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Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
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2
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Low-Energy Electron Generation for Biomolecular Damage Inquiry: Instrumentation and Methods. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Technological advancement has produced a variety of instruments and methods to generate electron beams that have greatly assisted in the extensive theoretical and experimental efforts devoted to investigating the effect of secondary electrons with energies approximately less than 100 eV, which are referred as low-energy electrons (LEEs). In the past two decades, LEE studies have focused on biomolecular systems, which mainly consist of DNA and proteins and their constituents as primary cellular targets of ionizing radiation. These studies have revealed that compared to other reactive species produced by high-energy radiation, LEEs have distinctive pathways and considerable efficiency in inducing lethal DNA lesions. The present work aims to briefly discuss the current state of LEE production technology and to motivate further studies and improvements of LEE generation techniques in relation to biological electron-driven processes associated with such medical applications as radiation therapy and cancer treatment.
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3
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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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4
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Lemelin V, Bass AD, Sanche L. Low energy (6-18 eV) electron scattering from condensed thymidine (dT) III: absolute electronic excitation cross sections. Phys Chem Chem Phys 2020; 22:8364-8372. [PMID: 32266899 DOI: 10.1039/d0cp00198h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Absolute cross sections (CSs) for electronic excitation by low-energy electron (LEE) scattering, from condensed thymidine (dT) in the 6-18 eV incident energy range, were measured by high-resolution electron energy loss spectroscopy (HREELS). Various electron energy loss (EEL) spectra were acquired using 1 ML of dT condensed on a multilayer film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex DNA constituents to be studied by HREELS and these spectra provide the first LEE energy-loss data for electronic excitation of a nucleoside. CSs for transitions to the states 13A', 13A'', 23A', 21A', 33A', 23A'', 43A', 33A'', 53A' and 51A' of dT were extracted from the EEL spectra. These states correlate to those previously measured for the thymine moiety. Two broad resonances are observed in the energy dependence of the CSs at around 8 and 10 eV; these energies are close to those found in earlier gas- and solid-phase studies on the interaction of LEEs with dT, thymine and related molecules. A quantitative comparison between the electronic CSs of dT and those of thymine and tetrahydrofuran indicates that no variation is induced in the electronic CSs of thymine upon chemically binding to a deoxyribose group.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - A D Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - L Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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5
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Lemelin V, Bass AD, Cloutier P, Sanche L. Low energy (1-19 eV) electron scattering from condensed thymidine (dT) II: comparison of vibrational excitation cross sections with those of tetrahydrofuran and the recalibrated values of thymine. Phys Chem Chem Phys 2019; 21:23818-23825. [PMID: 31503272 DOI: 10.1039/c9cp03448j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Recent measurements of absolute vibrational cross sections (CSs) for low-energy electron (LEE) scattering from condensed thymidine (dT) allows comparison with CSs of its constituents; thymine and tetrahydrofuran (THF). To facilitate this comparison, the vibrational CSs of condensed thymine were remeasured at six electron incident energies and a correction was applied to the earlier thymine CS values measured by Lévesque et al. [Nucl. Instrum. Methods Phys. Res., Sect. B, 2003, 208, 225]. The incident energy dependence of the CS of each vibrational mode of dT is compared with the corresponding modes in thymine and/or THF. It is found that the magnitude of the CSs of the thymine breathing mode and the C-C stretch mode of THF are greatly attenuated in dT. Finally, the magnitudes of the total vibrational CSs of each molecule are compared. Below 4 eV, the total vibrational CSs of dT is greater than each of its two constituents. Interestingly, at higher energy (>6 eV), the magnitude of the total vibrational CS of dT is roughly equal to that of THF and is greater than thymine by only 15% at 10 eV, showing that the CSs of dT cannot be approximated by the addition of the CSs of its constituents over the entire energy range. These comparisons are discussed in terms of the basic principles involved in the formation and decay of shape resonances, which are known to be responsible for major enhancements of LEE-induced vibrational excitation at low electron energies.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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6
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Lemelin V, Bass AD, Cloutier P, Sanche L. Low energy (1-19 eV) electron scattering from condensed thymidine (dT) I: absolute vibrational excitation cross sections. Phys Chem Chem Phys 2019; 21:23808-23817. [PMID: 31503266 DOI: 10.1039/c9cp03447a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Absolute cross sections (CSs) for vibrational excitation by electrons of energy between 1-19 eV scattering from condensed thymidine (dT) were measured by means of high-resolution electron energy loss spectroscopy (HREELS). The CSs were extracted from electron energy loss spectra of dT condensed on multilayers film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex molecules to be studied in condensed phase by HREELS. The magnitudes of the vibrational CSs lie within the 10-17 cm2 range. Structures observed in the energy dependence of the vibrational CSs under 3 eV and around 4 eV were compared with previous results of gas- and solid-phase studies on dT and related molecules (e.g., thymine and tetrahydrofuran). These structures were attributed to the formation of shape resonances.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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7
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Clustered DNA Damages induced by 0.5 to 30 eV Electrons. Int J Mol Sci 2019; 20:ijms20153749. [PMID: 31370253 PMCID: PMC6695612 DOI: 10.3390/ijms20153749] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022] Open
Abstract
Low-energy electrons (LEEs) of energies ≤30 eV are generated in large quantities by ionizing radiation. These electrons can damage DNA; particularly, they can induce the more detrimental clustered lesions in cells. This type of lesions, which are responsible for a large portion of the genotoxic stress generated by ionizing radiation, is described in the Introduction. The reactions initiated by the collisions of 0.5-30 eV electrons with oligonucleotides, duplex DNA, and DNA bound to chemotherapeutic platinum drugs are explained and reviewed in the subsequent sections. The experimental methods of LEE irradiation and DNA damage analysis are described with an emphasis on the detection of cluster lesions, which are considerably enhanced in DNA-Pt-drug complexes. Based on the energy dependence of damage yields and cross-sections, a mechanism responsible for the clustered lesions can be attributed to the capture of a single electron by the electron affinity of an excited state of a base, leading to the formation of transient anions at 6 and 10 eV. The initial capture is followed by electronic excitation of the base and dissociative attachment-at other DNA sites-of the electron reemitted from the temporary base anion. The mechanism is expected to be universal in the cellular environment and plays an important role in the formation of clustered lesions.
