1
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Cadet J, Angelov D, Di Mascio P, Wagner JR. Contribution of oxidation reactions to photo-induced damage to cellular DNA. Photochem Photobiol 2024; 100:1157-1185. [PMID: 38970297 DOI: 10.1111/php.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/08/2024]
Abstract
This review article is aimed at providing updated information on the contribution of immediate and delayed oxidative reactions to the photo-induced damage to cellular DNA/skin under exposure to UVB/UVA radiations and visible light. Low-intensity UVC and UVB radiations that operate predominantly through direct excitation of the nucleobases are very poor oxidizing agents giving rise to very low amounts of 8-oxo-7,8-dihydroguanine and DNA strand breaks with respect to the overwhelming bipyrimidine dimeric photoproducts. The importance of these two classes of oxidatively generated damage to DNA significantly increases together with a smaller contribution of oxidized pyrimidine bases upon UVA irradiation. This is rationalized in terms of sensitized photooxidation reactions predominantly mediated by singlet oxygen together with a small contribution of hydroxyl radical that appear to also be implicated in the photodynamic effects of the blue light component of visible light. Chemiexcitation-mediated formation of "dark" cyclobutane pyrimidine dimers in UVA-irradiated melanocytes is a recent major discovery that implicates in the initial stage, a delayed generation of reactive oxygen and nitrogen species giving rise to triplet excited carbonyl intermediate and possibly singlet oxygen. High-intensity UVC nanosecond laser radiation constitutes a suitable source of light to generate pyrimidine and purine radical cations in cellular DNA via efficient biphotonic ionization.
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Affiliation(s)
- Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule LMBC, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University, Balçova, Izmir, Turkey
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - J Richard Wagner
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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2
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Richer M, Heidar-Zadeh F, Ríos-Gutiérrez M, Yang XD, Ayers PW. Spin-Polarized Conceptual Density Functional Theory from the Convex Hull. J Chem Theory Comput 2024; 20:4616-4628. [PMID: 38819213 DOI: 10.1021/acs.jctc.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We present a new, nonarbitrary, internally consistent, and unambiguous framework for spin-polarized conceptual density-functional theory (SP-DFT). We explicitly characterize the convex hull of energy, as a function of the number of electrons and their spin, as the only accessible ground states in spin-polarized density functional theory. Then, we construct continuous linear and quadratic models for the energy. The nondifferentiable linear model exactly captures the simplicial geometry of the complex hull about the point of interest and gives exact representations for the conceptual DFT reactivity indicators. The continuous quadratic energy model is the paraboloid of maximum curvature, which most tightly encloses the point of interest and neighboring vertices. The quadratic model is invariant to the choice of coordinate system (i.e., {N, S} vs {Nα, Nβ}) and reduces to a sensible formulation of spin-free conceptual DFT in the appropriate limit. Using the quadratic model, we generalize the Parr functions {P+(r), P-(r)} (and their derivatives with respect to number of electrons) to this new spin-polarized framework, integrating the Parr function concept into the context of (spin-polarized) conceptual DFT, and extending it to include higher-order effects.
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Affiliation(s)
- Michelle Richer
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Xiaotian Derrick Yang
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul W Ayers
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
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3
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Kanamori T, Kaneko S, Hamamoto K, Yuasa H. Mapping the diffusion pattern of 1O 2 along DNA duplex by guanine photooxidation with an appended biphenyl photosensitizer. Sci Rep 2023; 13:288. [PMID: 36690669 PMCID: PMC9871026 DOI: 10.1038/s41598-023-27526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
To realize nucleic acid-targeting photodynamic therapy, a photosensitizer should be attached at the optimal position on a complementary oligonucleotide, where a guanine photooxidation is maximized. Here we show the photooxidation of 22 DNA duplexes with varied lengths between a 1O2-generating biphenyl photosensitizer attached at a midchain thymine in a strand and the single guanine reactant in the other strand. The best photooxidation efficiencies are achieved at 9, 10, and 21 base intervals, which coincides with the pitch of 10.5 base pairs per turn in a DNA duplex. The low efficiencies for near and far guanines are due to quenching of the biphenyl by guanine and dilution of 1O2 by diffusion, respectively. The 1O2-diffusion mapping along DNA duplex provides clues to the development of efficient and selective photosensitizer agents for nucleic acid-targeting photodynamic therapy, as well as an experimental demonstration of diffusion of a particle along cylindrical surface in molecular level.
