Skip to main content

Advertisement

Springer Nature Link
Log in

Proton-induced direct and indirect damage of plasmid DNA

  • Original Paper
  • Published:
Radiation and Environmental Biophysics Aims and scope Submit manuscript

Abstract

Clustered DNA damage induced by 10, 20 and 30 MeV protons in pBR322 plasmid DNA was investigated. Besides determination of strand breaks, additional lesions were detected using base excision repair enzymes. The plasmid was irradiated in dry form, where indirect radiation effects were almost fully suppressed, and in water solution containing only minimal residual radical scavenger. Simultaneous irradiation of the plasmid DNA in the dry form and in the solution demonstrated the contribution of the indirect effect as prevalent. The damage composition slightly differed when comparing the results for liquid and dry samples. The obtained data were also subjected to analysis concerning different methodological approaches, particularly the influence of irradiation geometry, models used for calculation of strand break yields and interpretation of the strand breaks detected with the enzymes. It was shown that these parameters strongly affect the results.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  • Adhikary A, Becker D, Palmer BJ, Heizer AN, Sevilla MD (2012) Direct formation of the C5′-radical in the sugar-phosphate backbone of DNA by high-energy radiation. J Phys Chem B 116(20):5900–5906

    Article  Google Scholar 

  • Adhikary A, Becker D, Sevilla MD (2014) Electron spin resonance of radicals in irradiated DNA. In: Lund A, Shiotani M (eds) Applications of EPR in radiation research. Springer, Berlin, pp 299–352

    Google Scholar 

  • Asaithamby A, Hu B, Chen DJ (2011) Unrepaired clustered DNA lesions induce chromosome breakage in human cells. PNAS 108(20):8293–8298

    Article  Google Scholar 

  • Berger MJ, Coursey JS, Zucker MA, Chang J (2005) ESTAR, PSTAR, and ASTAR: computer programs for calculating stopping-power and range tables for electrons, protons, and helium ions (version 1.2.3). http://physics.nist.gov/Star. Accessed 30 Oct 2014

  • Bin JH, Allinger K, Assmann W, Dollinger G, Drexler GA, Friedl AA, Habs D, Hilz P, Hoerlein R, Humble N, Karsch S, Khrennikov K, Kiefer D, Krausz F, Ma WJ, Michalski D, Molls M, Raith S, Reinhardt S, Röper B, Schmid TE, Tajima T, Wenz J, Zlobinskaya O, Schreiber J, Wilkens JJ (2012) A laser-driven nanosecond proton source for radiobiological studies. Appl Phys Lett 101:243701–243704

    Article  ADS  Google Scholar 

  • Bolivar F, Rodriguez RL, Greene PJ, Betlach MC, Heyneker HL, Boyer HW, Crosa JH, Falkow S (1977) Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2(2):95–113

    Article  Google Scholar 

  • Bolton PR, Borghesi M, Brenner C, Carroll DC, De Martinis C, Flacco A, Floquet V, Fuchs J, Gallegos J, Dn Giove, Green JS, Green S, Jones B, Kirby D, McKenna P, Neely D, Nuesslin F, Prasad R, Reinhardt S, Roth M, Schramm U, Scott GG, Ter-Avetisyan S, Tolley M, Turchetti G, Wilkens JJ (2014) Instrumentation for diagnostics and control of laser-accelerated proton (ion) beams. Phys Med 30(3):255–270

    Article  Google Scholar 

  • Cowan R, Collis CM, Grigg GW (1987) Breakage of double-stranded DNA due to single-stranded nicking. J Theor Biol 127:229–245

    Article  Google Scholar 

  • Do TT, Tang VJ, Konigsfeld K, Aguilera JA, Perry CC, Milligan JR (2012) Damage clusters after gamma irradiation of a nanoparticulate plasmid DNA peptide condensate. Radiat Environ Biophys 51(1):43–52

