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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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Chatterjee K, Dopfer O. Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine. Phys Chem Chem Phys 2020; 22:17275-17290. [PMID: 32685941 DOI: 10.1039/d0cp02919j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1-2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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Dong Y, Wang Y, Zhuang P, Fu X, Zheng Y, Sanche L. Role of Transient Anions in Chemoradiation Therapy: Base Modifications, Cross-Links, and Cluster Damages Induced to Cisplatin-DNA Complexes by 1–20 eV Electrons. J Phys Chem B 2020; 124:3315-3325. [DOI: 10.1021/acs.jpcb.0c00946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yanfang Dong
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yaxiao Wang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Puxiang Zhuang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Xianzhi Fu
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
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Dong Y, Gao Y, Liu W, Gao T, Zheng Y, Sanche L. Clustered DNA Damage Induced by 2-20 eV Electrons and Transient Anions: General Mechanism and Correlation to Cell Death. J Phys Chem Lett 2019; 10:2985-2990. [PMID: 31099579 DOI: 10.1021/acs.jpclett.9b01063] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The mechanisms of action of low-energy electrons (LEEs) generated in large quantities by ionizing radiation constitute an essential element of our understanding of early events in radiolysis and radiobiology. We present the 2-20 eV electron energy dependence of the yields of base damage (BD), BD-related cross-links (CLs), and non-double-strand break (NDSB) clustered damage induced in DNA. These new yield functions are generated by the impact of LEEs on plasmid DNA films. The damage is analyzed by gel electrophoresis with and without enzyme treatment. Maxima at 5 and 10 eV in BDs and BD-related CLs yield functions, and two others, at 6 and 10 eV, in those of NDSB clustered damage are ascribed to core-excited transient anions that decay into bond-breaking channels. The mechanism causing all types of DNA damages can be attributed to the capture of a single electron by a base followed by multiple different electron transfer pathways.
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Affiliation(s)
- Yanfang Dong
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Wenhui Liu
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Ting Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine , Université de Sherbrooke , Sherbrooke , QC , Canada J1H 5N4
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Zhou L, Liu W, Brodeur N, Cloutier P, Zheng Y, Sanche L. Absolute cross sections for chemoradiation therapy: Damages to cisplatin-DNA complexes induced by 10 eV electrons. J Chem Phys 2019; 150:195101. [PMID: 31117770 DOI: 10.1063/1.5090259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In chemoradiation therapy, the synergy between the radiation and the chemotherapeutic agent (CA) can result in a super-additive treatment. A priori, this increased effectiveness could be estimated from model calculations, if absolute cross sections (ACSs) involved in cellular damage are substantially higher, when the CA binds to DNA. We measure ACSs for damages induced by 10 eV electrons, when DNA binds to the CA cisplatin as in chemotherapy. At this energy, DNA is damaged essentially by the decay of core-excited transient anions into bond-breaking channels. Films of cisplatin-DNA complexes of ratio 5:1 with thicknesses 10, 15, and 20 nm were irradiated in vacuum during 5-30 s. Conformation changes were quantified by electrophoresis and yields extrapolated from exposure-response curves. Base damages (BDs) were revealed and quantified by enzymatic treatment. The ACSs were generated from these yields by two mathematical models. For 3197 base-pair plasmid DNA, ACS for single strand breaks, double strand breaks (DSBs), crosslinks, non-DSB cluster damages, and total BDs is 71 ± 2, 9.3 ± 0.4, 10.1 ± 0.3, 8.2 ± 0.3, and 115 ± 2 ×10-15 cm2, respectively. These ACSs are higher than those of nonmodified DNA by factors of 1.6 ± 0.1, 2.2 ± 0.1, 1.3 ± 0.1, 1.3 ± 0.3, and 2.1 ± 0.4, respectively. Since LEEs are produced in large quantities by radiolysis and strongly interact with biomolecules, we expect such enhancements to produce substantial additional damages in the DNA of the nucleus of cancer cells during concomitant chemoradiation therapy. The increase damage appears sufficiently large to justify more elaborate simulations, which could provide a quantitative evaluation of molecular sensitization by Pt-CAs.