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8
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Bugris V, Harmat V, Ferenc G, Brockhauser S, Carmichael I, Garman EF. Radiation-damage investigation of a DNA 16-mer. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:998-1009. [PMID: 31274421 DOI: 10.1107/s160057751900763x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
In macromolecular crystallography, a great deal of effort has been invested in understanding radiation-damage progression. While the sensitivity of protein crystals has been well characterized, crystals of DNA and of DNA-protein complexes have not thus far been studied as thoroughly. Here, a systematic investigation of radiation damage to a crystal of a DNA 16-mer diffracting to 1.8 Å resolution and held at 100 K, up to an absorbed dose of 45 MGy, is reported. The RIDL (Radiation-Induced Density Loss) automated computational tool was used for electron-density analysis. Both the global and specific damage to the DNA crystal as a function of dose were monitored, following careful calibration of the X-ray flux and beam profile. The DNA crystal was found to be fairly radiation insensitive to both global and specific damage, with half of the initial diffraction intensity being lost at an absorbed average diffraction-weighted dose, D1/2, of 19 MGy, compared with 9 MGy for chicken egg-white lysozyme crystals under the same beam conditions but at the higher resolution of 1.4 Å. The coefficient of sensitivity of the DNA crystal was 0.014 Å2 MGy-1, which is similar to that observed for proteins. These results imply that the significantly greater radiation hardness of DNA and RNA compared with protein observed in a DNA-protein complex and an RNA-protein complex could be due to scavenging action by the protein, thereby protecting the DNA and RNA in these studies. In terms of specific damage, the regions of DNA that were found to be sensitive were those associated with some of the bound calcium ions sequestered from the crystallization buffer. In contrast, moieties farther from these sites showed only small changes even at higher doses.
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Affiliation(s)
- Valéria Bugris
- X-ray Crystallography Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Veronika Harmat
- X-ray Crystallography Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Sándor Brockhauser
- X-ray Crystallography Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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9
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McKee AD, Schaible MJ, Rosenberg RA, Kundu S, Orlando TM. Low energy secondary electron induced damage of condensed nucleotides. J Chem Phys 2019; 150:204709. [PMID: 31153208 DOI: 10.1063/1.5090491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C-O-P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10-18 cm2) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. The C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (∼5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.
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Affiliation(s)
- A D McKee
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - R A Rosenberg
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - S Kundu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - T M Orlando
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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10
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Braud I, Zamith S, Cuny J, Zheng L, L’Hermite JM. Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study. J Chem Phys 2019; 150:014303. [DOI: 10.1063/1.5044481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Isabelle Braud
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC) UMR5626, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Linjie Zheng
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC) UMR5626, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jean-Marc L’Hermite
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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11
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Pshenichnyuk SA, Modelli A, Komolov AS. Interconnections between dissociative electron attachment and electron-driven biological processes. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1461347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute of Molecule and Crystal Physics – Subdivision of the Ufa Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Alberto Modelli
- Dipartimento di Chimica ‘G. Ciamician’, Università di Bologna, Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, Ravenna, Italy
| | - Alexei S. Komolov
- Department of Solid State Electronics, St. Petersburg State University, St. Petersburg, Russia
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Kohanoff J, McAllister M, Tribello GA, Gu B. Interactions between low energy electrons and DNA: a perspective from first-principles simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:383001. [PMID: 28617676 DOI: 10.1088/1361-648x/aa79e3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts with the interaction of radiation-either photons or swift ions-and the biological medium, which causes electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, and strand breaks in plasmid DNA in particular (Boudaiffa et al 2000 Science 287 1658-60). These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage. In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.
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Affiliation(s)
- Jorge Kohanoff
- Atomistic Simulation Centre, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
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Gao L, Bu Y. Protonation-modulated localization of excess electrons in histidine aqueous solutions revealed by ab initio molecular dynamics simulations: anion-centered versus cation-centered localization. Phys Chem Chem Phys 2017; 19:13807-13818. [PMID: 28508903 DOI: 10.1039/c7cp01847a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we present an ab initio molecular dynamics simulation study on the interaction of an excess electron (EE) with histidine in its aqueous solution. Two different configurations of histidine (imidazole group protonated or not) are considered to reflect its different existing forms in neutral or slightly acidic surroundings. The simulation results indicate that localizations of EEs in different aqueous histidine solutions are quite different and are strongly affected by protonation of the side chain imidazole group and are thus pH-controlled. In neutral aqueous histidine solution, an EE localizes onto the carboxyl anionic group of the amino acid backbone after a relatively lengthy diffuse state, performing just like in an aliphatic amino acid solution. But in weakly acidic solution in which the side chain imidazole group is protonated, an EE undergoes a short lifetime diffuse state and finally localizes on the protonated imidazole group. We carefully examine these two different localization dynamics processes and analyze the competition between different dominating groups in their corresponding electron localization mechanisms. To explain the difference, we investigate the frontier molecular orbitals of these two systems and find that their energy levels and compositions are important to determine these differences. These findings can provide helpful information to understand the interaction mechanisms of low energy EEs with amino acids and even oligopeptides, especially with aromatic rings.