    Article  Google Scholar 

  • Durante M, Cucinotta FA (2008) Heavy ion carcinogenesis and human space exploration. Nat Rev Cancer 8:465–472

    Article  Google Scholar 

  • Gebicki S, Gebicki JM (1999) Crosslinking of DNA and proteins induced by protein hydroperodixes. Biochem J 338:629–636

    Article  Google Scholar 

  • Georgakilas AG, O’Neill P, Stewart RD (2013) Induction and repair of clustered DNA lesions: What do we know so far? Radiat Res 180(1):100–109

    Article  Google Scholar 

  • Girdhani S, Sachs R, Hlatky L (2013) Biological effects of proton radiation: What we know and don’t know. Radiat Res 179(3):257–272

    Article  Google Scholar 

  • Gulston M, Fulford J, Jenner T, de Lara C, O’Neill P (2002) Clustered DNA damage induced by γ radiation in human fibroblasts (HF19), hamster (V79-4) cells and plasmid DNA is revealed as Fpg and Nth sensitive sites. Nucleic Acid Res 30(15):3464–3472

    Article  Google Scholar 

  • Hada M, Georgakilas AG (2008) Formation of clustered DNA damage after high-LET irradiation: a review. J Radiat Res 49(3):203–210

    Article  Google Scholar 

  • Hall EJ, Hei TK (2003) Genomic instability and bystander effects induced by high-LET radiation. Oncogene 22(45):7034–7042

    Article  Google Scholar 

  • ICRU Report 16 (1970) Linear energy transfer. International Commission on Radiation Units and Measurements

  • Klimczak U, Ludwig DC, Mark F, Rettberg P, Schulte-Frohlinde D (1993) Irradiation of plasmid and phage DNA in water-alcohol mixtures: strand breaks and lethal damage as a function of scavenger concentration. Int J Radiat Biol 64(5):497–510

    Article  Google Scholar 

  • Kraft SD, Richter C, Zeil K, Baumann M, Beyreuther E, Bock S, Bussmann M, Cowan TE, Dammene Y, Enghardt W, Helbig U, Karsch L, Kluge T, Laschinsky L, Lessmann E, Metzkes J, Naumburger D, Sauerbrey R, Schurer M, Sobiella M, Woithe J, Schramm U, Pawelke J (2010) Dose-dependent biological damage of tumour cells by laser-accelerated proton beams. New J Phys 12:085003

    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(1):41–54

    Article  Google Scholar 

  • Malka V, Faure J, Gauduel YA, Lefebvre E, Rousse A, Phuoc KT (2008) Principles and applications of compact laser-plasma accelerators. Nat Phys 4(6):447–453

    Article  Google Scholar 

  • McMahon SJ, Currell FJ (2011) A robust curve-fitting procedure for the analysis of plasmid DNA strand break data from gel electrophoresis. Radiat Res 175(6):797–805

    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(11):1475–1483

    Article  Google Scholar 

  • Pachnerová Brabcová K, Sihver L, Yasuda N, Matuo Y, Štěpán V, Davídková M (2014) Clustered DNA damage on subcellular level: effect of scavengers. Radiat Environ Biophys 53(4):705–712

    Article  Google Scholar 

  • Pachnerová Brabcová K, Štěpán V, Karamitros M, Karabín M, Dostálek P, Incerti S, Davídková M, Sihver L (2015) Contribution of indirect effects to clustered damage in DNA irradiated with protons. Radiat Prot Dosim. doi:10.1093/rpd/ncv15

    Google Scholar 

  • Prise KM, Pullar CHL, Michael BD (1999) A study of endonuclease III-sensitive sites in irradiated DNA: detection of α-particle-induced oxidative damage. Carcinogenesis 20(5):905–909

    Article  Google Scholar 

  • Semenenko VA, Stewart RD (2006) Fast Monte Carlo simulation of DNA damage formed by electrons and light ions. Phys Med Biol 51(7):1693–1706