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Affiliation(s)
- Limei Zhou
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, People's Republic of China
| | - Wenhui Liu
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, People's Republic of China
| | - Nicolas Brodeur
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté of Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre Cloutier
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté of Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, People's Republic of China
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté of Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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6
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Gu J, Wang J, Leszczynski J. Electron interaction with a DNA duplex: dCpdC:dGpdG. Phys Chem Chem Phys 2016; 18:13657-65. [PMID: 27139598 DOI: 10.1039/c6cp01408a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron attachment to double-stranded cytosine-rich DNA, dCpdC:dGpdG, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 eV. The excess electron may reside on the nucleobase at the 5' position (dC˙(-)pdC:dGpdG) or at the 3' position (dCpdC˙(-):dGpdG). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dC1H˙pdC:dG2-H(-)pdG and dCpdC2H˙:dGpdG1-H(-). These distonic radical anions are found to be approximately 1 to 4 kcal mol(-1) more stable than the normal radical anions. Intra-strand cytosine π→π transition energies are below the electron detachment energy. Inter-strand π→π transitions of the excess electron from C to G are predicted to be less than 2.79 eV. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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7
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Kopyra J, Abdoul-Carime H. Temperature dependence of the cross section for the fragmentation of thymine via dissociative electron attachment. J Chem Phys 2015; 142:174303. [PMID: 25956096 DOI: 10.1063/1.4919638] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Providing experimental values for absolute Dissociative Electron Attachment (DEA) cross sections for nucleobases at realistic biological conditions is a considerable challenge. In this work, we provide the temperature dependence of the cross section, σ, of the dehydrogenated thymine anion (T - H)(-) produced via DEA. Within the 393-443 K temperature range, it is observed that σ varies by one order of magnitude. By extrapolating to a temperature of 313 K, the relative DEA cross section for the production of the dehydrogenated thymine anion at an incident energy of 1 eV decreases by 2 orders of magnitude and the absolute value reaches approximately 6 × 10(-19) cm(2). These quantitative measurements provide a benchmark for theoretical prediction and also a contribution to a more accurate description of the effects of ionizing radiation on molecular medium.
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Affiliation(s)
- Janina Kopyra
- Faculty of Science, Siedlce University, 3 Maja 54, 08-110 Siedlce, Poland
| | - Hassan Abdoul-Carime
- Université de Lyon; Université Claude Bernard Lyon1; Institut de Physique Nucléaire de Lyon, CNRS/IN2P3 UMR 5822, 43 Bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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8
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Bao Q, Chen Y, Zheng Y, Sanche L. Cisplatin Radiosensitization of DNA Irradiated with 2-20 eV Electrons: Role of Transient Anions. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014; 118:15516-15524. [PMID: 26793285 PMCID: PMC4716812 DOI: 10.1021/jp503706h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Platinum chemotherapeutic agents, such as cisplatin (cis-diamminedichloroplatinum(II)), can act as radiosensitizers when bound covalently to nuclear DNA in cancer cells. This radiosensitization is largely due to an increase in DNA damage induced by low-energy secondary electrons, produced in large quantities by high-energy radiation. We report the yields of single- and double-strand breaks (SSB and DSB) and interduplex cross-links (CL) induced by electrons of 1.6-19.6 eV (i.e., the yield functions) incident on 5 monolayer (ML) films of cisplatin-DNA complexes. These yield functions are compared with those previously recorded with 5 ML films of unmodified plasmid DNA. Binding of five cisplatin molecules to plasmid DNA (3197 base pairs) enhances SSB, DSB, and CL by factors varying, from 1.2 to 2.8, 1.4 to 3.5, and 1.2 to 2.7, respectively, depending on electron energy. All yield functions exhibit structures around 5 and 10 eV that can be attributed to enhancement of bond scission, via the initial formation of core-excited resonances associated with π → π* transitions of the bases. This increase in damage is interpreted as arising from a modification of the parameters of the corresponding transient anions already present in nonmodified DNA, particularly those influencing molecular dissociation. Two additional resonances, specific to cisplatin-modified DNA, are formed at 13.6 and 17.6 eV in the yield function of SSB. Furthermore, cisplatin binding causes the induction of DSB by electrons of 1.6-3.6 eV, i.e., in an energy region where a DSB cannot be produced by a single electron in pure DNA. Breaking two bonds with a subexcitation-energy electron is tentatively explained by a charge delocalization mechanism, where a single electron occupies simultaneously two σ* bonds linking the Pt atom to guanine bases on opposite strands.