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Affiliation(s)
- Takashi Kanamori
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan.
| | - Shota Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan
| | - Koji Hamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan
| | - Hideya Yuasa
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan.
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4
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Fu J, Xu Y, Arts EJ, Bai Z, Chen Z, Zheng Y. Viral disinfection using nonthermal plasma: A critical review and perspectives on the plasma-catalysis system. CHEMOSPHERE 2022; 309:136655. [PMID: 36191766 DOI: 10.1016/j.chemosphere.2022.136655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
The transmission of viral infections via aerosol has become a serious threat to public health. This has produced an ever-increasing demand for effective forms of viral inactivation technology/processes. Plasma technology is rising in popularity and gaining interest for viral disinfection use. Due to its highly effectively disinfection and flexible operation, non-thermal plasma (NTP) is a promising technology in decontaminating bacteria or virus from air or surfaces. This review discusses the fundamentals of non-thermal plasma and the disinfection mechanisms of the biocidal agents produced in plasma, including ultraviolet (UV) photons, reactive oxygen species, and reactive nitrogen species. Perspectives on the role of catalysts and its potential applications in cold plasma disinfection are discussed.
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Affiliation(s)
- Jile Fu
- School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Fine Chemicals Green Manufacturing, Henan Normal University, Xinxiang, 453007, China; Department of Chemical and Biochemical Engineering, Western University, London, Ontario, Canada
| | - Yiyi Xu
- Department of Chemical and Biochemical Engineering, Western University, London, Ontario, Canada
| | - Eric J Arts
- Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Zhengyu Bai
- School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Collaborative Innovation Center of Henan Province for Fine Chemicals Green Manufacturing, Henan Normal University, Xinxiang, 453007, China.
| | - Zhongwei Chen
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada.
| | - Ying Zheng
- Department of Chemical and Biochemical Engineering, Western University, London, Ontario, Canada.
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5
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Moe MM, Saito T, Tsai M, Liu J. Singlet O 2 Oxidation of the Radical Cation versus the Dehydrogenated Neutral Radical of 9-Methylguanine in a Watson-Crick Base Pair. Consequences of Structural Context. J Phys Chem B 2022; 126:5458-5472. [PMID: 35849846 DOI: 10.1021/acs.jpcb.2c03748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In DNA, guanine is the most susceptible to oxidative damage by exogenously and endogenously produced electronically excited singlet oxygen (1O2). The reaction mechanism and the product outcome strongly depend on the nucleobase ionization state and structural context. Previously, exposure of a monomeric 9-methylguanine radical cation (9MG•+, a model guanosine compound) to 1O2 was found to result in the formation of an 8-peroxide as the initial product. The present work explores the 1O2 oxidation of 9MG•+ and its dehydrogenated neutral form [9MG - H]• within a Watson-Crick base pair consisting of one-electron-oxidized 9-methylguanine-1-methylcytosine [9MG·1MC]•+. Emphasis is placed on entangling the base pair structural context and intra-base pair proton transfer with and consequences thereof on the singlet oxygenation of guanine radical species. Electrospray ionization coupled with guided-ion beam tandem mass spectrometry was used to study the formation and reaction of guanine radical species in the gas phase. The 1O2 oxidation of both 9MG•+ and [9MG - H]• is exothermic and proceeds barrierlessly either in an isolated monomer or within a base pair. Single- and multi-referential theories were tested for treating spin contaminations and multi-configurations occurring in radical-1O2 interactions, and reaction potential energy surfaces were mapped out to support experimental findings. The work provides a comprehensive profile for the singlet oxygenation of guanine radicals in different charge states and in the absence and the presence of base pairing. All results point to an 8-peroxide as the major oxidation product in the experiment, and the oxidation becomes slightly more favorable in a neutral radical form. On the basis of a variety of reaction pathways and product profiles observed in the present and previous studies, the interplay between guanine structure, base pairing, and singlet oxygenation and its biological implications are discussed.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194 Hiroshima, Japan