    Article  Google Scholar 

  • Shikazono N, Noguchi M, Fujii K, Urushibara A, Yokoya A (2009) The yield, processing, and biological consequences of clustered DNA damage induced by ionizing radiation. J Radiat Res 50(1):27–36

    Article  Google Scholar 

  • Śmiałek MA (2012) Early models of DNA damage formation. J Phys Conf Ser 373(1):012013

    ADS  Google Scholar 

  • Śmiałek MA, Jones NC, Hoffmann SV, Mason NJ (2013) Measuring the density of DNA films using ultraviolet-visible interferometry. Phys Rev E 87:060701

    Google Scholar 

  • Stefančíková L, Porcel E, Eustache P, Li S, Salado D, Marco S, Guerquin-Kern JL, Réfrégiers M, Tillement O, Lux F, Lacombe S (2014) Cell localisation of gadolinium-based nanoparticles and related radiosensitising efficacy in glioblastoma cells. Cancer Nanotechnol. doi:10.1186/s12645-014-0006-6

  • Sui L, Wang Y, Wang X, Kong FQ, Liu JC, Zhou PK (2013) Clustered DNA damage induced by protons radiation in plasmid DNA. Chin Sci Bull 58(26):3217–3223

    Article  Google Scholar 

  • Sutherland BM, Bennett PV, Saparbaev M, Sutherland JC, Laval J (2001) Clustered DNA damages as dosemeters for ionising radiation exposure and biological responses. Radiat Prot Dosim 97(1):33–38

    Article  Google Scholar 

  • Swarts SG, Sevilla MD, Becker D, Tokar CJ, Wheeler KT (1992) Radiation-induced DNA damage as a function of hydration: I. Release of unaltered bases. Radiat Res 129(3):333–344

    Article  Google Scholar 

  • Terato H, Ide H (2004) Clustered DNA damage induced by heavy ion particles. Biol Sci Space 18(4):206–215

    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(1):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- and double-strand breaks and nucleobase lesions in fully hydrated plasmid DNA films irradiated with high-LET charged particles. Radiat Res 177(5):614–627

    Article  Google Scholar 

  • von Sonntag C (2006) Free-radical-induced DNA damage and its repair, a chemical perspective. Springer, Berlin

    Book  Google Scholar 

  • Watanabe M (2007) The first target of radiation carcinogenesis is not DNA. Int Congr Ser 1299:21–24

    Article  Google Scholar 

  • Willers H, Dahm-Daphi J, Powel SN (2004) Repair of radiation damage to DNA. Brit J Cancer 90:1297–1301

    Article  Google Scholar 

  • Wyer JA, Butterworth KT, Hirst DG, Latimer CJ, Montenegro EC, Shah MB, Currell FJ (2009) Fragmentation and plasmid strand breaks in pure and gold-doped DNA irradiated by beams of fast hydrogen atoms. Phys Med Biol 54(15):4705–4721

    Article  Google Scholar 

  • Yogo A, Sato K, Nishikino M, Maeda T, Sakaki H, Hori T, Ogura K, Nishiuchi M, Teshima T, Nishimura H, Kondo K, Bolton PR, Kawanishi S (2011) Measurement of DNA double-strand break yield in human cancer cells by high-current, short-duration bunches of laser-accelerated protons. Jpn J Appl Phys 50(10):106401

    Article  ADS  Google Scholar 

  • Ziegler JF, Ziegler MD, Biersack JP (2010) SRIM—The stopping and range of ions in matter (2010). Nucl Instrum Methods B 268(11–12):1818–1823

    Article  ADS  Google Scholar 

  • Zlobinskaya O, Siebenwirth C, Greubel C, Hable V, Hertenberger R, Humble N, Reinhardt S, Michalski D, Röper B, Multhoff G, Dollinger G, Wilkens JJ, Schmid TE (2014) The effects of ultra-high dose rate proton irradiation on growth delay in the treatment of human tumour xenofrafts in nude mice. Radiat Res 181(2):177–183