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Affiliation(s)
- Liang Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
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14
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Hahn MB, Meyer S, Kunte HJ, Solomun T, Sturm H. Measurements and simulations of microscopic damage to DNA in water by 30 keV electrons: A general approach applicable to other radiation sources and biological targets. Phys Rev E 2017; 95:052419. [PMID: 28618479 DOI: 10.1103/physreve.95.052419] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 12/28/2022]
Abstract
The determination of the microscopic dose-damage relationship for DNA in an aqueous environment is of a fundamental interest for dosimetry and applications in radiation therapy and protection. We combine geant4 particle-scattering simulations in water with calculations concerning the movement of biomolecules to obtain the energy deposit in the biologically relevant nanoscopic volume. We juxtaposition these results to the experimentally determined damage to obtain the dose-damage relationship at a molecular level. This approach is tested for an experimentally challenging system concerning the direct irradiation of plasmid DNA (pUC19) in water with electrons as primary particles. Here a microscopic target model for the plasmid DNA based on the relation of lineal energy and radiation quality is used to calculate the effective target volume. It was found that on average fewer than two ionizations within a 7.5-nm radius around the sugar-phosphate backbone are sufficient to cause a single strand break, with a corresponding median lethal energy deposit being E_{1/2}=6±4 eV. The presented method is applicable for ionizing radiation (e.g., γ rays, x rays, and electrons) and a variety of targets, such as DNA, proteins, or cells.
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Affiliation(s)
- Marc Benjamin Hahn
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Susann Meyer
- Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam, Germany and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Hans-Jörg Kunte
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany and Technical University Berlin, D-10587 Berlin, Germany
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15
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Pshenichnyuk SA, Komolov AS. Why Can Unnatural Electron Acceptors Protect Photosynthesizing Organisms but Kill the Others? J Phys Chem B 2017; 121:749-757. [DOI: 10.1021/acs.jpcb.6b12007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute
of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospeκt Oktyabrya 151, 450075 Ufa, Russia
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Alexei S. Komolov
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
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16
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Pshenichnyuk SA, Modelli A, Lazneva EF, Komolov AS. Role of Resonance Electron Attachment in Phytoremediation of Halogenated Herbicides. J Phys Chem B 2016; 120:12098-12104. [DOI: 10.1021/acs.jpcb.6b10149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute
of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospeκt Oktyabrya 151, 450075 Ufa, Russia
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Alberto Modelli
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, via S. Alberto 163, 48123 Ravenna, Italy
| | - Eleonora F. Lazneva
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Alexei S. Komolov
- St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
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17
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Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Choofong S, Cloutier P, Sanche L, Wagner JR. Base Release and Modification in Solid-Phase DNA Exposed to Low-Energy Electrons. Radiat Res 2016; 186:520-530. [PMID: 27802110 DOI: 10.1667/rr14476.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ionization generates a large number of secondary low-energy electrons (LEEs) with a most probable energy of approximately 10 eV, which can break DNA bonds by dissociative electron attachment (DEA) and lead to DNA damage. In this study, we investigated radiation damage to dry DNA induced by X rays (1.5 keV) alone on a glass substrate or X rays combined with extra LEEs (average energy of 5.8 eV) emitted from a tantalum (Ta) substrate under an atmosphere of N2 and standard ambient conditions of temperature and pressure. The targets included calf-thymus DNA and double-stranded synthetic oligonucleotides. We developed analytical methods to measure the release of non-modified DNA bases from DNA and the formation of several base modifications by LC-MS/MS with isotopic dilution for precise quantification. The results show that the yield of non-modified bases as well as base modifications increase by 20-30% when DNA is deposited on a Ta substrate compared to that on a glass substrate. The order of base release (Gua > Ade > Thy ∼ Cyt) agrees well with several theoretical studies indicating that Gua is the most susceptible site toward sugar-phosphate cleavage. The formation of DNA damage by LEEs is explained by DEA leading to the release of non-modified bases involving the initial cleavage of N1-C1', C3'-O3' or C5'-O5' bonds. The yield of base modifications was lower than the release of non-modified bases. The main LEE-induced base modifications include 5,6-dihydrothymine (5,6-dHT), 5,6-dihydrouracil (5-dHU), 5-hydroxymethyluracil (5-HmU) and 5-formyluracil (5-ForU). The formation of base modifications by LEEs can be explained by DEA and cleavage of the C-H bond of the methyl group of Thy (giving 5-HmU and 5-ForU) and by secondary reactions of H atoms and hydride anions that are generated by primary LEE reactions followed by subsequent reaction with Cyt and Thy (giving 5,6-dHU and 5,6-dHT).