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Avenue, Long Island City, New York 11101, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
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6
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Benny J, Saito T, Moe MM, Liu J. Singlet O 2 Reactions with Radical Cations of 8-Bromoguanine and 8-Bromoguanosine: Guided-Ion Beam Mass Spectrometric Measurements and Theoretical Treatments. J Phys Chem A 2021; 126:68-79. [PMID: 34941276 DOI: 10.1021/acs.jpca.1c09552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
8-Bromoguanosine is generated in vivo as a biomarker for early inflammation. Its formation and secondary reactions lead to a variety of biological sequelae at inflammation sites, most of which are mutagenic and linked to cancer. Herein, we report the formation of radical cations of 8-bromoguanine (8BrG•+) and 8-bromoguanosine (8BrGuo•+) and their reactions toward the lowest excited singlet molecular oxygen (1O2)─a common reactive oxygen species generated in biological systems. This work aims to investigate synergistic, oxidatively generated damage of 8-brominated guanine and guanosine that may occur upon ionizing radiation, one-electron oxidation, and 1O2 oxidation. Capitalizing on measurements of reaction product ions and cross sections of 8BrG•+ and 8BrGuo•+ with 1O2 using guided-ion beam tandem mass spectrometry and augmented by computational modeling of the prototype reaction system, 8BrG•+ + 1O2, using the approximately spin-projected ωB97XD/6-31+G(d,p) density functional theory, the coupled cluster DLPNO-CCSD(T)/aug-cc-pVTZ and the multireference CASPT2(21,15)/6-31G**, probable reaction products, and potential energy surfaces (PESs) were mapped out. 8BrG•+ and 8BrGuo•+ present similar exothermic oxidation products, and their reaction efficiencies with 1O2 increase with decreasing collision energy. Both single- and multireference theories predicted that the two most energetically favorable reaction pathways correspond to 1O2-addition to the C8 and C5-positions of 8BrG•+, respectively. The CASPT2-calculated PES represents the best quantitative agreement with the experimental benchmark, in that the oxidation exothermicity is close to the water hydration energy of product ions and, thus, is able to eliminate a water ligand in the product ions.
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Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194 Hiroshima, Japan
| | - May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
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7
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Ravanat JL, Dumont E. Reactivity of Singlet Oxygen with DNA, an Update. Photochem Photobiol 2021; 98:564-571. [PMID: 34931317 DOI: 10.1111/php.13581] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 11/28/2022]
Abstract
The reactivity of singlet oxygen with DNA constituents and in particular with the guanine base has been studied during more than four decades but the exact mechanisms by which such a reactive oxygen species reacts with DNA is still a matter of debate. In this review article, a summary of the data that were obtained from several laboratories and using complementary experimental and theoretical approaches are presented. Reaction mechanisms of 1 O2 with guanine and its oxidation product 8-oxo7,8-dihydroguanine are presented both at the nucleoside level and when the base is inserted into DNA since significant differences have been observed. Efforts have been made to propose tentative mechanisms to explain the conflicting results that were sometimes reported and hypotheses have been put forward to tentatively explain still contradictory observations.