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Affiliation(s)
- Qianhong Bao
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, P. R. China
| | - Yunfeng Chen
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, P. R. China
| | - Yi Zheng
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, P. R. China
| | - Léon Sanche
- Group in the Radiation Sciences, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
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9
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Gu J, Xie Y, Schaefer HF. Benchmarking the Electron Affinity of Uracil. J Chem Theory Comput 2014; 10:609-12. [DOI: 10.1021/ct400958d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS, Shanghai 201203, People’s Republic of China
| | - Yaoming Xie
- Center for Computational
Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2525, United States
| | - Henry F. Schaefer
- Center for Computational
Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2525, United States
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Storoniak P, Rak J, Ko YJ, Wang H, Bowen KH. Photoelectron spectroscopic and density functional theoretical studies of the 2′-deoxycytidine homodimer radical anion. J Chem Phys 2013; 139:075101. [DOI: 10.1063/1.4817779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Ko YJ, Storoniak P, Wang H, Bowen KH, Rak J. Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions. J Chem Phys 2012. [PMID: 23206036 DOI: 10.1063/1.4767053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine, (rU)(2)(●-). It features a broad band consisting of an onset of ∼1.2 eV and a maximum at the electron binding energy (EBE) ranging from 2.0 to 2.5 eV. Calculations performed at the B3LYP∕6-31++G∗∗ level of theory suggest that the PES is dominated by dimeric radical anions in which one uridine nucleoside, hosting the excess charge on the base moiety, forms hydrogen bonds via its O8 atom with hydroxyl of the other neutral nucleoside's ribose. The calculated adiabatic electron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimers show an excellent agreement with the experimental values. The anionic complexes consisting of two intermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers. Despite the fact that uracil-uracil anionic homodimers are additionally stabilized by barrier-free electron-induced proton transfer, their relative thermodynamic stabilities and the calculated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)(2)(●-).
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Affiliation(s)
- Yeon Jae Ko
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Gu J, Leszczynski J, Schaefer HF. Interactions of electrons with bare and hydrated biomolecules: from nucleic acid bases to DNA segments. Chem Rev 2012; 112:5603-40. [PMID: 22694487 DOI: 10.1021/cr3000219] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS, PR China.
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Chomicz L, Rak J, Storoniak P. Electron-induced elimination of the bromide anion from brominated nucleobases. A computational study. J Phys Chem B 2012; 116:5612-9. [PMID: 22510158 DOI: 10.1021/jp3008738] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The enhancement of radiodamage to DNA labeled with halonucleobases is attributed to the reactive radical produced from a halonucleobase by the attachment of an electron. We examined at the B3LYP/6-31++G** level electron capture by four brominated nucleobases (BrNBs): 8-bromo-9-methyladenine, 8-bromo-9-methylguanine, 5-bromo-1-methylcytosine, and 5-bromo-1-methyluracil followed by the release of the bromide anion and a nucleobase radical. We demonstrate that neutral BrNBs in both gas and aqueous phases are better electron acceptors than unsubstituted NBs and that resulting anion radicals, BrNBs(•-), can easily transform into the product complex of the bromide anion and the nucleobase radical ([Br(-)···NB(•)]). The overall thermodynamic stimulus for the process starting with the neutral BrNB and ending with the isolated bromide anion and the NB(•) radical is similar in the case of all four BrNBs studied, which suggests their comparable radiosensitizing capabilities.
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Affiliation(s)
- Lidia Chomicz
- Department of Chemistry, University of Gdańsk , Sobieskiego 18, 80-952 Gdańsk, Poland
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Abdoul-Carime H, König-Lehmann C, Kopyra J, Farizon B, Farizon M, Illenberger E. Dissociative electron attachment to amino-acids: The case of Leucine. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Ion-beam irradiation provides a promising treatment for some types of cancer. This promise is due mainly to the selective deposition of energy into a relatively small volume (the Bragg peak), thus reducing damage to healthy tissue. Recent observations that electrons with energies below the ionization potential of DNA can cause covalent damage to the bases and backbone have led to investigations into the ability of low-energy (<1 keV·Da−1) ion beams to damage double-stranded DNA. It has been clearly demonstrated that these low-energy ions induce a mixture of single- and double-strand breaks to dried DNA in vacuo. These effects depend upon the number of ions incident upon the DNA, the kinetic energy of the ions and on their charge state. This DNA damage may be important, as all radiotherapies will result in the production of low-energy secondary ions as radiation passes through tissues. Currently, their effects are neglected in treatment planning, and thus more work is required to quantify and understand DNA damage by low-energy ions.
