Quantitative analysis of dose dependent DNA fragmentation in dry pBR322 plasmid using long read sequencing and Monte Carlo simulations.
DNA damages
Ionizing radiation
Monte Carlo simulation
Nanopore sequencing
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
12 Aug 2024
12 Aug 2024
Historique:
received:
08
04
2024
accepted:
05
08
2024
medline:
13
8
2024
pubmed:
13
8
2024
entrez:
12
8
2024
Statut:
epublish
Résumé
Exposure to ionizing radiation can induce genetic aberrations via unrepaired DNA strand breaks. To investigate quantitatively the dose-effect relationship at the molecular level, we irradiated dry pBR322 plasmid DNA with 3 MeV protons and assessed fragmentation yields at different radiation doses using long-read sequencing from Oxford Nanopore Technologies. This technology applied to a reference DNA model revealed dose-dependent fragmentation, as evidenced by read length distributions, showing no discernible radiation sensitivity in specific genetic sequences. In addition, we propose a method for directly measuring the single-strand break (SSB) yield. Furthermore, through a comparative study with a collection of previous works on dry DNA irradiation, we show that the irradiation protocol leads to biases in the definition of ionizing sources. We support this scenario by discussing the size distributions of nanopore sequencing reads in the light of Geant4 and Geant4-DNA simulation toolkit predictions. We show that integrating long-read sequencing technologies with advanced Monte Carlo simulations paves a promising path toward advancing our comprehension and prediction of radiation-induced DNA fragmentation.
Identifiants
pubmed: 39134627
doi: 10.1038/s41598-024-69406-3
pii: 10.1038/s41598-024-69406-3
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
18650Informations de copyright
© 2024. The Author(s).
Références
Yousefzadeh, M. et al. DNA damage-how and why we age?. Elife 10, e62852 (2021).
pubmed: 33512317
pmcid: 7846274
doi: 10.7554/eLife.62852
UNSCEAR 2008 Report Volume I. United Nations: Scientific Committee on the Effects of Atomic Radiation. www.unscear.org/unscear/en/publications/2008_1.html .
Lord, C. J. & Ashworth, A. The DNA damage response and cancer therapy. Nature 481, 287–294 (2012).
pubmed: 22258607
doi: 10.1038/nature10760
Shepard, C., Yost, D. C. & Kanai, Y. Electronic excitation response of DNA to high-energy proton radiation in water. Phys. Rev. Lett. 130, 118401 (2023).
pubmed: 37001078
doi: 10.1103/PhysRevLett.130.118401
Shepard, C. & Kanai, Y. Ion-type dependence of DNA electronic excitation in water under proton, α-particle, and carbon ion irradiation: A first-principles simulation study. J. Phys. Chem. B 127, 10700–10709 (2023).
pubmed: 37943091
doi: 10.1021/acs.jpcb.3c05446
Li, L., Story, M. & Legerski, R. J. Cellular responses to ionizing radiation damage. Int. J. Radiat. Oncol. Biol. Phys. 49, 1157–1162 (2001).
pubmed: 11240259
doi: 10.1016/S0360-3016(00)01524-8
Heller, C., Duke, T. & Viovy, J. L. Electrophoretic mobility of DNA in gels. II. Systematic experimental study in agarose gels. Biopolymers 34, 249–259 (1994).
doi: 10.1002/bip.360340211
Viovy, J.-L. Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms. Rev. Mod. Phys. 72, 813–872 (2000).
doi: 10.1103/RevModPhys.72.813
Maayah, Y., Nusrat, H., Pang, G. & Tambasco, M. Assessing the DNA damaging effectiveness of ionizing radiation using plasmid DNA. Int. J. Mol. Sci. 23, 12459 (2022).
pubmed: 36293322
pmcid: 9604049
doi: 10.3390/ijms232012459
McMahon, S. J. & Currell, F. J. A robust curve-fitting procedure for the analysis of plasmid DNA strand break data from gel electrophoresis. Radiat. Res. 175, 797–805 (2011).
pubmed: 21466384
doi: 10.1667/RR2514.1
Birren, B. W., Lai, E., Hood, L. & Simon, M. I. Pulsed field gel electrophoresis techniques for separating 1- to 50-kilobase DNA fragments. Anal. Biochem. 177, 282–286 (1989).
