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Induction of DNA damage, including abasic sites, in plasmid DNA by carbon ion and X-ray irradiation

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Abstract

DNA from plasmid pUC18 was irradiated with low-LET (13 keV/μm) or high-LET (60 keV/μm) carbon ions or X-rays (4 keV/μm) in solutions containing several concentrations of Tris (0.66–200 mM) to determine the yield of abasic (AP) sites and the effect of scavenging capacity. The yield of AP sites, detected as single-strand breaks (SSB) after digestion with E. coli endonuclease IV (Nfo), was compared with that of SSB and base lesions. At higher concentrations of Tris, the yields of single or clustered AP sites were significantly lower than those of single or clustered base lesions. The relative yields of single AP sites and AP clusters were less than 10 and 7 %, respectively, of the total damage produced at a scavenger capacity mimicking that in cells. The dependence of the yield of AP sites on scavenging capacity was similar to that of prompt strand breaks. The ratios of the yield of isolated AP sites to that of SSB induced by carbon ion or X-ray irradiation were relatively constant at 0.45 ± 0.15 over the tested range of scavenger capacity, although the ratio of SSB to double-strand breaks (DSB) showed the characteristic dependence on both scavenging capacity and radiation quality. These results indicate that the reaction of water radiolysis products, presumably OH radicals, with the sugar-phosphate moieties in the DNA backbone induces both AP sites and SSB with similar efficiency. Direct ionization of DNA is notably more involved in the production of DSB and base lesion clusters than in the production of AP site clusters.

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References

  • Alden CJ, Kim SH (1979) Solvent-accessible surfaces of nucleic acids. J Mol Biol 132:411–434

    Article  Google Scholar 

  • Becker D, Razskazovskii Y, Callaghan MU, Sevilla MD (1996) Electron spin resonance of DNA irradiated with a heavy-ion beam(16O8+): evidence for damage to the deoxyribose phosphate backbone. Radiat Res 146:361–368

    Article  Google Scholar 

  • Bjoras M, Luna L, Johnson B, Hoff E, Haug T, Rognes T, Seeberg E (1997) Opposite base-dependent reactions of a human base excision repair enzyme on DNA containing 7,8-dihydro-8-oxoguanine and abasic sites. EMBO J 16:6314–6322

    Article  Google Scholar 

  • Chevillard S, Radicella JP, Levalois C, Lebeau J, Poupon MF, Oudard S, Dutrillaux B, Boiteux S (1998) Mutations in OGG1, a gene involved in the repair of oxidative DNA damage, are found in human lung and kidney tumours. Oncogene 16:3083–3086

    Article  Google Scholar 

  • Demple B, Sung JS (2005) Molecular and biological roles of Ape1 protein in mammalian base excision repair. DNA Repair 4:1442–1449

    Article  Google Scholar 

  • Eccles LJ, Lomax ME, O’Neill P (2010) Hierarchy of lesion processing governs the repair, double-strand break formation and mutability of three-lesion clustered DNA damage. Nucl Acids Res 38:1123–1134

    Article  Google Scholar 

  • Flaherty DM, Monick MM, Hunninghake GW (2001) AP endonucleases and the many functions of Ref-1. Am J Respir Cell Mol Biol 25:664–667

    Google Scholar 

  • Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoeras M, Cunningham RP, Tainer JA (2008) DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol 15:515–522

    Article  Google Scholar 

  • Georgakilas AG, Bennett PV, Wilson DM, Sutherland BM (2004) Processing of bistranded abasic DNA clusters in gamma-irradiated human hematopoietic cells. Nucl Acids Res 32:5609–5620

    Article  Google Scholar 

  • Goodhead DT (1994) Initial events in the cellular effects of ionizing-radiations—clustered damage in DNA. Int J Radiat Biol 65:7–17

    Article  Google Scholar 

  • Hanai R, Yazu M, Hieda K (1998) On the experimental distinction between ssbs and dsbs in circular DNA. Int J Radiat Biol 73:475–479