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Marcum JC, Halevi A, Weber JM. Photodamage to isolated mononucleotides—photodissociation spectra and fragment channels. Phys Chem Chem Phys 2009; 11:1740-51. [DOI: 10.1039/b819273a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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17
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18
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Vall-llosera G, Huels MA, Coreno M, Kivimäki A, Jakubowska K, Stankiewicz M, Rachlew E. Photofragmentation of 2-Deoxy-D-Ribose Molecules in the Gas Phase. Chemphyschem 2008; 9:1020-9. [DOI: 10.1002/cphc.200700635] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Zheng Y, Cloutier P, Hunting DJ, Wagner JR, Sanche L. Phosphodiester and N-glycosidic bond cleavage in DNA induced by 4-15 eV electrons. J Chem Phys 2007; 124:64710. [PMID: 16483232 DOI: 10.1063/1.2166364] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Thin molecular films of the short single strand of DNA, GCAT, were bombarded under vacuum by electrons with energies between 4 and 15 eV. Ex vacuo analysis by high-pressure liquid chromatography of the samples exposed to the electron beam revealed the formation of a multitude of products. Among these, 12 fragments of GCAT were identified by comparison with reference compounds and their yields were measured as a function of electron energy. For all energies, scission of the backbone gave nonmodified fragments containing a terminal phosphate, with negligible amounts of fragments without the phosphate group. This indicates that phosphodiester bond cleavage by 4-15 eV electrons involves cleavage of the C-O bond rather than the P-O bond. The yield functions exhibit maxima at 6 and 10-12 eV, which are interpreted as due to the formation of transient anions leading to fragmentation. Below 15 eV, these resonances dominate bond dissociation processes. All four nonmodified bases are released from the tetramer, by cleavage of the N-glycosidic bond, which occurs principally via the formation of core-excited resonances located around 6 and 10 eV. The formation of the other nonmodified products leading to cleavage of the phosphodiester bond is suggested to occur principally via two different mechanisms: (1) the formation of a core-excited resonance on the phosphate unit followed by dissociation of the transient anion and (2) dissociation of the CO bond of the phosphate group formed by resonance electron transfer from the bases. In each case, phosphodiester bond cleavage leads chiefly to the formation of stable phosphate anions and sugar radicals with minimal amounts of alkoxyl anions and phosphoryl radicals.
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Affiliation(s)
- Yi Zheng
- Group in the Radiation Sciences, Faculty of Medicine, Université de Sherbrooke, Québec, Canada.
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22
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Cai Z, Dextraze ME, Cloutier P, Hunting D, Sanche L. Induction of strand breaks by low-energy electrons (8-68 eV) in a self-assembled monolayer of oligonucleotides: effective cross sections and attenuation lengths. J Chem Phys 2007; 124:024705. [PMID: 16422624 DOI: 10.1063/1.2141505] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Self-assembled monolayers of 5'-32P-labeled 3'-thiolated oligonucleotides chemisorbed on gold were bombarded by low-energy electrons (LEE) of 8-68 eV. Shorter 5'-32P-oligonucleotides produced by LEE-induced strand breaks were separated with denaturing polyacrylamide gel electrophoresis and quantified by phosphor imaging. The yields of short oligonucleotides (y) decrease exponentially with their length (n), following the equation y=ae-bn, where a and b are constants, which are related to the average effective cross section per nucleotide for DNA strand break (sigmaeff) and the attenuation length (AL=1b) of LEE, respectively. The AL decreases with LEE energies from 2.5+/-0.6 nm at 8 eV to 0.8+/-0.1 nm at 68 eV, whereas sigmaeff increases from (3+/-1)x10(-18) to (5.1+/-1.6)x10(-17) cm2 within the same energy range. The energy dependence of sigmaeff shows a resonance peak of (2.8+/-0.9)x10(-17) cm2 at 18 eV superimposed on a monotonically rising curve. Transient electron attachment to a sigma* anion state of the deoxyribose group, followed by dipolar dissociation into H- and the corresponding positive-ion radical, leading to C-O bond cleavage, is proposed to account for this maximum.