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Affiliation(s)
- Surakarn Choofong
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Pierre Cloutier
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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19
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Wu X, Gao L, Liu J, Yang H, Wang S, Bu Y. Excess electron reactivity in amino acid aqueous solution revealed by ab initio molecular dynamics simulation: anion-centered localization and anion-relayed electron transfer dissociation. Phys Chem Chem Phys 2016; 17:26854-63. [PMID: 26399512 DOI: 10.1039/c5cp03720d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies on the structure, states, and reactivity of excess electrons (EEs) in biological media are of great significance. Although there is information about EE interaction with desolvated biological molecules, solution effects are hardly explored. In this work, we present an ab initio molecular dynamics simulation study on the interaction and reactivity of an EE with glycine in solution. Our simulations reveal two striking results. Firstly, a pre-solvated EE partially localizes on the negatively charged -COO(-) group of the zwitterionic glycine and the remaining part delocalizes over solvent water molecules, forming an anion-centered quasi-localized structure, due to relative alignment of the lowest unoccupied molecular orbital energy levels of potential sites for EE residence in the aqueous solution. Secondly, after a period of anion-centered localization of an EE, the zwitterionic glycine is induced to spontaneously fragment through the cleavage of the N-Cα bond, losing ammonia (deamination), and leaving a ˙CH2-COO(-) anion radical, in good agreement with experimental observations. Introduction of the same groups (-COO(-) or -NH3(+)) in the side chain (taking lysine and aspartic acid as examples) can affect EE localization, with the fragmentation of the backbone part of these amino acids dependent on the properties of the side chain groups. These findings provide insights into EE interaction mechanisms with the backbone parts of amino acids and low energy EE induced fragmentation of amino acids and even peptides and proteins.
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Affiliation(s)
- Xiuxiu Wu
- School of Chemistry & Chemical Engineering, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China.
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20
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Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF. RNA protects a nucleoprotein complex against radiation damage. Acta Crystallogr D Struct Biol 2016; 72:648-57. [PMID: 27139628 PMCID: PMC4854314 DOI: 10.1107/s2059798316003351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/26/2016] [Indexed: 11/10/2022] Open
Abstract
Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.
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Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry I Street, Portsmouth PO1 2DY, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Markus Gerstel
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Mikhail B. Shevtsov
- Laboratory of Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
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21
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Pshenichnyuk SA, Modelli A, Lazneva EF, Komolov AS. Hypothesis for the Mechanism of Ascorbic Acid Activity in Living Cells Related to Its Electron-Accepting Properties. J Phys Chem A 2016; 120:2667-76. [DOI: 10.1021/acs.jpca.6b02272] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute of Molecule and Crystal Physics,
Ufa Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya
151, 450075 Ufa, Russia
- Physics Faculty, St. Petersburg State University, Uljanovskaja 1, 198504 St. Petersburg, Russia
| | - Alberto Modelli
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, via S. Alberto 163, 48123 Ravenna, Italy
| | - Eleonora F. Lazneva
- Physics Faculty, St. Petersburg State University, Uljanovskaja 1, 198504 St. Petersburg, Russia
| | - Alexei S. Komolov
- Physics Faculty, St. Petersburg State University, Uljanovskaja 1, 198504 St. Petersburg, Russia
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22
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Zhao J, Wang M, Fu A, Yang H, Bu Y. Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations. Chemphyschem 2015; 16:2348-56. [DOI: 10.1002/cphc.201500040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Indexed: 11/07/2022]
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23
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Bury C, Garman EF, Ginn HM, Ravelli RBG, Carmichael I, Kneale G, McGeehan JE. Radiation damage to nucleoprotein complexes in macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:213-24. [PMID: 25723923 PMCID: PMC4344358 DOI: 10.1107/s1600577514026289] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/30/2014] [Indexed: 05/23/2023]
Abstract
Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.
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Affiliation(s)
- Charles Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Helen Mary Ginn
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Raimond B. G. Ravelli
- Institute of Nanoscopy, Maastricht University, PO Box 616, Maastricht 6200 MD, The Netherlands
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Geoff Kneale
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY, UK
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY, UK
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24
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Alizadeh E, Orlando TM, Sanche L. Biomolecular damage induced by ionizing radiation: the direct and indirect effects of low-energy electrons on DNA. Annu Rev Phys Chem 2015; 66:379-98. [PMID: 25580626 DOI: 10.1146/annurev-physchem-040513-103605] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many experimental and theoretical advances have recently allowed the study of direct and indirect effects of low-energy electrons (LEEs) on DNA damage. In an effort to explain how LEEs damage the human genome, researchers have focused efforts on LEE interactions with bacterial plasmids, DNA bases, sugar analogs, phosphate groups, and longer DNA moieties. Here, we summarize the current understanding of the fundamental mechanisms involved in LEE-induced damage of DNA and complex biomolecule films. Results obtained by several laboratories on films prepared and analyzed by different methods and irradiated with different electron-beam current densities and fluencies are presented. Despite varied conditions (e.g., film thicknesses and morphologies, intrinsic water content, substrate interactions, and extrinsic atmospheric compositions), comparisons show a striking resemblance in the types of damage produced and their yield functions. The potential of controlling this damage using molecular and nanoparticle targets with high LEE yields in targeted radiation-based cancer therapies is also discussed.
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Affiliation(s)
- Elahe Alizadeh
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, J1H 5N4 Sherbrooke, Canada
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25
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Bacchus-Montabonel MC, Calvo F. Nanohydration of uracil: emergence of three-dimensional structures and proton-induced charge transfer. Phys Chem Chem Phys 2015; 17:9629-33. [DOI: 10.1039/c5cp00611b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stepwise hydration of uracil proceeds three dimensionally above three molecules and qualitatively changes the response to proton damage.