pubmed: 2729546
doi: 10.1016/0003-2697(89)90052-3
Xu, X. et al. Direct observation of damage clustering in irradiated DNA with atomic force microscopy. Nucleic Acids Res. 48, e18 (2020).
pubmed: 31840169
doi: 10.1093/nar/gkz1159
Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, K. F. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348–1365 (2021).
pubmed: 34750572
pmcid: 8988251
doi: 10.1038/s41587-021-01108-x
Jain, M., Olsen, H. E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239 (2016).
pubmed: 27887629
pmcid: 5124260
doi: 10.1186/s13059-016-1103-0
Jain, M., Olsen, H. E., Akeson, M. & Abu-Shumays, R. Adaptation of human ribosomal RNA for nanopore sequencing of canonical and modified nucleotides. Methods Mol. Biol. 2298, 53–74 (2021).
pubmed: 34085238
doi: 10.1007/978-1-0716-1374-0_4
Friedland, W. et al. Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping. Sci. Rep. 7, 45161 (2017).
pubmed: 28345622
pmcid: 5366876
doi: 10.1038/srep45161
Nikjoo, H., Uehara, S., Emfietzoglou, D. & Cucinotta, F. A. Track-structure codes in radiation research. Radiat. Meas. 41, 1052–1074 (2006).
doi: 10.1016/j.radmeas.2006.02.001
Francis, Z., Villagrasa, C. & Clairand, I. Simulation of DNA damage clustering after proton irradiation using an adapted DBSCAN algorithm. Comput. Methods Programs Biomed. 101, 265–270 (2011).
pubmed: 21232812
doi: 10.1016/j.cmpb.2010.12.012
Nikjoo, H., O’Neill, P., Terrissol, M. & Goodhead, D. T. Quantitative modelling of DNA damage using Monte Carlo track structure method. Radiat. Environ. Biophys. 38, 31–38 (1999).
pubmed: 10384953
doi: 10.1007/s004110050135
Bernal, M. A. et al. Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. Phys. Med. 31, 861–874 (2015).
pubmed: 26653251
doi: 10.1016/j.ejmp.2015.10.087
Incerti, S. et al. The geant4-dna project. Int. J. Model. Simul. Sci. Comput. 01, 157–178 (2010).
doi: 10.1142/S1793962310000122
Incerti, S. et al. Comparison of GEANT4 very low energy cross section models with experimental data in water. Med. Phys. 37, 4692–4708 (2010).
pubmed: 20964188
doi: 10.1118/1.3476457
Incerti, S. et al. Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA project. Med. Phys. 45, e722–e739 (2018).
doi: 10.1002/mp.13048
Chatzipapas, K. P. et al. Simulation of DNA damage using Geant4-DNA: An overview of the “molecularDNA” example application. Precis. Radiat. Oncol. 7, 4–14 (2023).
doi: 10.1002/pro6.1186
Lin, B., Hui, J. & Mao, H. Nanopore technology and its applications in gene sequencing. Biosensors (Basel) 11, 214 (2021).
pubmed: 34208844
doi: 10.3390/bios11070214
Balbas, P., Soberon, X., Bolivar, F. & Rodriguez, R. L. CHAPTER 1: The plasmid, pBR322. In Vectors (eds Rodriguez, R. L. & Denhardt, D. T.) 5–41 (Butterworth-Heinemann, 1988). https://doi.org/10.1016/B978-0-409-90042-2.50007-6 .
doi: 10.1016/B978-0-409-90042-2.50007-6
Sahlin, K. & Medvedev, P. Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis. Nat. Commun. 12, 2 (2021).
pubmed: 33397972
pmcid: 7782715
doi: 10.1038/s41467-020-20340-8
Bourret, S. et al. Fluorescence time-lapse imaging of single cells targeted with a focused scanning charged-particle microbeam. Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 325, 27–34 (2014).
doi: 10.1016/j.nimb.2014.02.004
Ushigome, T. et al. 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, 614–627 (2012).
pubmed: 22206232
doi: 10.1667/RR2701.1
Wyer, J. A. et al. Fragmentation and plasmid strand breaks in pure and gold-doped DNA irradiated by beams of fast hydrogen atoms. Phys. Med. Biol. 54, 4705–4721 (2009).
