Localization Estimation of Ionizing Radiation-Induced Abasic Sites in DNA in the Solid State Using Fluorescence Resonance Energy Transfer

Radiation Research

Volumn 183, Issue 1, 2015, Pages 105-113

  Akamatsu, Ken ^a   Shikazono, Naoya ^a   Saito, Takeshi ^b  

^a JAPAN ATOMIC ENERGY AGENCY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COBALT 60; COMPLEMENTARY DNA; DEOXYRIBONUCLEASE I; DOUBLE STRANDED DNA; FLUORESCENT DYE; OLIGOMER; URACIL DNA GLYCOSIDASE; DNA;

APYRIMIDINIC SITE; ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; DNA DAMAGE; DNA REPAIR; ENERGY TRANSFER; EXCISION REPAIR; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUOROMETRY; GAMMA IRRADIATION; HEAT TREATMENT; IONIZING RADIATION; PRIORITY JOURNAL; RADIATION DOSE; ALPHA RADIATION; CHEMISTRY; GAMMA RADIATION; GENETICS;

ALPHA PARTICLES; DNA; DNA DAMAGE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GAMMA RAYS; RADIATION DOSAGE;

EID: 84925282809     PISSN: 00337587     EISSN: 19385404     Source Type: Journal    
DOI: 10.1667/RR13780.1     Document Type: Article

References (43)

