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Hervé du Penhoat MA, Souchaud A, Rajpal A, Vuilleumier R, Gaigeot MP, Tavernelli I, Fujii K, Yokoya A, Díaz-Tendero S, Politis MF. Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment. Phys Chem Chem Phys 2024; 26:15693-15704. [PMID: 38766756 DOI: 10.1039/d4cp00489b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Ab initio molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.
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Affiliation(s)
| | | | - Aashini Rajpal
- IMPMC, Sorbonne Université, UMR CNRS 7590, MNHN, Paris, France.
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | | | - Kentaro Fujii
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Sergio Díaz-Tendero
- Departamento de Química, Universidad Autónoma de Madrid, Madrid, Spain
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Marie-Françoise Politis
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
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Yokoya A, Obata Y. Core level ionization or excitation and Auger relaxation induce clustered DNA damage. Enzymes 2022; 51:79-100. [PMID: 36336411 DOI: 10.1016/bs.enz.2022.08.006] [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] [Indexed: 06/16/2023]
Abstract
Ionizing radiation causes various types of DNA damage, such as single- (SSBs) and double-strand breaks (DSBs), nucleobase lesions, abasic sites (AP sites), and cross-linking between complementary strands of DNA or DNA and proteins. DSBs are among the most harmful type of DNA damage, inducing serious genetic effects such as cell lethality and mutation. Nucleobase lesions and AP sites, on the other hand, may be less deleterious and are promptly repaired by base excision repair (BER) pathways. Recently, biochemical approaches to quantify nucleobase lesions and AP sites have revealed certain types of non-strand break lesions as harmful DNA damage, called clustered DNA damage. Such clusters can retard nucleobase excision repair enzymes, and can sometimes be converted to DSBs by BER catalysis. This unique character of clustered DNA damage strongly depends on the spatial density of ionization or excitation events occurring at the track end of initial radiation or low energy secondary electrons. In particular, the photoelectric effect of elements comprising biological molecules, followed by emission of Auger electrons, are key factors in determining the future fate of each clustered damage site. This chapter describes biological studies of clustered nucleobase lesions with SSBs or AP sites, and mechanistical studies on core level excitation and Auger relaxation giving rise to clustered DNA damage.
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Affiliation(s)
- Akinari Yokoya
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba-shi, Japan; Graduate School of Science and Engineering, Ibaraki University, Mito, Japan.
| | - Yui Obata
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba-shi, Japan; Graduate School of Science and Engineering, Ibaraki University, Mito, Japan
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Khalili F, Vafaee M, Shokri B. Attosecond charge migration following oxygen K-shell ionization in DNA bases and base pairs. Phys Chem Chem Phys 2021; 23:23005-23013. [PMID: 34611693 DOI: 10.1039/d1cp02920g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Core ionization of DNA begins a cascade of events which could lead to cellular inactivation or death. The created core-hole following an impulse inner-shell ionization of molecules naturally decays in the auger timescale. We simulated charge migration (CM) phenomena following an impulsive core ionization of individual DNA bases at the oxygen K-edge which occurs before Auger decay of the oxygen. Our approach is based on real-time time dependent density functional theory (RT-TDDFT). It is shown that the pronounced hole fluctuation observed around bonds of the initial core-hole results in various valence orbital migrations. Also, the same photo-core-ionized dynamics is studied for the related base pairs. We investigate the role of base pairing and H-bonding interactions in the attosecond CM dynamics. In particular, the creation of a core-hole in the oxygen involved in H-bonding leads to an enhancement of charge migration relative to the respective single bases. Importantly, the hole oscillation of the adenine-thymine base pair upon creation of a core-hole at the oxygen, which does not contribute to the donor-acceptor interactions (not H-bonded), decreases compared to the single thymine base. Understanding the detailed dynamics of the localized core-hole initiating CM process would open the way for chemically controlling DNA damage/repair in the future.
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Affiliation(s)
- Fatemeh Khalili
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran.
| | - Mohsen Vafaee
- Department of Chemistry, Tarbiat Modares University, P. O. Box 14115-175, Tehran, Iran.
| | - Babak Shokri
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran. .,Laser-Plasma Research Institute, Shahid Beheshti University, Velenjak, Tehran 19839, Iran
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Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays. QUANTUM BEAM SCIENCE 2019. [DOI: 10.3390/qubs3040024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.