pubmed: 19590119
doi: 10.1088/0031-9155/54/15/005
Vyšín, L. et al. Proton-induced direct and indirect damage of plasmid DNA. Radiat. Environ. Biophys. 54, 343–352 (2015).
pubmed: 26007308
doi: 10.1007/s00411-015-0605-6
Souici, M. et al. Single- and double-strand breaks of dry DNA exposed to protons at Bragg-peak energies. J. Phys. Chem. B 121, 497–507 (2017).
pubmed: 28045263
doi: 10.1021/acs.jpcb.6b11060
Urushibara, A. et al. LET dependence of the yield of single-, double-strand breaks and base lesions in fully hydrated plasmid DNA films by
pubmed: 17852554
doi: 10.1080/09553000701616072
Nikjoo, H. et al. Radiation track, DNA damage and response: A review. Rep. Prog. Phys. 79, 116601 (2016).
pubmed: 27652826
doi: 10.1088/0034-4885/79/11/116601
Nakano, M. et al. Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory. Chem. Phys. Lett. 660, 250–255 (2016).
doi: 10.1016/j.cplett.2016.08.032
Krajina, B. A. & Spakowitz, A. J. Large-scale conformational transitions in supercoiled DNA revealed by coarse-grained simulation. Biophys. J. 111, 1339–1349 (2016).
pubmed: 27705758
pmcid: 5052444
doi: 10.1016/j.bpj.2016.07.045
Marko, J. F. & Siggia, E. D. Statistical mechanics of supercoiled DNA. Phys. Rev. E 52, 2912–2938 (1995).
doi: 10.1103/PhysRevE.52.2912
Swarts, S. G., Sevilla, M. D., Becker, D., Tokar, C. J. & Wheeler, K. T. Radiation-induced DNA damage as a function of hydration: I. Release of Unaltered Bases. Radiat. Res. 129, 333–344 (1992).
pubmed: 1542721
doi: 10.2307/3578034
Yokoya, A. et al. Yields of strand breaks and base lesions induced by soft X-rays in plasmid DNA. Radiat. Prot. Dosim. 122, 86–88 (2006).
doi: 10.1093/rpd/ncl408
Zein, S. A. et al. Electron transport in DNA bases: An extension of the Geant4-DNA Monte Carlo toolkit. Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 488, 70–82 (2021).
doi: 10.1016/j.nimb.2020.11.021
Krim, M. et al. Cross sections, stopping power and Bragg peak range calculation of proton collisions with the DNA base adenine. Jpn. J. Appl. Phys. 58, 096001 (2019).
doi: 10.7567/1347-4065/ab35b0
Tan, Z., Xia, Y., Zhao, M. & Liu, X. Proton stopping power in a group of bioorganic compounds over the energy range of 0.05–10 MeV. Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 248, 1–6 (2006).
doi: 10.1016/j.nimb.2006.04.073
Barberet, P., Jouve, J., Sorieul, S., Alfaurt, P. & Mathieu, L. AIFIRA: A light ion beam facility for ion beam analysis and irradiation. Eur. Phys. J. Plus 136, 67 (2021).
doi: 10.1140/epjp/s13360-020-01045-9
Ziegler, J. F., Ziegler, M. D. & Biersack, J. P. SRIM: The stopping and range of ions in matter (2010). Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 268, 1818–1823 (2010).
doi: 10.1016/j.nimb.2010.02.091
Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
pubmed: 29750242
pmcid: 6137996
doi: 10.1093/bioinformatics/bty191
Lampe, N. et al. Mechanistic DNA damage simulations in Geant4-DNA part 1: A parameter study in a simplified geometry. Phys. Med. 48, 135–145 (2018).
pubmed: 29628360
doi: 10.1016/j.ejmp.2018.02.011
Agostinelli, S. et al. Geant4: A simulation toolkit. Nucl. Instrum. Methods Phys. Res. Sect. A Accel. Spectrom. Detect. Assoc. Equip. 506, 250–303 (2003).
doi: 10.1016/S0168-9002(03)01368-8
Sakata, D. et al. Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA. Sci. Rep. 10, 20788 (2020).
pubmed: 33247225
pmcid: 7695857
doi: 10.1038/s41598-020-75982-x