    Article  Google Scholar 

  • Haring M, Rudiger H, Demple B, Boiteux S, Epe B (1994) Recognition of oxidized abasic sites by repair endonucleases. Nucl Acids Res 22:2010–2015

    Article  Google Scholar 

  • Hodgkins PS, Fairman MP, O’Neill P (1996) Rejoining of gamma-radiation-induced single-strand breaks in plasmid DNA by human cell extracts: dependence on the concentration of the hydroxyl radical scavenger, tris. Radiat Res 145:24–30

    Article  Google Scholar 

  • Konigsfeld KM, Lee M, Urata MS, Aguilera JA, Milligan JR (2012) Free terminal amine in DNA- binding peptides alter the product distribution from guanine radicals produced by single electron oxidation. Int J Radiat Biol 88:230–238

    Article  Google Scholar 

  • Kuznetsov NA, Koval VV, Nevinsky GA, Douglas KT, Zharkov DO, Fedorova OS (2007) Kinetic conformational analysis of human 8-oxoguanine-DNA glycosylase. J Biol Chem 282:1029–1038

    Article  Google Scholar 

  • Leloup C, Garty G, Assaf G, Cristovão A, Breskin A, Chechik R, Shchemelinin S, Paz-Elizur T, Livneh Z, Schulte RW, Bashkirov V, Milligan JR, Grosswendt B (2005) Evaluation of lesion clustering in irradiated plasmid DNA. Int J Radiat Biol 81:41–54

    Article  Google Scholar 

  • Lomax ME, Salje H, Cunniffe S, O’Neill P (2005) 8-OxoA inhibits the incision of an AP site by the DNA glycosylases Fpg, Nth and the AP endonuclease HAP1. Radiat Res 163:79–84

    Article  Google Scholar 

  • Milligan JR, Arnold AD, Ward JF (1992) The effect of superhelical density on the yield of single-strand breaks in gamma-irradiated plasmid DNA. Radiat Res 132:69–73

    Article  Google Scholar 

  • Milligan JR, Aguilera JA, Nguyen TTD, Paglinawan RA, Ward JF (2000) DNA strand-break yields after post-irradiation incubation with base excision repair endonucleases implicate hydroxyl radical pairs in double-strand break formation. Int J Radiat Biol 76:1475–1483

    Article  Google Scholar 

  • Nakamura J, Walker VE, Upton PB, Chiang SY, Kow YW, Swenberg JA (1998) Highly sensitive apurinic/apyrimidinic site assay can detect spontaneous and chemically induced depurination under physiological conditions. Cancer Res 58:222–225

    Google Scholar 

  • Sharma KKK, Milligan JR, Bernhard WA (2008) Multiplicity of DNA single-strand breaks produced in pUC18 exposed to the direct effects of ionizing radiation. Radiat Res 170:156–162

    Article  Google Scholar 

  • Shikazono N, O’Neill P (2009) Biological consequences of potential repair intermediates of clustered base damage site in Escherichia coli. Mutat Res 669:162–168

    Article  Google Scholar 

  • Sutherland BM, Bennett PV, Sidorkina O, Laval J (2000) Clustered DNA damages induced in isolated DNA and in human cells by low doses of ionizing radiation. Proc Natl Acad Sci US Am 97:103–108

    Article  ADS  Google Scholar 

  • Taucher-Scholz G, Kraft G (1999) Influence of radiation quality on the yield of DNA strand breaks in SV40 DNA irradiated in solution. Radiat Res 151:595–604

    Article  Google Scholar 

  • Terato H, Tanaka R, Nakaarai Y, Nohara T, Doi Y, Iwai S, Hirayama R, Furusawa Y, Ide H (2008) Quantitative analysis of isolated and clustered DNA damage induced by gamma-rays, carbon ion beams, and iron ion beams. J Radiat Res 49:133–146