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Affiliation(s)
- Zhongli Cai
- Group in the Radiation Sciences, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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Naaman R, Sanche L. Low-Energy Electron Transmission through Thin-Film Molecular and Biomolecular Solids. Chem Rev 2007; 107:1553-79. [PMID: 17439288 DOI: 10.1021/cr040200j] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R Naaman
- Department of Chemical Physics, Weizmann Institute, Rehovot, Israel 76100
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24
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Evangelista FA, Schaefer HF. Hydrogen Atom and Hydride Anion Addition to Adenine: Structures and Energetics. Chemphyschem 2006; 7:1471-80. [PMID: 16810726 DOI: 10.1002/cphc.200600049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The radicals and anions derived from the 9H tautomer of adenine by adding a hydrogen atom to one of the four double bonds of the adenine framework have been studied. Computations were carried out using a carefully calibrated density functional (B3LYP) method and basis set (DZP++). Optimized geometries, energies, and vibrational frequencies are predicted for eight radicals and anions. The radicals are found to lie in a range of 22 kcal mol(-1), with the radical derived by addition to the C(8) carbon atom being the lowest lying energetically. The anions are predicted to be bound species in the gas phase with an energetic range of 43 kcal mol(-1). Anions produced by addition of a hydride ion to adenine carbon atoms are found to be the most favorable. Six of the anions are predicted to be stable species with respect to electron detachment. The adiabatic electron affinities, vertical electron affinities, and vertical detachment energies are computed for the first time. Electron affinities for these radicals range from 0.0 to 2.0 eV. Radicals produced by addition to a nitrogen atom have near-zero adiabatic electron affinities, while radicals produced by addition at carbon atoms have considerably higher electron affinities.
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Ray SG, Daube SS, Leitus G, Vager Z, Naaman R. Chirality-induced spin-selective properties of self-assembled monolayers of DNA on gold. PHYSICAL REVIEW LETTERS 2006; 96:036101. [PMID: 16486734 DOI: 10.1103/physrevlett.96.036101] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2005] [Indexed: 05/06/2023]
Abstract
Here we show that self-assembled monolayers on gold of double-stranded DNA oligomers interact with polarized electrons similarly to a strong and oriented magnetic field. The direction of the field for right-handed DNA is away from the substrate. Moreover, the layer shows very high paramagnetic susceptibility. Interestingly, thiolated single-stranded DNA oligomers on gold do not show this effect. The new findings are rationalized based on recent results in which high paramagnetism was measured for diamagnetic films adsorbed on diamagnetic substrates.
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Affiliation(s)
- S G Ray
- Department of Chemical Physics, The Weizmann Institute, Rehovot 76100, Israel
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26
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Gold RS, Maxim J, Halepaska DJ, Wales ME, Johnson DA, Wild JR. Electron beam irradiation as protection against the environmental release of recombinant molecules for biomaterials applications. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2005; 16:79-89. [PMID: 15796306 DOI: 10.1163/1568562052843357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In biomaterials applications there exists a need to protect against the environmental release of recombinant microorganisms and transmissible genetic material and to prevent the recovery of proprietary genetic information. Irradiation technologies have long been used to eliminate microorganisms associated with spoilage and contamination and recent studies have demonstrated that moderate doses of irradiation may be used to sterilize medically important proteins without causing adverse effects in their desirable biological properties. Recombinant Escherichia coli cells expressing organophosphate hydrolase (OPH, E.C. 3.1.8.1), an important enzyme for the detection and decontamination of neurotoxic pesticides and chemical warfare agents, were subjected to electron beam irradiation to gauge its effect on enzymatic activity, cell viability and DNA recoverability. Bacterial samples were irradiated at 2, 20 and 200 kGy using a 10 MeV electron source. Irradiation levels of 2 to 20 kGy were sufficient to eliminate viable cells without affecting OPH enzymatic activity. Biologically active DNA was recovered via PCR from all samples through the 20 kGy irradiation level. While DNA was not recovered from samples at the 200 kGy exposure level, protein activity was reduced by 19 to 78%, depending on the method of cell preparation. These results demonstrate that irradiation can be effective in preventing the release of recombinant organisms intended for use in biomaterials applications without eliminating enzymatic activity and suggests that further research may indicate specific conditions whereby DNA recovery can be eliminated while retaining sufficient enzymatic activity for targeted biomaterials applications.