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Affiliation(s)
| | - Florent Calvo
- Laboratoire Interdisciplinaire de Physique
- Rue de La Piscine
- Campus Saint Martin d'Hères
- 38000 Grenoble
- France
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26
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Kouass Sahbani S, Sanche L, Cloutier P, Bass AD, Hunting DJ. Loss of cellular transformation efficiency induced by DNA irradiation with low-energy (10 eV) electrons. J Phys Chem B 2014; 118:13123-31. [PMID: 25325149 DOI: 10.1021/jp508170c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Low energy electrons (LEEs) of energies less than 20 eV are generated in large quantities by ionizing radiation in biological matter. While LEEs are known to induce single (SSBs) and double strand breaks (DSBs) in DNA, their ability to inactivate cells by inducing nonreparable lethal damage has not yet been demonstrated. Here we observe the effect of LEEs on the functionality of DNA, by measuring the efficiency of transforming Escherichia coli with a [pGEM-3Zf (-)] plasmid irradiated with 10 eV electrons. Highly ordered DNA films were prepared on pyrolitic graphite by molecular self-assembly using 1,3-diaminopropane ions (Dap(2+)). The uniformity of these films permits the inactivation of approximately 50% of the plasmids compared to <10% using previous methods, which is sufficient for the subsequent determination of their functionality. Upon LEE irradiation, the fraction of functional plasmids decreased exponentially with increasing electron fluence, while LEE-induced isolated base damage, frank DSB, and non DSB-cluster damage increased linearly with fluence. While DSBs can be toxic, their levels were too low to explain the loss of plasmid functionality observed upon LEE irradiation. Similarly, non-DSB cluster damage, revealed by transforming cluster damage into DSBs by digestion with repair enzymes, also occurred relatively infrequently. The exact nature of the lethal damage remains unknown, but it is probably a form of compact cluster damage in which the lesions are too close to be revealed by purified repair enzymes. In addition, this damage is either not repaired or is misrepaired by E. coli, since it results in plasmid inactivation, when they contain an average of three lesions. Comparison with previous results from a similar experiment performed with γ-irradiated plasmids indicates that the type of clustered DNA lesions, created directly on cellular DNA by LEEs, may be more difficult to repair than those produced by other species from radiolysis.
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Affiliation(s)
- Saloua Kouass Sahbani
- Department of Nuclear Medicine & Radiobiology, Faculty of Medicine, Université de Sherbrooke , Sherbrooke, Quebec, Canada J1H 5N4
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27
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Smyth M, Kohanoff J, Fabrikant II. Electron-induced hydrogen loss in uracil in a water cluster environment. J Chem Phys 2014; 140:184313. [DOI: 10.1063/1.4874841] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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28
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Luo X, Zheng Y, Sanche L. DNA strand breaks and crosslinks induced by transient anions in the range 2-20 eV. J Chem Phys 2014; 140:155101. [PMID: 26792947 PMCID: PMC4716823 DOI: 10.1063/1.4870519] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The energy dependence of the yields of single and double strand breaks (SSB and DSB) and crosslinks induced by electron impact on plasmid DNA films is measured in the 2-20 eV range. The yield functions exhibit two strong maxima, which are interpreted to result from the formation of core-excited resonances (i.e., transient anions) of the bases, and their decay into the autoionization channel, resulting in π → π* electronic transitions of the bases followed by electron transfer to the C-O σ* bond in the phosphate group. Occupancy of the σ* orbital ruptures the C-O bond of the backbone via dissociative electron attachment, producing a SSB. From a comparison of our results with those of other works, including theoretical calculations and electron-energy-loss spectra of the bases, the 4.6 eV peak in the SSB yield function is attributed to the resonance decay into the lowest electronically excited states of the bases; in particular, those resulting from the transitions 13A'(π2 → π3*) and 13A″(n2 → π3*) of thymine and 13A'(π → π*) of cytosine. The strongest peak at 9.6 eV in the SSB yield function is also associated with electron captured by excited states of the bases, resulting mostly from a multitude of higher-energy π → π* transitions. The DSB yield function exhibits strong maxima at 6.1 and 9.6 eV. The peak at 9.6 eV is probably related to the same resonance manifold as that leading to SSB, but the other at 6.1 eV may be more restricted to decay into the electronic state 13A' (π → π*) of cytosine via autoionization. The yield function of crosslinks is dominated by a broad peak extending over the 3.6-11.6 eV range with a sharper one at 17.6 eV. The different line shape of the latter function, compared to that of SSB and DSB, appears to be due to the formation of reactive radical sites in the initial supercoiled configuration of the plasmid, which react with the circular form (i.e., DNA with a SSB) to produce a crosslink.
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Affiliation(s)
- Xinglan Luo
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Yi Zheng
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Léon Sanche
- Group in the Radiation Sciences, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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29
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Gu B, Smyth M, Kohanoff J. Protection of DNA against low-energy electrons by amino acids: a first-principles molecular dynamics study. Phys Chem Chem Phys 2014; 16:24350-8. [DOI: 10.1039/c4cp03906h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The physical shielding and chemical stabilizing of the low energy electron by glycine around the thymine through proton transfer.