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Affiliation(s)
- Jean-Luc Ravanat
- CEA, CNRS, CIBEST, SyMMES, Univ. Grenoble Alpes, Grenoble, France
| | - Elise Dumont
- ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Univ Lyon, Lyon, France.,Institut Universitaire de France, Paris, France
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8
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Jin ZY, Fatima H, Zhang Y, Shao Z, Chen XJ. Recent Advances in Bio‐Compatible Oxygen Singlet Generation and Its Tumor Treatment. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202100176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zheng Yang Jin
- The First Affiliated Hospital of Wenzhou Medical University Wenzhou Zhejiang 325015 P. R. China
| | - Hira Fatima
- Western Australia School of Mines: Minerals Energy and Chemical Engineering (WASM‐MECE) Curtin University Perth Western Australia 6102 Australia
| | - Yue Zhang
- The First Affiliated Hospital of Wenzhou Medical University Wenzhou Zhejiang 325015 P. R. China
| | - Zongping Shao
- Western Australia School of Mines: Minerals Energy and Chemical Engineering (WASM‐MECE) Curtin University Perth Western Australia 6102 Australia
- State Key Laboratory of Materials‐Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University Nanjing Jiangsu 211816 P. R. China
| | - Xiang Jian Chen
- The First Affiliated Hospital of Wenzhou Medical University Wenzhou Zhejiang 325015 P. R. China
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9
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Jiang T, Monari A, Dumont E, Bignon E. Molecular Mechanisms Associated with Clustered Lesion-Induced Impairment of 8-oxoG Recognition by the Human Glycosylase OGG1. Molecules 2021; 26:molecules26216465. [PMID: 34770874 PMCID: PMC8587150 DOI: 10.3390/molecules26216465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
The 8-oxo-7,8-dihydroguanine, referred to as 8-oxoG, is a highly mutagenic DNA lesion that can provoke the appearance of mismatches if it escapes the DNA Damage Response. The specific recognition of its structural signature by the hOGG1 glycosylase is the first step along the Base Excision Repair pathway, which ensures the integrity of the genome by preventing the emergence of mutations. 8-oxoG formation, structural features, and repair have been matters of extensive research; more recently, this active field of research expended to the more complicated case of 8-oxoG within clustered lesions. Indeed, the presence of a second lesion within 1 or 2 helix turns can dramatically impact the repair yields of 8-oxoG by glycosylases. In this work, we use μs-range molecular dynamics simulations and machine-learning-based postanalysis to explore the molecular mechanisms associated with the recognition of 8-oxoG by hOGG1 when embedded in a multiple-lesion site with a mismatch in 5′ or 3′. We delineate the stiffening of the DNA–protein interactions upon the presence of the mismatches, and rationalize the much lower repair yields reported with a 5′ mismatch by describing the perturbation of 8-oxoG structural features upon addition of an adjacent lesion.
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Affiliation(s)
- Tao Jiang
- Laboratoire de Chimie—UMR CNRS 5182, ENS de Lyon, Université de Lyon, 46 Allée d’Italie, F-69000 Lyon, France; (T.J.); (E.D.)
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques—UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, Boulevard des Aiguillettes, F-54506 Vandoeuvre-les-Nancy, France;
- Université de Paris and CNRS, ITODYS, F-75006 Paris, France
| | - Elise Dumont
- Laboratoire de Chimie—UMR CNRS 5182, ENS de Lyon, Université de Lyon, 46 Allée d’Italie, F-69000 Lyon, France; (T.J.); (E.D.)