    Article  Google Scholar 

Download references

Acknowledgments

This work has been supported by ESA Project No. ESTEC/ITT AO/1-7146/12/NL/GLC “Radiation Biological End Effects Models and Interfaces to Physics Models” and MEYS CR Project No. LD12008. L. Vyšín and L. Juha appreciate a partial financial support provided by the Czech Science Foundation under the Grant No. 13-28721S. M. Vlk is grateful for a partial financial support by MEYS CR Project No. LK21310. The irradiation has been realized at the CANAM (Center of Accelerators and Nuclear Analytical Methods) supported by the MEYS CR Project No. LM 2011019. The authors also appreciate valuable comments of Dr. Amitava Adhikary.

Author information

Authors and Affiliations

  1. Institute of Physics CAS, Na Slovance 1999/2, 182 21, Prague, Czech Republic

    Luděk Vyšín & Libor Juha

  2. FNSPE, Czech Technical University in Prague, Břehová 7, 115 19, Prague, Czech Republic

    Luděk Vyšín & Martin Vlk

  3. Nuclear Physics Institute CAS, Na Truhlářce 39/64, 180 00, Prague, Czech Republic

    Kateřina Pachnerová Brabcová, Richard Wagner & Marie Davídková

  4. CNRS/IN2P3, Centre d’Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Université de Bordeaux, Chemin du Solarium, BP 120, 33 175, Gradignan, France

    Václav Štěpán & Sebastien Incerti

  5. Laboratoire Collisions Agregats Réactivité, IRSAMC, CNRS, UMR 5589, Université de Toulouse, UPS, 31062, Toulouse, France

    Patrick Moretto-Capelle, Pierre Cafarelli, Romain Casta, Jean Philippe Champeaux & Martine Sence

  6. LBCMCP, CNRS, UMR 5088, Université de Toulouse, UPS, 31062, Toulouse, France

    Beatrix Bugler & Gaelle Legube

  7. Nuclear Physics Institute CAS, Husinec – Řež 130, 250 68, Řež, Czech Republic

    Jan Štursa & Václav Zach

Authors
  1. Luděk Vyšín
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Kateřina Pachnerová Brabcová
    View author publications

    You can also search for this author inPubMed Google Scholar

  3. Václav Štěpán
    View author publications

    You can also search for this author inPubMed Google Scholar

  4. Patrick Moretto-Capelle
    View author publications

    You can also search for this author inPubMed Google Scholar

  5. Beatrix Bugler
    View author publications

    You can also search for this author inPubMed Google Scholar

  6. Gaelle Legube
    View author publications

    You can also search for this author inPubMed Google Scholar

  7. Pierre Cafarelli
    View author publications

    You can also search for this author inPubMed Google Scholar

  8. Romain Casta
    View author publications

    You can also search for this author inPubMed Google Scholar

  9. Jean Philippe Champeaux
    View author publications

    You can also search for this author inPubMed Google Scholar

  10. Martine Sence
    View author publications

    You can also search for this author inPubMed Google Scholar

  11. Martin Vlk
    View author publications

    You can also search for this author inPubMed Google Scholar

  12. Richard Wagner
    View author publications

    You can also search for this author inPubMed Google Scholar

  13. Jan Štursa
    View author publications

    You can also search for this author inPubMed Google Scholar

  14. Václav Zach
    View author publications

    You can also search for this author inPubMed Google Scholar

  15. Sebastien Incerti
    View author publications

    You can also search for this author inPubMed Google Scholar

  16. Libor Juha
    View author publications

    You can also search for this author inPubMed Google Scholar

  17. Marie Davídková
    View author publications

    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence to Kateřina Pachnerová Brabcová.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Vyšín, L., Pachnerová Brabcová, K., Štěpán, V. et al. Proton-induced direct and indirect damage of plasmid DNA. Radiat Environ Biophys 54, 343–352 (2015). https://doi.org/10.1007/s00411-015-0605-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00411-015-0605-6

Keywords