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Affiliation(s)
- Bin Gu
- Department of Physics
- Nanjing University of Information Science and Technology
- Nanjing 210044, China
- Atomistic Simulation Centre
- Queen's University Belfast
| | - Maeve Smyth
- Atomistic Simulation Centre
- Queen's University Belfast
- Belfast BT7 1NN, UK
| | - Jorge Kohanoff
- Atomistic Simulation Centre
- Queen's University Belfast
- Belfast BT7 1NN, UK
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30
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Massey S, Bass AD, Sanche L. Note: Transient negative ions as initiators of oxygen fixation in <20 eV electron-irradiated DNA. J Chem Phys 2013; 139:186101. [DOI: 10.1063/1.4829770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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31
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Cauët E, Bogatko S, Liévin J, De Proft F, Geerlings P. Electron-Attachment-Induced DNA Damage: Instantaneous Strand Breaks. J Phys Chem B 2013; 117:9669-76. [DOI: 10.1021/jp406320g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilie Cauët
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
- Service de Chimie Quantique
et Photophysique, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, CPi160/09, B-1050 Brussels, Belgium
| | - Stuart Bogatko
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
| | - Jacques Liévin
- Service de Chimie Quantique
et Photophysique, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, CPi160/09, B-1050 Brussels, Belgium
| | - Frank De Proft
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
| | - Paul Geerlings
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
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32
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Alizadeh E, Sanche L. The Role of Humidity and Oxygen Level on Damage to DNA Induced by Soft X-rays and Low-Energy Electrons. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2013; 117:22445-22453. [PMID: 24976877 PMCID: PMC4072655 DOI: 10.1021/jp403350j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Single- and double-strand breaks induced by soft X-rays (1.5 keV) and photo-emitted LEEs (0-30 eV) were measured in dry and humid thin films of plasmid DNA irradiated under different controllable levels of oxygen at standard ambient temperature and pressure (SATP). G values derived from these experiments shows that the presence of H2O and changing the atmosphere from N2 to O2, while keeping all other experimental parameters constant, increases the formation of DSBs by factors of 4.5 and 11.8 for X-rays and LEEs, respectively. Under an oxygenated environment in humid DNA films, the additional LEE-induced damage resulting from the combination of water and oxygen exhibits a supper-additive effect, which leads to the formation of DSBs with a G value almost 7 times higher than that obtained by X-ray photons. These results indicate that O2, H2O and LEEs effectively contribute synergistically to enhance the formation of DSBs.
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Affiliation(s)
- Elahe Alizadeh
- Group of Radiation Sciences, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada J1H5N4
| | - Léon Sanche
- Group of Radiation Sciences, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada J1H5N4
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33
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Alizadeh E, Sanz AG, García G, Sanche L. Radiation Damage to DNA: The Indirect Effect of Low Energy Electrons. J Phys Chem Lett 2013; 4:820-825. [PMID: 24976899 PMCID: PMC4071054 DOI: 10.1021/jz4000998] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We report the effect of DNA hydration level on damage yields induced by soft X-rays and photo-emitted low energy electrons (LEEs) in thin films of plasmid DNA irradiated in N2 at atmospheric pressure under different humidity levels. Contrary to a dilute solution of DNA, the number of H2O molecules per nucleotide (Γ) in these films can be varied from Γ=2.5 to ~33, where Γ≤20 corresponds to layers of hydration and Γ=33 to an additional bulk-like water layer. Our results indicate that DNA damage induced by LEEs does not increase significantly until the second hydration shell is formed. However, this damage increases dramatically as DNA coverage approaches bulk-like hydration conditions. A number of phenomena are invoked to account for these behaviors including: dissociative electron transfer from water-interface electron traps to DNA bases, quenching of dissociative electron attachment to DNA and quenching of dissociative electronically excited states of H2O in contact with DNA.
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Affiliation(s)
- Elahe Alizadeh
- Groupe en Sciences des Radiations, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Corresponding Author: , Tel: +1 819 346 1110 (15863), Fax: +1 819 564 5442
| | - Ana G. Sanz
- Instituto de Física Fundumental, Consejo Suporior de Investigaciones Científicas, Madrid, Spain
| | - Gustavo García
- Instituto de Física Fundumental, Consejo Suporior de Investigaciones Científicas, Madrid, Spain
| | - Léon Sanche
- Groupe en Sciences des Radiations, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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34
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Becker D, Adhikary A, Tetteh ST, Bull AW, Sevilla MD. Kr-86 ion-beam irradiation of hydrated DNA: free radical and unaltered base yields. Radiat Res 2012; 178:524-37. [PMID: 23106211 DOI: 10.1667/rr3066.3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields.
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Affiliation(s)
- David Becker
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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Fabrikant II, Caprasecca S, Gallup GA, Gorfinkiel JD. Electron attachment to molecules in a cluster environment. J Chem Phys 2012; 136:184301. [PMID: 22583281 DOI: 10.1063/1.4706604] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Low-energy dissociative electron attachment (DEA) to the CF(2)Cl(2) and CF(3)Cl molecules in a water cluster environment is investigated theoretically. Calculations are performed for the water trimer and water hexamer. It is shown that the DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster, and that this cross section grows as the number of water molecules in the cluster increases. This growth is explained by a trapping effect that is due to multiple scattering by water molecules while the electron is trapped in the cluster environment. The trapping increases the resonance lifetime and the negative ion survival probability. This confirms qualitatively existing experiments on electron attachment to the CF(2)Cl(2) molecule placed on the surface of H(2)O ice. The DEA cross sections are shown to be very sensitive to the position of the attaching molecule within the cluster and the orientation of the electron beam relative to the cluster.
