare the molecular decomposition of 2-deoxy-D-ribose induced by 0.6 keV electron irradiation or by 0.5keV ultrasoft X-ray irradiation. MATERIALS AND METHODS A thin film of 2-deoxy-D-ribose was irradiated by two radiation sources: low-energy (approximately 0.6 keV) electrons and ultrasoft X-rays (approximately 0.5 keV). The positive ions that were desorbed from the sample during the irradiation were measured using a quadrupole mass spectrometer. The spectral changes in the X-ray absorption near edge structure (XANES) were also examined after the irradiation. RESULTS AND DISCUSSION The ions that were desorbed from 2-deoxy-D-ribose due to electron irradiation were mainly H+, CHx+, C2Hx+, CO+, CHxO+, C3Hx+, C2HxO+ and C3sHO+ (x=1, 2, and 3) ions. These ions were the same as those observed in desorption due to ultrasoft X-ray irradiation. The XANES spectral changes induced by electron irradiation showed C-O bond cleavage in the molecule and C=O bond formation in the surface residues. These results show that intensive molecular decomposition of the furanose ring structure was induced by both types of irradiation. It is inferred that these irradiation products are primarily produced by secondary electrons (several tens of eV), which are thought to be generated by both types of irradiation when they are applied to the 2-deoxy-D-ribose sample.
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Affiliation(s)
- Kentaro Fujii
- Radiation Risk Analysis Laboratory, Japan Atomic Energy Research Institute, 2-4 Shirakatashirane, Tokai, Ibaraki 319-1195 Japan.
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Abstract
PURPOSE The extreme radiotoxicity of Auger electrons and their exquisite capacity to irradiate specific molecular sites has prompted scientists to extensively investigate their radiobiological effects. Their efforts have been punctuated by quadrennial international symposia that have focused on biophysical aspects of Auger processes. The latest meeting, the 6th International Symposium on Physical, Molecular, Cellular, and Medical Aspects of Auger Processes, was held 5-6 July 2007 at Harvard Medical School in Boston, Massachusetts, USA. This article provides a review of the research in this field that was published during the years 2004-2007, the period that has elapsed since the previous meeting. CONCLUSION The field has advanced considerably. A glimpse of the potential of this unique form of ionizing radiation to contribute to future progress in a variety of fields of study is proffered.
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Affiliation(s)
- Roger W Howell
- Department of Radiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA.
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Vall-llosera G, Huels MA, Coreno M, Kivimäki A, Jakubowska K, Stankiewicz M, Rachlew E. Photofragmentation of 2-Deoxy-D-Ribose Molecules in the Gas Phase. Chemphyschem 2008; 9:1020-9. [DOI: 10.1002/cphc.200700635] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Akamatsu K. A novel methodology for characterizing strand-break termini and damaged bases in plasmid DNA exposed to ionizing radiation. Anal Biochem 2007; 362:229-35. [PMID: 17258165 DOI: 10.1016/j.ab.2006.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/03/2006] [Accepted: 12/04/2006] [Indexed: 10/23/2022]
Abstract
We have developed a de novo methodology to characterize radiation damage in DNA. An enzyme system consisting of the 3'-->5' exonuclease snake venom phosphodiesterase (SVPD) and calf intestine alkaline phosphatase (CIAP) was used to examine the 3' termini of strand-break sites. In this study, we hypothesized that the strand-break termini can be divided into two categories: CIAP-independent SVPD sites and CIAP-dependent SVPD sites. The former consists of strand-break termini that can be recognized directly and digested by SVPD without CIAP pretreatment, whereas the latter includes the termini that cannot be digested by SVPD without CIAP pretreatment. In addition, the apparent radiation-chemical yield (G value) can be estimated using the level of intact 2'-deoxynucleotides produced during a 15-min incubation with SVPD. The G value for total strand breaks in fully dried DNA irradiated with (60)Co gamma-rays was estimated to be 0.1 micromol/J. Moreover, the G values of CIAP-dependent and CIAP-independent SVPD sites were estimated to be 0.078 and 0.024 micromol/J, respectively. These values suggest that 3'-phosphate termini are more likely to be produced than 3' termini without phosphate. Furthermore, piperidine-treated irradiated plasmid DNA was also treated with the same enzyme system to examine the piperidine-labile sites. As a result of the treatment, the G value of the CIAP-dependent SVPD sites increased to 0.16 micromol/J, whereas no significant increase was seen in the G value of the CIAP-independent SVPD sites. This observation implies that most piperidine-labile damaged bases can be eliminated to form apurinic/apyrimidinic sites, which are completely removed by piperidine treatment to form 3' phosphate termini, and that prompt CIAP-independent SVPD sites are piperidine resistant.
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Affiliation(s)
- Ken Akamatsu
- Radiation Effect Analysis Group, Nuclear Science and Engineering Directorate, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-Mura, Naka-Gun, Ibaraki, Japan.
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Akamatsu K, Fujii K, Yokoya A. Qualitative and quantitative analyses of the decomposition products that arise from the exposure of thymine to monochromatic ultrasoft X rays and 60Co gamma rays in the solid state. Radiat Res 2004; 161:442-50. [PMID: 15038767 DOI: 10.1667/3151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
HPLC analyses of condensed thymine irradiated with monochromatic synchrotron ultrasoft X rays in the energy region around nitrogen and oxygen K-shell edges were performed. Cobalt-60 gamma rays were used as a reference radiation. The radiation chemical dose response of each separated thymine decomposition product was also determined. Uracil (U), 5-(hydroxymethyl)uracil (HMU), 5,6-dihydrothymine (DHT), 5-formyluracil (foU) and four main unknown products were found in the HPLC chromatogram of the sample irradiated with ultrasoft X rays in vacuo. Similar spectra of the products were also found in the gamma-ray experiment; however, some unknown products that appeared after elution of the thymine peak were significantly larger than those in the ultrasoft X- ray experiment. This result indicates the difference in radiation quality. The G value of DHT produced by gamma radiation was 10 times larger than those produced by the ultrasoft X- ray photons with energies of 395 and 407 eV corresponding to below and on the nitrogen K-shell edge, respectively. This result suggests that the differences in the photon energy and/ or in the energy spectra of the secondary electron between ultrasoft X rays and gamma rays are causing differences in the process of the radiation chemistry. Moreover, the yields of all the thymine decomposition products induced by 538 eV photons (oxygen K-shell edge) were significantly smaller than those induced by photons around the nitrogen K-shell edge. The K-shell excitation of oxygen in thymine may efficiently promote the production of small thymine fragments susceptible to desorption from the sample.
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Affiliation(s)
- Ken Akamatsu
- Radiation Risk Laboratory, Department of Health Physics, Japan Atomic Energy Research Institute, 2-4 Shirakatashirane, Tokai, Naka, Ibaraki 319-1195, Japan.
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