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Hervé du Penhoat MA, Moraga NRG, Gaigeot MP, Vuilleumier R, Tavernelli I, Politis MF. Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation. J Phys Chem A 2018; 122:5311-5320. [PMID: 29846073 DOI: 10.1021/acs.jpca.8b04787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we studied the fragmentation dynamics of 2-deoxy-d-ribose (DR) in solution that arises from the double ionization of a water molecule in its primary hydration shell. This process was modeled in the framework of ab initio molecular dynamics. The charge unbalanced in the solvent molecules produces a Coulomb explosion with the consequent release of protons with kinetic energy in the few electronvolts range, which collide with the surrounding molecules in solution inducing further chemical reactions. In particular, we observe proton collisions with the solute molecule DR, which leads to a complete ring opening. In DNA, damage to the DR moiety may lead to DNA strand breaking. This mechanism can be understood as one of the possible steps in the radiation-induced fragmentation of DNA chains.
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Affiliation(s)
| | | | - Marie-Pierre Gaigeot
- LAMBE UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement , Université d'Evry val d'Essonne, Université Paris-Saclay, CEA, CNRS , Blvd F. Mitterrand , 91025 Evry , France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Ivano Tavernelli
- IBM Research-Zurich , Säumerstrasse 4 , 8803 Rüschlikon , Switzerland
| | - Marie-Fraņcoise Politis
- LAMBE UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement , Université d'Evry val d'Essonne, Université Paris-Saclay, CEA, CNRS , Blvd F. Mitterrand , 91025 Evry , France
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Sage E, Shikazono N. Radiation-induced clustered DNA lesions: Repair and mutagenesis. Free Radic Biol Med 2017; 107:125-135. [PMID: 27939934 DOI: 10.1016/j.freeradbiomed.2016.12.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 12/18/2022]
Abstract
Clustered DNA lesions, also called Multiply Damaged Sites, is the hallmark of ionizing radiation. It is defined as the combination of two or more lesions, comprising strand breaks, oxidatively generated base damage, abasic sites within one or two DNA helix turns, created by the passage of a single radiation track. DSB clustered lesions associate DSB and several base damage and abasic sites in close vicinity, and are assimilated to complex DSB. Non-DSB clustered lesions comprise single strand break, base damage and abasic sites. At radiation with low Linear Energy Transfer (LET), such as X-rays or γ-rays clustered DNA lesions are 3-4 times more abundant than DSB. Their proportion and their complexity increase with increasing LET; they may represent a large part of the damage to DNA. Studies in vitro using engineered clustered DNA lesions of increasing complexity have greatly enhanced our understanding on how non-DSB clustered lesions are processed. Base excision repair is compromised, the observed hierarchy in the processing of the lesions within a cluster leads to the formation of SSB or DSB as repair intermediates and increases the lifetime of the lesions. As a consequence, the chances of mutation drastically increase. Complex DSB, either formed directly by irradiation or by the processing of non-DSB clustered lesions, are repaired by slow kinetics or left unrepaired and cause cell death or pass mitosis. In surviving cells, large deletions, translocations, and chromosomal aberrations are observed. This review details the most recent data on the processing of non-DSB clustered lesions and complex DSB and tends to demonstrate the high significance of these specific DNA damage in terms of genomic instability induction.
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Affiliation(s)
- Evelyne Sage
- Institut Curie, PSL Research University, CNRS, UMR3347, F-91405 Orsay, France.
| | - Naoya Shikazono
- Quantum Beam Science Research Directorate, National Institutes of Quantum and Radiological Science and Technology, Kansai Photon Science Institute, 8-1-7 Umemidai, Kizugawa-Shi, Kyoto 619-0215, Japan.