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Affiliation(s)
- I I Fabrikant
- Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom.
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Kumar SVK, Pota T, Peri D, Dongre AD, Rao BJ. Low energy electron induced damage to plasmid DNA pQE30. J Chem Phys 2012; 137:045101. [DOI: 10.1063/1.4737182] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Alizadeh E, Sanche L. Precursors of solvated electrons in radiobiological physics and chemistry. Chem Rev 2012; 112:5578-602. [PMID: 22724633 DOI: 10.1021/cr300063r] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elahe Alizadeh
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
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Mirsaleh-Kohan N, Bass AD, Cloutier P, Massey S, Sanche L. Low energy electron stimulated desorption from DNA films dosed with oxygen. J Chem Phys 2012; 136:235104. [PMID: 22779623 PMCID: PMC3820536 DOI: 10.1063/1.4729781] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Desorption of anions stimulated by 1-18 eV electron impact on self-assembled monolayer (SAM) films of single DNA strands is measured as a function of film temperature (50-250 K). The SAMs, composed of 10 nucleotides, are dosed with O(2). The OH(-) desorption yields increase markedly with exposure to O(2) at 50 K and are further enhanced upon heating. In contrast, the desorption yields of O(-), attributable to dissociative electron attachment to trapped O(2) molecules decrease with heating. Irradiation of the DNA films prior to the deposition of O(2) shows that this surprising increase in OH(-) desorption, at elevated temperatures, arises from the reaction of O(2) with damaged DNA sites. These results thus appear to be a manifestation of the so-called "oxygen fixation" effect, well known in radiobiology.
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Affiliation(s)
- Nasrin Mirsaleh-Kohan
- Groupe en sciences des radiations, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Adaniya H, Slaughter DS, Osipov T, Weber T, Belkacem A. A momentum imaging microscope for dissociative electron attachment. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:023106. [PMID: 22380078 DOI: 10.1063/1.3685244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe an experimental approach to image the three-dimensional (3D) momentum distribution of the negative ions arising from dissociative electron attachment (DEA). The experimental apparatus employs a low energy pulsed electron gun, an effusive gas source and a 4π solid-angle ion momentum imaging spectrometer consisting of a pulsed ion extraction field, an electrostatic lens, and a time- and position-sensitive detector. The time-of-flight and impact position of each negative ion are measured event by event in order to image the full 3D ion momentum sphere. The system performance is tested by measuring the anion momentum distributions from two DEA resonances, namely H(-) from H(2)O(-) ((2)B(1)) and O(-) from O(2)(-) ((2)Π(u)). The results are compared with existing experimental and theoretical data.
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Affiliation(s)
- H Adaniya
- Lawrence Berkeley National Laboratory, Chemical Sciences, Berkeley, California 94720, USA
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Alizadeh E, Sanche L. Induction of Strand Breaks in DNA films by Low Energy Electrons and Soft X-ray under Nitrous Oxide Atmosphere. Radiat Phys Chem Oxf Engl 1993 2012; 81:33-39. [PMID: 24976692 DOI: 10.1016/j.radphyschem.2011.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Five-monolayer (5ML) plasmid DNA films deposited on glass and tantalum substrates were exposed to Al Kα X-rays of 1.5 keV under gaseous nitrous oxide (N2O) at atmospheric pressure and temperature. Whereas the damage yields for DNA deposited on glass are due to soft X-rays, those arising from DNA on tantalum are due to both the interaction of low energy photoelectrons from the metal and X-rays. Then, the differences in the yields of damage on glass and tantalum substrates, essentially arises from interaction of essentially low-energy electrons (LEEs) with DNA molecules and the surrounding atmosphere. The G-values (i.e., the number of moles of product per Joule of energy absorbed) for DNA strand breaks induced by LEEs (GLEE) and the lower limit of G-values for soft X-ray photons (GXL) were calculated and the results compared to those from previous studies under atmospheric conditions and other ambient gases, such as N2 and O2. Under N2O, the G-values for loss of supercoiled DNA are 103±15 nmol/J for X-rays, and 737±110 nmol/J for LEEs. Compared to corresponding values in an O2 atmosphere, the effectiveness of X-rays to damage DNA in N2O is less, but the G value for LEEs in N2O is more than twice the corresponding value for an oxygenated environment. This result indicates a higher effectiveness for LEEs relative to N2 and O2 environments in causing SSB and DSB in an N2O environment. Thus, the previously observed radiosensitization of cells by N2O may not be only due to OH• radicals but also to the reaction of LEE with N2O molecules near DNA. The previous experiments with N2 and O2 and the present one demonstrate the possibility to investigate damage induced by LEEs to biomolecules under various type of surrounding atmospheres.
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Affiliation(s)
- Elahe Alizadeh
- Groupe en science des radiations, Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, J1H 5N4, Sherbrooke, Canada
| | - Léon Sanche
- Groupe en science des radiations, Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, J1H 5N4, Sherbrooke, Canada
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Smyth M, Kohanoff J. Excess electron localization in solvated DNA bases. PHYSICAL REVIEW LETTERS 2011; 106:238108. [PMID: 21770551 DOI: 10.1103/physrevlett.106.238108] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 05/02/2011] [Indexed: 05/31/2023]
Abstract
We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.
