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Chen X, Karmaker N, Cloutier P, Bass AD, Zheng Y, Sanche L. Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity. J Phys Chem B 2022; 126:5443-5457. [PMID: 35834372 DOI: 10.1021/acs.jpcb.2c03664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions. The yields of single- and double-strand breaks, other cluster damage, isolated base lesions, and crosslinks were measured by electrophoresis and enzyme treatment. The films were deposited on oriented graphite or polycrystalline tantalum, with or without DNA autoassembly via diaminopropane (Dap) intercalation. Yields were correlated with the influence of vacuum, film uniformity, surface density, substrates, and the DNA environment. Aided by surface potential measurements and scanning electron microscopy and atomic force microscopy images, the lyophilized Dap-DNA films were found to be the most practical high-quality targets. These studies pave the way to the fabrication of LEE target-films composed of plasmids intercalated with biomolecules that could mimic the cellular environment; for example, as a first step, by replacing Dap with an amino acid.
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Affiliation(s)
- Xingju Chen
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P. R. China
| | - Nanda Karmaker
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre Cloutier
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Andrew D Bass
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P. R. China.,Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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Gao Y, Zheng Y, Sanche L. Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents. Int J Mol Sci 2021; 22:7879. [PMID: 34360644 PMCID: PMC8345953 DOI: 10.3390/ijms22157879] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/18/2022] Open
Abstract
The complex physical and chemical reactions between the large number of low-energy (0-30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.
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Affiliation(s)
- Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, China;
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, China;
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
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Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA. Int J Mol Sci 2019; 21:ijms21010111. [PMID: 31877939 PMCID: PMC6981450 DOI: 10.3390/ijms21010111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 12/27/2022] Open
Abstract
The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A4), d(A8), d(A12), d(A16), and d(A20)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A4) to d(A16), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A20), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA20 sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy.
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Ribar A, Huber SE, Smiałek MA, Tanzer K, Neustetter M, Schürmann R, Bald I, Denifl S. Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment. Phys Chem Chem Phys 2018; 20:5578-5585. [PMID: 29410988 DOI: 10.1039/c7cp07697e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
2-Amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) and ethylenediaminetetraacetic acid (EDTA) are key components of biological buffers and are frequently used as DNA stabilizers in irradiation studies. Such surface or liquid phase studies are done with the aim to understand the fundamental mechanisms of DNA radiation damage and to improve cancer radiotherapy. When ionizing radiation is used, abundant secondary electrons are formed during the irradiation process, which are able to attach to the molecular compounds present on the surface. In the present study we experimentally investigate low energy electron attachment to TRIS and methyliminodiacetic acid (MIDA), an analogue of EDTA, supported by quantum chemical calculations. The most prominent dissociation channel for TRIS is through hydroperoxyl radical formation, whereas the dissociation of MIDA results in the formation of formic and acetic acid. These compounds are well-known to cause DNA modifications, like strand breaks. The present results indicate that buffer compounds may not have an exclusive protecting effect on DNA as suggested previously.
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Affiliation(s)
- Anita Ribar
- Institute for Ion Physics and Applied Physics and Center of Molecular Biosciences Innsbruck, Leopold Franzens University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
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Khalil T, Boulanouar O, Heintz O, Fromm M. Auto-assembly of nanometer thick, water soluble layers of plasmid DNA complexed with diamines and basic amino acids on graphite: Greatest DNA protection is obtained with arginine. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 71:231-239. [DOI: 10.1016/j.msec.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/02/2016] [Accepted: 10/07/2016] [Indexed: 11/30/2022]
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Fromm M, Boulanouar O. Low energy electrons and ultra-soft X-rays irradiation of plasmid DNA. Technical innovations. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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McAllister M, Smyth M, Gu B, Tribello GA, Kohanoff J. Understanding the Interaction between Low-Energy Electrons and DNA Nucleotides in Aqueous Solution. J Phys Chem Lett 2015; 6:3091-3097. [PMID: 26267207 DOI: 10.1021/acs.jpclett.5b01011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Reactions that can damage DNA have been simulated using a combination of molecular dynamics and density functional theory. In particular, the damage caused by the attachment of a low energy electron to the nucleobase. Simulations of anionic single nucleotides of DNA in an aqueous environment that was modeled explicitly have been performed. This has allowed us to examine the role played by the water molecules that surround the DNA in radiation damage mechanisms. Our simulations show that hydrogen bonding and protonation of the nucleotide by the water can have a significant effect on the barriers to strand breaking reactions. Furthermore, these effects are not the same for all four of the bases.