    Article  Google Scholar 

  • Urushibara A, Shikazono N, O’Neill P, Fujii K, Wada S, Yokoya A (2008) 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 84:23–33

    Article  Google Scholar 

  • Ushigome T, Shikazono N, Fujii K, Watanabe R, Suzuki M, Tsuruoka C, Tauchi H, Yokoya A (2012) Yield of single-, double-strand breaks and nucleobase lesions in fully hydrated plasmid DNA films irradiated with high-LET charged particles. Radiat Res 177:614–627

    Article  Google Scholar 

  • von Sonntag C (2006) DNA and double-stranded oligonucleotides. In: von Sonntag C (ed) Free-radical-induced DNA damage and its repair. Springer-Verlag, Germany, pp 357–482

  • Ward JF (1988) DNA damage produced by ionizing-radiation in mammalian-cells - identities, mechanisms of formation, and reparability. Prog Nucl Acid Res Mol Biol 35:95–125

    Article  Google Scholar 

  • Watanabe R, Wada S, Funayama T, Kobayashi Y, Satio K, Furusawa Y (2011) Monte Carlo simulation of radial distribution of DNA strand breaks along the C and Ne ion paths. Radiat Prot Dosim 143:186–190

    Article  Google Scholar 

  • Yokoya A, Cunniffe SMT, O’Neill P (2002) Effect of hydration on the induction of strand breaks and base lesions in plasmid DNA films by gamma-radiation. J Am Chem Soc 124:8859–8866

    Article  Google Scholar 

  • Yokoya A, Fujii K, Ushigome T, Shikazono N, Urushibara A, Watanabe R (2006) Yields of strand breaks and base lesions induced by soft X-rays in plasmid DNA. Radiat Prot Dosim 122:86–88

    Article  Google Scholar 

  • Yokoya A, Shikazono N, Fujii K, Urushibara A, Akamatsu K, Watanabe R (2008) DNA damage induced by the direct effect of radiation. Radiat Phys Chem 77:1280–1285

    Article  ADS  Google Scholar 

  • Yokoya A, Fujii K, Shikazono N, Ukai M (2011a) Spectroscopic study of radiation-induced DNA lesions and their susceptibility to enzymatic repair. In: Hatano Y, Katsumura Y, Mozumder A (eds) Charged particle and photon interactions with matter. Taylor and Francis, New York, pp 543–574

  • Yokoya A, Shikazono N, Fujii K, Noguchi M, Urushibara A (2011b) A novel technique using DNA denaturation to detect multiply induced single-strand breaks in a hydrated plasmid DNA molecule by X-ray and 4He2+ ion irradiation. Radiat Prot Dosim 143:219–225

    Article  Google Scholar 

  • Zharkov DO, Rosenquist TA, Gerchman SE, Grollman AP (2000) Substrate specificity and reaction mechanism of murine 8-oxoguanine-DNA glycosylase. J Biol Chem 275:28607–28617

    Article  Google Scholar 

Download references

Acknowledgments

We gratefully acknowledge Professor Akira Tachibana at the Department of Environmental Sciences, Faculty of Science, Ibaraki University, for his useful suggestions throughout this work. We also gratefully acknowledge the workers at the Research Group for Radiation and Biomolecular Science for their useful suggestions on the irradiation experiments. This work was supported by JSPS KAKENHI Grant Numbers 21310041 and 23651049 and by the Research Project at NIRS-HIMAC (project number 22B446 and 21B368).

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Correspondence to Akinari Yokoya.

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Shiina, T., Watanabe, R., Shiraishi, I. et al. Induction of DNA damage, including abasic sites, in plasmid DNA by carbon ion and X-ray irradiation. Radiat Environ Biophys 52, 99–112 (2013). https://doi.org/10.1007/s00411-012-0447-4

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  • DOI: https://doi.org/10.1007/s00411-012-0447-4

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