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Affiliation(s)
- Maeve Smyth
- Atomistic Simulation Centre, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
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Alizadeh E, Cloutier P, Hunting D, Sanche L. Soft X-ray and low energy electron-induced damage to DNA under N2 and O2 atmospheres. J Phys Chem B 2011; 115:4523-31. [PMID: 21452797 PMCID: PMC3846624 DOI: 10.1021/jp200947g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
DNA damage induced by low energy electrons (LEEs) and soft X-rays is measured under dry nitrogen and oxygen at atmospheric pressure and temperature. Five-monolayer plasmid DNA films deposited on tantalum and glass substrates are exposed to Al K(α) X-rays of 1.5 keV in the two different environments. From the damage yields for DNA, G values are extracted for X-rays and LEEs. The G values for LEEs are 3.5 and 3.4 higher than those for X-ray photons under N(2) and O(2) atmospheres, respectively. Because most of the measured damage is in the form of single strand breaks (SSB), this result indicates a much higher effectiveness for LEEs relative to X-rays in causing SSB in both environments. The results indicate that the oxygen fixation mechanism, which is highly effective in increasing radiobiological effectiveness, under aerobic conditions, is operative on the type of damage created at the early stage of DNA radiolysis by LEEs.
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Affiliation(s)
- Elahe Alizadeh
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
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Markus TZ, Daube SS, Naaman R. Cooperative effect in the electronic properties of human telomere sequence. J Phys Chem B 2011; 114:13897-903. [PMID: 20942452 DOI: 10.1021/jp1064038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The contribution of sequence elements of human telomere DNA to the interaction of DNA with electrons has been analyzed. By applying wavelength dependent low-energy photoelectron transmission and two-photon photoemission spectroscopy, we investigated the density of states of DNA oligomers with partial sequence elements of the human telomere assembled as monolayers on gold. The findings demonstrate the role of the resonance states in the DNA in accepting electrons and the effect of the sequence on these states. When guanine (G) bases are clustered together, the resonance negative ion state is stabilized, as compared to oligomers containing the same number of G bases but distributed within the sequence. The electron-capturing probability of the human telomere-like oligomer, a sequence with an additional single adenine (A) base adjacent to the G cluster, is dramatically enhanced compared to the other oligomers studied, most likely due to the enhancement of the density of states near the highest occupied molecular orbital.
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Affiliation(s)
- Tal Z Markus
- Department of Chemical Physics, Weizmann Institute, Rehovot 76100, Israel
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Orlando TM, Oh D, Chen Y, Aleksandrov AB. Low-energy electron diffraction and induced damage in hydrated DNA. J Chem Phys 2008; 128:195102. [PMID: 18500900 DOI: 10.1063/1.2907722] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Elastic scattering of 5-30 eV electrons within the B-DNA 5'-CCGGCGCCGG-3' and A-DNA 5'-CGCGAATTCGCG-3' DNA sequences is calculated using the separable representation of a free-space electron propagator and a curved wave multiple scattering formalism. The disorder brought about by the surrounding water and helical base stacking leads to a featureless amplitude buildup of elastically scattered electrons on the sugar and phosphate groups for all energies between 5 and 30 eV. However, some constructive interference features arising from diffraction are revealed when examining the structural waters within the major groove. These appear at 5-10, 12-18, and 22-28 eV for the B-DNA target and at 7-11, 12-18, and 18-25 eV for the A-DNA target. Although the diffraction depends on the base-pair sequence, the energy dependent elastic scattering features are primarily associated with the structural water molecules localized within 8-10 A spheres surrounding the bases and/or the sugar-phosphate backbone. The electron density buildup occurs in energy regimes associated with dissociative electron attachment resonances, direct electronic excitation, and dissociative ionization. Since diffraction intensity can be localized on structural water, compound H2O:DNA states may contribute to energy dependent low-energy electron induced single and double strand breaks.
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Affiliation(s)
- Thomas M Orlando
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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Dingfelder M, Ritchie RH, Turner JE, Friedland W, Paretzke HG, Hamm RN. Comparisons of calculations with PARTRAC and NOREC: transport of electrons in liquid water. Radiat Res 2008; 169:584-94. [PMID: 18439039 DOI: 10.1667/rr1099.1] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 01/10/2008] [Indexed: 11/03/2022]
Abstract
Monte Carlo computer models that simulate the detailed, event-by-event transport of electrons in liquid water are valuable for the interpretation and understanding of findings in radiation chemistry and radiation biology. Because of the paucity of experimental data, such efforts must rely on theoretical principles and considerable judgment in their development. Experimental verification of numerical input is possible to only a limited extent. Indirect support for model validity can be gained from a comparison of details between two independently developed computer codes as well as the observable results calculated with them. In this study, we compare the transport properties of electrons in liquid water using two such models, PARTRAC and NOREC. Both use interaction cross sections based on plane-wave Born approximations and a numerical parameterization of the complex dielectric response function for the liquid. The models are described and compared, and their similarities and differences are highlighted. Recent developments in the field are discussed and taken into account. The calculated stopping powers, W values, and slab penetration characteristics are in good agreement with one another and with other independent sources.
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Affiliation(s)
- M Dingfelder
- Department of Physics, East Carolina University, Greenville, NC 27858, USA.
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Shukla MK, Leszczynski J. Radiation Induced Molecular Phenomena In Nucleic Acids: A Brief Introduction. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2008. [DOI: 10.1007/978-1-4020-8184-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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