1. Goodhead DT. Initial events in the cellular effects of ionizing radiations: clustered damage in DNA. Int J Radiat Biol 1994; 65: 7-17.
2. Ward JF. The complexity of DNA damage: relevance to biological consequences. Int J Radiat Biol 1994; 66: 427-32.
3. Boudaïffa B, Cloutier P, Hunting D, Huels MA, Sanche L. Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons. Science 2000; 287: 1658-60.
4. Huels MA, Boudaïffa B, Cloutier P, Hunting D, Sanche L. Single, double, and multiple double strand breaks induced in DNA by 3 - 100 eV electrons. J Am Chem Soc 2003; 125: 4467-77.
5. Pearson CG, Shikazono N, Thacker J, O'Neill P. Enhanced mutagenic potential of 8-oxo-7,8-dihydroguanine when present within a clustered DNA damage site. Nucleic Acids Res 2004; 32: 263-70.
6. Shikazono N, Pearson C, O'Neill P, Thacker J. The roles of specific glycosylases in determining the mutagenic consequences of clustered DNA base damage. Nucleic Acids Res 2006; 34: 3722-30.
7. Harrison L, Hatahet Z, Purmal AA, Wallace SS. Multiply damaged sites in DNA: interactions with Escherichia coli endonuclease III and VIII. Nucleic Acids Res 1998; 26: 932-41.
8. Shikazono N, Akamatsu K, Takahashi M, Noguchi M, Urushibara A, O'Neill P, et al. Significance of DNA polymerase I in in vivo processing of clustered DNA damage. Mutat Res 2013; 749: 9-15.
9. Harrison L, Brame KL, Geltz LE, Landry AM. Closely opposed apurinic /apyrimidinic sites are converted to double strand breaks in Escherichia coli even in the absence of exonuclease III, endonuclease IV, nucleotide excision repair and AP lyase cleavage. DNA Repair 2006; 5: 324-35.
10. D'souza DI, Harrison L. Repair of clustered uracil DNA damage in Escherichia coli. Nucleic Acids Res 2003; 31: 4573-81.
11. Malyarchuk S, Brame KL, Youngblood R, Shi R, Harrison L. Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli. Nucleic Acids Res 2004; 32: 5721-31.
12. Sutherland BM, Bennett PV, Sidorkina O, Laval J. Clustered damages and total lesions induced in DNA by ionizing radiation: oxidized bases and strand breaks. Biochemistry 2000; 39: 8026-31.
13. Georgakilas AG, Bennett PV, Sutherland BM. High efficiency detection of bi-stranded abasic clusteres in c-irradiated DNA by putrescine. Nucleic Acids Res 2002; 30: 2800-8.
14. Hada M, Georgakilas AG. Formation of clustered DNA damage after high-LET irradiation: a review. J Radiat Res 2008; 49: 203-10.
15. Terato H, Tanaka R, Nakaarai Y, Nohara T, Doi Y, Iwai S, et al. Quantitative analysis of isolated and clustered DNA damage induced by gamma-rays, carbon ion beams, and iron ion beams. J Radiat Res 2008; 49: 133-46.
16. Chaudhry MA, Weinfeld M. The action of Escherichia coli endonuclease III on multiply damaged sites in DNA. J Mol Biol 1995; 249: 914-22.
17. Chaudhry MA, Weinfeld M. Reactivity of human apurinic/ apyrimidinic endonuclease and Escherichia coli exonuclease IIIwith bistranded abasic sites in DNA. J Biol Chem 1997; 272: 15650-55.
18. Ottolenghi A, Merzagora M, Paretzke HG. DNA complex lesions induced by protons and a-particles: track structure characteristics determining linear energy transfer and particle type dependence. Radiat Environ Biophys 1997; 36: 97-103.
19. Holley WR, Chatterjee A. Clusters of DNA damage induced by ionizing radiation: formation of short DNA fragments. I. Theoretical modeling. Radiat Res 1996; 145: 188-99.
20. Nikjoo H, Uehara S, Wilson WE, Hoshi M, Goodhead DT. Track structure in radiation biology: theory and application. Int J Radiat Biol 1998; 73: 355-64.
21. Nikjoo H, O'Neill P, Wilson WE, Goodhead DT. Computational approach for determining the spectrum of DNA damage induced by ionizing radiation. Radiat Res 2001; 156: 577-83.
22. Nikjoo H, O'Neill P, Goodhead DT, Terrissol M. Computational modeling of low-energy electron-induced DNA damage by early physical and chemical events. Int J Radiat Biol 1997; 71: 467-83.
23. Akamatsu K, Shikazono N. A methodology for estimating localization of apurinic/apyrimidinic sites in DNA using fluorescence Resonance Energy Transfer. Anal Biochem 2013; 433: 171-80.
24. Albani JR. Principles and applications of fluorescence spectroscopy. Oxford: Blackwell; 2007. p. 197.
25. Rosa S, Fortini P, Karran P, Bignami M, Dogliotti E. Processing in vivo of an abasic site reacted with methoxylamine: a new assay for the detection of abasic sites formed in vivo. Nucleic Acids Res 1991; 19: 5569-74.
26. Ide H, Akamatsu K, Kimura Y, Michiue K, Makino K, Asaeda A, et al. Synthesis and damage specificity of a novel probes for the detection of abasic sites in DNA. Biochemistry 1993; 32: 8276-83.
27. Nakamura J, Walker VE, Upton PB, Chiang S-Y, Kow YW, Swenberg JA. Highly sensitive apurinic/apyrimidinic site assay can detect spontaneous and chemically induced depurination under physiological conditions. Cancer Res 1998; 58: 222-5.
28. Pogozelski WK, Tullius TD. Oxidative strand scission of nucleic acids: routes initiated by hydrogen abstraction from the sugar moiety. Chem Rev 1998; 98: 1089-107.
29. Johnson I, Spence MTZ. Molecular probes handbook, a guide to fluorescent probes and labeling technologies. 11th ed. Carlsbad: Life Technologies; 2010. p. 39.
30. 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.
31. X-ray mass attenuation coefficients. Table 4. Gaithersburg, MD: National Institute of Standards and Technology (NIST). (http://1.usa.gov/1tYKl2A)
32. Tanaka A, Watanabe H, Shimizu T, Inoue M, Kikuchi M, Kobayashi Y, et al. Penetration controlled irradiation with ion beams for biological study. Nucl Instr Meth B 1997; 129: 42-8.
33. Tanaka S, Fukuda M, Nishimura K, Watanabe H, Yamano N. IRACM: a code system to calculate induced radioactivity produced by ions and neutrons. JAERI-Data/Code 97-019. Tokai, Ibaraki: Japan Atomic Energy Research Institute; 1997: 97-019.
34. 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 4He2+ ion irradiation. Int J Radiat Biol 2008; 84: 23-33.
35. Hada M, Sutherland BM. Spectrum of complex DNA damages depends on the incident radiation. Radiat Res 2006; 165: 223-30.
36. Marras SAE, Kramer FR, Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res 2002; 30: e122.
37. Gromova M, Nardin R, Cadet J. Direct effect of heavy ions and electrons on 20-deoxyguanosine in the solid state. J Chem Soc Perkin Trans 2 1998: 1365-74.
38. Gromova M, Balanzat E, Gervais B, Nardin R, Cadet J. The direct effect of heavy ions and electrons on thymidine in the solid state. Int J Radiat Biol 1998; 74: 81-97.
39. Moribayashi K. Incorporation of the effect of the composite electric fields of molecular ions as a simulation tool for biological damage due to heavy- ion irradiation. Phys Rev 2011; 84: 012702.
40. Magee JL, Chatterjee, A. Radiation Chemistry of heavy-particle tracks. 1. General considerations. J Phys Chem 1980; 84: 3529-36.
41. Mozumder A. Trackcore radius of charged particles at relativistic speed in condensed media. J Chem Phys 1974; 60: 1145-8.
42. Becker D, Razskazovskii Y, Callaghan MU, Sevilla MD. Electron spin resonance of DNA irradiated with a heavy-ion beam (16O+8): evidence for damage to the deoxyribose phosphate backbone. Radiat Res 1996; 146: 361-8.
43. Akamatsu K. Grappling with problems in analytical science for radiation damage in DNA. Radiat Chem 2010; 89: 3-8.