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Affiliation(s)
- Maeve McAllister
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Maeve Smyth
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Bin Gu
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
- ‡Department of Physics, Nanjing University of Information Science and Technology, Nanjing 21004, China
| | - Gareth A Tribello
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jorge Kohanoff
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
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Gomes PJ, Ferraria AM, Botelho do Rego AM, Hoffmann SV, Ribeiro PA, Raposo M. Energy Thresholds of DNA Damage Induced by UV Radiation: An XPS Study. J Phys Chem B 2015; 119:5404-11. [DOI: 10.1021/acs.jpcb.5b01439] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. J. Gomes
- CEFITEC,
Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - A. M. Ferraria
- Centro
de Química-Física Molecular and IN, Instituto Superior
Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - A. M. Botelho do Rego
- Centro
de Química-Física Molecular and IN, Instituto Superior
Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - S. V. Hoffmann
- ISA,
Department of Physics and Astronomy, Aarhus University, Ny Munkegade
120, Building 1520, DK-8000 Aarhus C, Denmark
| | - P. A. Ribeiro
- CEFITEC,
Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - M. Raposo
- CEFITEC,
Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Minaev BF, Shafranyosh MI, Svida YY, Sukhoviya MI, Shafranyosh II, Baryshnikov GV, Minaeva VA. Fragmentation of the adenine and guanine molecules induced by electron collisions. J Chem Phys 2015; 140:175101. [PMID: 24811665 DOI: 10.1063/1.4871881] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Secondary electron emission is the most important stage in the mechanism of radiation damage to DNA biopolymers induced by primary ionizing radiation. These secondary electrons ejected by the primary electron impacts can produce further ionizations, initiating an avalanche effect, leading to genome damage through the energy transfer from the primary objects to sensitive biomolecular targets, such as nitrogenous bases, saccharides, and other DNA and peptide components. In this work, the formation of positive and negative ions of purine bases of nucleic acids (adenine and guanine molecules) under the impact of slow electrons (from 0.1 till 200 eV) is studied by the crossed electron and molecular beams technique. The method used makes it possible to measure the molecular beam intensity and determine the total cross-sections for the formation of positive and negative ions of the studied molecules, their energy dependences, and absolute values. It is found that the maximum cross section for formation of the adenine and guanine positive ions is reached at about 90 eV energy of the electron beam and their absolute values are equal to 2.8 × 10(-15) and 3.2 × 10(-15) cm(2), respectively. The total cross section for formation of the negative ions is 6.1 × 10(-18) and 7.6 × 10(-18) cm(2) at the energy of 1.1 eV for adenine and guanine, respectively. The absolute cross-section values for the molecular ions are measured and the cross-sections of dissociative ionization are determined. Quantum chemical calculations are performed for the studied molecules, ions and fragments for interpretation of the crossed beams experiments.
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Affiliation(s)
- B F Minaev
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | | | - Yu Yu Svida
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | - M I Sukhoviya
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | | | - G V Baryshnikov
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | - V A Minaeva
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
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Boulanouar O, Fromm M, Bass AD, Cloutier P, Sanche L. Absolute cross section for loss of supercoiled topology induced by 10 eV electrons in highly uniform /DNA/1,3-diaminopropane films deposited on highly ordered pyrolitic graphite. J Chem Phys 2013; 139:055104. [PMID: 23927289 PMCID: PMC3812120 DOI: 10.1063/1.4817323] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It was recently shown that the affinity of doubly charged, 1-3 diaminopropane (Dap(2+)) for DNA permits the growth on highly ordered pyrolitic graphite (HOPG) substrates, of plasmid DNA films, of known uniform thickness [O. Boulanouar, A. Khatyr, G. Herlem, F. Palmino, L. Sanche, and M. Fromm, J. Phys. Chem. C 115, 21291-21298 (2011)]. Post-irradiation analysis by electrophoresis of such targets confirms that electron impact at 10 eV produces a maximum in the yield of single strand breaks that can be associated with the formation of a DNA(-) transient anion. Using a well-adapted deterministic survival model for the variation of electron damage with fluence and film thickness, we have determined an absolute cross section for strand-break damage by 10 eV electrons and inelastic scattering attenuation length in DNA-Dap complex films.
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Affiliation(s)
- Omar Boulanouar
- Laboratoire de Chimie Physique et Rayonnements – Alain Chambaudet, LRC CEA, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Michel Fromm
- Laboratoire de Chimie Physique et Rayonnements – Alain Chambaudet, LRC CEA, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Andrew D. Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et de Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec J1H 5N4, Canada
| | - Pierre Cloutier
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et de Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec J1H 5N4, Canada
| | - Léon Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et de Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec J1H 5N4, Canada
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