- Institut Universitaire de France, 5 rue Descartes, F-75005 Paris, France
| | - Emmanuelle Bignon
- Laboratoire de Physique et Chimie Théoriques—UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, Boulevard des Aiguillettes, F-54506 Vandoeuvre-les-Nancy, France;
- Correspondence:
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10
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Baptista MS, Cadet J, Greer A, Thomas AH. Photosensitization Reactions of Biomolecules: Definition, Targets and Mechanisms. Photochem Photobiol 2021; 97:1456-1483. [PMID: 34133762 DOI: 10.1111/php.13470] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/13/2021] [Indexed: 02/07/2023]
Abstract
Photosensitization reactions have been demonstrated to be largely responsible for the deleterious biological effects of UV and visible radiation, as well as for the curative actions of photomedicine. A large number of endogenous and exogenous photosensitizers, biological targets and mechanisms have been reported in the past few decades. Evolving from the original definitions of the type I and type II photosensitized oxidations, we now provide physicochemical frameworks, classifications and key examples of these mechanisms in order to organize, interpret and understand the vast information available in the literature and the new reports, which are in vigorous growth. This review surveys in an extended manner all identified photosensitization mechanisms of the major biomolecule groups such as nucleic acids, proteins, lipids bridging the gap with the subsequent biological processes. Also described are the effects of photosensitization in cells in which UVA and UVB irradiation triggers enzyme activation with the subsequent delayed generation of superoxide anion radical and nitric oxide. Definitions of photosensitized reactions are identified in biomolecules with key insights into cells and tissues.
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Affiliation(s)
| | - Jean Cadet
- Département de Médecine Nucléaire et de Radiobiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, Brooklyn, NY, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Andrés H Thomas
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CCT La Plata-CONICET, La Plata, Argentina
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11
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Miclot T, Corbier C, Terenzi A, Hognon C, Grandemange S, Barone G, Monari A. Forever Young: Structural Stability of Telomeric Guanine Quadruplexes in the Presence of Oxidative DNA Lesions*. Chemistry 2021; 27:8865-8874. [PMID: 33871121 DOI: 10.1002/chem.202100993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 01/13/2023]
Abstract
Human telomeric DNA, in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine (8oxoG) lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.
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Affiliation(s)
- Tom Miclot
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.,Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Camille Corbier
- Université de Lorraine and CNRS, CRAN UMR 7039, 54000, Nancy, France
| | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | | | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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12
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Bignon E, Gillet N, Chan CH, Jiang T, Monari A, Dumont E. Recognition of a tandem lesion by DNA bacterial formamidopyrimidine glycosylases explored combining molecular dynamics and machine learning. Comput Struct Biotechnol J 2021; 19:2861-2869. [PMID: 34093997 PMCID: PMC8141532 DOI: 10.1016/j.csbj.2021.04.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/30/2022] Open
Abstract
The combination of several closely spaced DNA lesions, which can be induced by a single radical hit, constitutes a hallmark in the DNA damage landscape and radiation chemistry. The occurrence of such a tandem base lesion gives rise to a strong coupling with the double helix degrees of freedom and induces important structural deformations, in contrast to DNA strands containing a single oxidized nucleobase. Although such complex lesions are known to be refractory to repair by DNA glycosylases, there is still a lack of structural evidence to rationalize these phenomena. In this contribution, we explore, by numerical modeling and molecular simulations, the behavior of the bacterial glycosylase responsible for base excision repair (MutM), specialized in excising oxidatively-damaged defects such as 7,8-dihydro-8-oxoguanine (8-oxoG). The difference in lesion recognition between a simple damage and a tandem lesion featuring an additional abasic site is assessed at atomistic resolution owing to microsecond molecular dynamics simulations and machine learning postprocessing, allowing to extensively pinpoint crucial differences in the interaction patterns of the damaged bases. Our results reveal substantial changes in the interaction network surrounding the 8-oxoG upon addition of an adjacent abasic site, leading to the perturbation of the intercalation triad which is crucial for lesion recognition and processing. The recognition process might also be impacted by a more constrained MutM-DNA binding upon tandem damage, as shown by the machine learning post-processing. This work advocates for the use of such high throughput numerical simulations for exploring the complex combinatorial chemistry of tandem DNA lesions repair and more generally local multiple damaged sites of the utmost significance in radiation chemistry.