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Affiliation(s)
- Akinari Yokoya
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Naka, Ibaraki, Japan
| | - Takashi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Tokyo, Japan
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Foray N. Aspects radiobiologiques des traitements anticancéreux par rayonnement synchrotron : bilan et perspectives. Cancer Radiother 2010; 14:145-54. [DOI: 10.1016/j.canrad.2009.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 11/26/2009] [Accepted: 12/03/2009] [Indexed: 10/19/2022]
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du Penhoat MAH, Eschenbrenner A, Abel F, Boissiere A, Guigner JM, Chetioui A, Politis MF, Touati A, Sage E, Jenner TJ, Stevens DL, Hill MA. Double-strand break induction and repair in V79-4 hamster cells: the role of core ionisations, as probed by ultrasoft X-rays. Int J Radiat Biol 2010; 86:205-19. [PMID: 20201649 DOI: 10.3109/09553000903419296] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To compare the induction of double-strand breaks (DSB) in cells irradiated by 250 and 350 eV ultrasoft X-rays and assess the residual yield of breaks 2 hours post irradiation in order to unravel the correlation between the sharp increase in cell-killing efficiency of ultrasoft X-rays above versus below the carbon-K threshold (284 eV) and the induction of core events in DNA atoms. MATERIALS AND METHODS V79-4 hamster cells were irradiated with synchrotron ultrasoft X-rays at isoattenuating energies of 250 eV and 350 eV. DSB were quantified using pulse field gel electrophoresis. RESULTS A significant increase in DSB induction was observed for 350 eV ultrasoft X-rays above the carbon-K threshold, compared to 250 eV below the threshold, per unit dose to the cell. The DSB induced by the 350 eV ultrasoft X-rays were less repaired 2 h after irradiation. CONCLUSION The increased DSB induction at 350 eV is attributed to the increase in the relative proportion of photon interactions in DNA resulting in significant dose inhomogeneity across the cell with a local increase in dose to DNA. It results from an increase in carbon-K shell interactions and the short range of the electrons produced. Core ionisations in DNA, through core-hole relaxation in conjunction with localised effects of spatially correlated low-energy photo- and Auger-electrons lead to an increase in number and the complexity of DSB.
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Affiliation(s)
- Marie-Anne Hervé du Penhoat
- Institut de Minéralogie et de Physique des Milieux Condensés, Université Pierre et Marie Curie-Paris6, UMR-CNRS 7590, Paris, France.
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Averbeck D. Does scientific evidence support a change from the LNT model for low-dose radiation risk extrapolation? HEALTH PHYSICS 2009; 97:493-504. [PMID: 19820459 DOI: 10.1097/hp.0b013e3181b08a20] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The linear no-threshold (LNT) model has been widely used to establish international rules and standards in radiation protection. It is based on the notion that the physical energy deposition of ionizing radiation (IR) increases carcinogenic risk linearly with increasing dose (i.e., the carcinogenic effectiveness remains constant irrespective of dose) and, within a factor of two, also with dose-rate. However, recent findings have strongly put into question the LNT concept and its scientific validity, especially for very low doses and dose-rates. Low-dose effects are more difficult to ascertain than high-dose effects. Epidemiological studies usually lack sufficient statistical power to determine health risks from very low-dose exposures. In this situation, studies of the fundamental mechanisms involved help to understand and assess short- and long-term effects of low-dose IR and to evaluate low-dose radiation risks. Several lines of evidence demonstrate that low-dose and low dose-rate effects are generally lower than expected from high-dose exposures. DNA damage signaling, cell cycle checkpoint activation, DNA repair, gene and protein expression, apoptosis, and cell transformation differ qualitatively and quantitatively at high- and low-dose IR exposures, and most animal and epidemiological data support this conclusion. Thus, LNT appears to be scientifically invalid in the low-dose range.
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Affiliation(s)
- Dietrich Averbeck
- Dietrich Averbeck, Institut Curie-Section de Recherche, UMR2027 CNRS/I.C., Centre Universitaire, F-91405 ORSAY Cedex, France.
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Fujii K, Yokoya A, Shikazono N. Induction of single strand breaks, and base lesions in plasmid DNA films induced by carbon, nitrogen, and oxygenKLLAuger process. Int J Radiat Biol 2009; 84:1104-11. [DOI: 10.1080/09553000802482564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Agrawala PK, Eschenbrenner A, du Penhoat MAH, Boissiere A, Politis MF, Touati A, Sage E, Chetioui A. Induction and repairability of DNA damage caused by ultrasoft X-rays: Role of core events. Int J Radiat Biol 2009; 84:1093-103. [DOI: 10.1080/09553000802478083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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