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Affiliation(s)
- R Shane Gold
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
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27
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Abstract
Many of the mutagenic or lethal effects of ionization radiation can be attributed to damage caused to the DNA by low-energy electrons. To gain insight on the parameters affecting this process, we measured the low-energy electron (<2 eV) transmission yield through self-assembled monolayers of short DNA oligomers. The electrons that are not transmitted are captured by the layer. Hence, the transmission reflects the capturing efficiency of the electrons by the layer. The dependence of the capturing probability on the base sequence was studied, as was the state of the captured electrons. It is found that the capturing probability scales with the number of G bases in the single-stranded oligomers and depends on their clustering level. Using two-photon photoelectron spectroscopy, we find that, once captured, the electrons do not reside on the bases. Rather, the state of the captured electrons is insensitive to the sequence of the oligomer. Double-stranded DNA does not capture electrons as efficiently as single-stranded oligomers; however, once captured, the electrons are bound more strongly than to the single strands.
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Affiliation(s)
- S G Ray
- Department of Chemical Physics and Chemical Research Support, Weizmann Institute, Rehovot 76100, Israel
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Evangelista FA, Schaefer HF. Structures and Energetics of Adenosine Radicals: (2‘-dAdo − H)•. J Phys Chem A 2004. [DOI: 10.1021/jp040361r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco A. Evangelista
- Scuola Normale Superiore di Pisa, 56126 Pisa, Italy, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2525
| | - Henry F. Schaefer
- Scuola Normale Superiore di Pisa, 56126 Pisa, Italy, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2525
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Weber JM, Ioffe IN, Berndt KM, Löffler D, Friedrich J, Ehrler OT, Danell AS, Parks JH, Kappes MM. Photoelectron spectroscopy of isolated multiply negatively charged oligonucleotides. J Am Chem Soc 2004; 126:8585-9. [PMID: 15238018 DOI: 10.1021/ja049736c] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet photoelectron spectroscopy in an ion beam was used to investigate the electronic properties of isolated DNA oligonucleotides [dA(5)-4H](4-) and [dT(5)-4H](4-), carrying four excess negative charges. We find the fourth adiabatic electron affinity to be slightly negative for [dA(5)-4H](4-), while it is positive for [dT(5)-4H](4-). This implies a significant influence of the base composition on energetics, which is in turn relevant for analytic applications and also for charge transport properties.
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Affiliation(s)
- J Mathias Weber
- Institut für Physikalische Chemie, Universität Karlsruhe, Kaiserstr. 12, D-76128 Karlsruhe, Germany.
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30
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Akamatsu K, Fujii K, Yokoya A. Qualitative and quantitative analyses of the decomposition products that arise from the exposure of thymine to monochromatic ultrasoft X rays and 60Co gamma rays in the solid state. Radiat Res 2004; 161:442-50. [PMID: 15038767 DOI: 10.1667/3151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
HPLC analyses of condensed thymine irradiated with monochromatic synchrotron ultrasoft X rays in the energy region around nitrogen and oxygen K-shell edges were performed. Cobalt-60 gamma rays were used as a reference radiation. The radiation chemical dose response of each separated thymine decomposition product was also determined. Uracil (U), 5-(hydroxymethyl)uracil (HMU), 5,6-dihydrothymine (DHT), 5-formyluracil (foU) and four main unknown products were found in the HPLC chromatogram of the sample irradiated with ultrasoft X rays in vacuo. Similar spectra of the products were also found in the gamma-ray experiment; however, some unknown products that appeared after elution of the thymine peak were significantly larger than those in the ultrasoft X- ray experiment. This result indicates the difference in radiation quality. The G value of DHT produced by gamma radiation was 10 times larger than those produced by the ultrasoft X- ray photons with energies of 395 and 407 eV corresponding to below and on the nitrogen K-shell edge, respectively. This result suggests that the differences in the photon energy and/ or in the energy spectra of the secondary electron between ultrasoft X rays and gamma rays are causing differences in the process of the radiation chemistry. Moreover, the yields of all the thymine decomposition products induced by 538 eV photons (oxygen K-shell edge) were significantly smaller than those induced by photons around the nitrogen K-shell edge. The K-shell excitation of oxygen in thymine may efficiently promote the production of small thymine fragments susceptible to desorption from the sample.
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Affiliation(s)
- Ken Akamatsu
- Radiation Risk Laboratory, Department of Health Physics, Japan Atomic Energy Research Institute, 2-4 Shirakatashirane, Tokai, Naka, Ibaraki 319-1195, Japan.
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Fujii K, Akamatsu K, Yokoya A. Ion Desorption from DNA Components Irradiated with 0.5 keV Ultrasoft X-Ray Photons. Radiat Res 2004; 161:435-41. [PMID: 15038768 DOI: 10.1667/rr3131] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Positive ion desorption from thin films of DNA components, 2-deoxy-d-ribose, thymine, thymidine (dThd), and thymidine 5'-monophosphate (dTMP) was investigated in the oxygen K- shell edge excitation region using synchrotron ultrasoft X rays (538 eV). A large number of molecular fragments, H(+), CH(x)(+), C(2)H(x)(+), CO(+), CH(x)O(+), C(3)H(x)(+), C(2)H(x)O(+) and C(3)H(x)O(+) (x = 1, 2 and 3), were observed as desorbed ions from 2-deoxy-d-ribose. Some of these ions are related to simultaneous bond scission at particular C-C and C-O (or C-C) bonds in the furanose ring structure in the 2-deoxy-d-ribose molecule, indicating that the impact of photons on the oxygen atom and the impact of ejected secondary electrons (e.g. Auger electrons) cause an intense destruction of the furanose ring structure. In thymine thin films, H(+), CH(x)(+), CO(+), CH(x)O(+), C(2)H(x)N(+) and CH(x)NO(+) (x = 1, 2 and 3) fragments were observed. The yields of these ions were smaller than the yields from 2-deoxy-d-ribose. The desorption of CH(3)(+) from thymine might induce a molecular conversion from thymine to uracil. The mass patterns of dThd and dTMP, and especially that of dTMP, were similar to that of 2-deoxy-d-ribose, indicating that a number of ions were generated at the sugar site, even in the nucleotide molecule. It is therefore predicted that the sugar moiety is more fragile than the thymine base.
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Affiliation(s)
- Kentaro Fujii
- Synchrotron Radiation Research Center, Japan Atomic Energy Research Institute, SPring-8, Mikazuki, Sayo, Hyogo 679-5148, Japan.
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Caron LG, Sanche L. Low-energy electron diffraction and resonances in DNA and other helical macromolecules. PHYSICAL REVIEW LETTERS 2003; 91:113201. [PMID: 14525424 DOI: 10.1103/physrevlett.91.113201] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2003] [Indexed: 05/24/2023]
Abstract
We propose a framework to calculate the intermolecular multiple elastic scattering of low-energy electrons from helical macromolecules and indicate how it affects the resonant capture cross section. Using a model of DNA, an appreciable enhancement of the elastic and resonant capture cross sections is predicted at incident energies below 15 eV. These results may qualitatively explain the observed prominence of low-energy resonances in strand breaking of plasmid DNA.
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Affiliation(s)
- L G Caron
- Groupe des Instituts de Recherche en Santé du Canada en Sciences des Radiations, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
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33
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Sanche L. Nanoscopic aspects of radiobiological damage: Fragmentation induced by secondary low-energy electrons. MASS SPECTROMETRY REVIEWS 2002; 21:349-369. [PMID: 12645089 DOI: 10.1002/mas.10034] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Low-energy electrons (LEEs) are produced in large quantities in any type of material irradiated by high-energy particles. In biological media, these electrons can fragment molecules and lead to the formation of highly reactive radicals and ions. The results of recent experiments performed on biomolecular films bombarded with LEEs under ultra-high vacuum conditions are reviewed in the present article. The major type of experiments, which measure fragments produced in such films as a function of incident electron energy (0.1-45 eV), are briefly described. Examples of the results obtained from DNA films are summarized along with those obtained from the fragmentation of elementary components of the DNA molecule (i.e., thin solid films of H(2)O, DNA bases, sugar analogs, and oligonucleotides) and proteins. By comparing the results of these different experiments, it is possible to determine fundamental mechanisms that are involved in the dissociation of biomolecules and the production of single- and double-strand breaks in DNA, and to show that base damage is dependent on the nature of the bases and on their sequence context. Below 15 eV, electron resonances (i.e., the formation of transient anions) play a dominant role in the fragmentation of all biomolecules investigated. These transient anions fragment molecules by decaying into dissociative electronically excited states or by dissociating into a stable anion and a neutral radical. These fragments usually initiate other reactions with nearby molecules, causing further chemical damage. The damage caused by transient anions is dependent on the molecular environment.
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Affiliation(s)
- Léon Sanche
- Group of the Canadian Institutes of Health Research in the Radiation Sciences, Faculté de médecine, Université de Sherbrooke, Canada J1H 5N4.
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