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Affiliation(s)
- Emmanuelle Bignon
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Chen-Hui Chan
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Tao Jiang
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000 Nancy, France
| | - Elise Dumont
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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13
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Saito T, Takano Y. Spin-projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B-DNA by Singlet Oxygen. Chemphyschem 2021; 22:561-568. [PMID: 33462992 PMCID: PMC8048875 DOI: 10.1002/cphc.202000978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/17/2021] [Indexed: 12/11/2022]
Abstract
Guanine is the most susceptible base to oxidation damage induced by reactive oxygen species including singlet oxygen (1 O2 , 1 Δg ). We clarify whether the first step of guanine oxidation in B-DNA proceeds via either a zwitterionic or a diradical intermediate. The free energy profiles are calculated by means of a combined quantum mechanical and molecular mechanical (QM/MM) method coupled with the adaptive biasing force (ABF) method. To describe the open-shell electronic structure of 1 O2 correctly, the broken-symmetry spin-unrestricted density functional theory (BS-UDFT) with an approximate spin projection (AP) correction is applied to the QM region. We find that the effect of spin contamination on the activation and reaction free energies is up to ∼8 kcal mol-1 , which is too large to be neglected. The QM(AP-ULC-BLYP)/MM-based free energy calculations also reveal that the reaction proceeds through a diradical transition state, followed by a conversion to a zwitterionic intermediate. Our computed activation energy of 5.2 kcal mol-1 matches experimentally observed range (0∼6 kcal mol-1 ).
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Affiliation(s)
- Toru Saito
- Department of Biomedical Information ScienceGraduate School of Information ScienceHiroshima City University3-4-1 Ozuka-Higashi, Asa-Minami-Ku731-3194HiroshimaJapan
| | - Yu Takano
- Department of Biomedical Information ScienceGraduate School of Information ScienceHiroshima City University3-4-1 Ozuka-Higashi, Asa-Minami-Ku731-3194HiroshimaJapan
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14
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Sun Y, Tsai M, Moe MM, Liu J. Dynamics and Multiconfiguration Potential Energy Surface for the Singlet O2 Reactions with Radical Cations of Guanine, 9-Methylguanine, 2′-Deoxyguanosine, and Guanosine. J Phys Chem A 2021; 125:1564-1576. [DOI: 10.1021/acs.jpca.1c00095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College 31-10 Thomson Avenue, Long Island City, New York 11101, United States
| | - May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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15
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Sun Y, Tsai M, Zhou W, Lu W, Liu J. Reaction Kinetics, Product Branching, and Potential Energy Surfaces of 1O 2-Induced 9-Methylguanine-Lysine Cross-Linking: A Combined Mass Spectrometry, Spectroscopy, and Computational Study. J Phys Chem B 2019; 123:10410-10423. [PMID: 31718186 DOI: 10.1021/acs.jpcb.9b08796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a kinetics and mechanistic study on the 1O2 oxidation of 9-methylguanine (9MG) and the cross-linking of the oxidized intermediate 2-amino-9-methyl-9H-purine-6,8-dione (9MOGOX) with Nα-acetyl-lysine-methyl ester (abbreviated as LysNH2) in aqueous solutions of different pH. Experimental measurements include the determination of product branching ratios and reaction kinetics using mass spectrometry and absorption spectroscopy, and the characterization of product structures by employing collision-induced dissociation. Strong pH dependence was revealed for both 9MG oxidation and the addition of nucleophiles (water and LysNH2) at the C5 position of 9MOGOX. The 1O2 oxidation rate constant of 9MG was determined to be 3.6 × 107 M-1·s-1 at pH 10.0 and 0.3 × 107 M-1·s-1 at pH 7.0, both of which were measured in the presence of 15 mM LysNH2. The ωB97XD density functional theory coupled with various basis sets and the SMD implicit solvation model was used to explore the reaction potential energy surfaces for the 1O2 oxidation of 9MG and the formation of C5-water and C5-LysNH2 adducts of 9MOGOX. Computational results have shed light on reaction pathways and product structures for the different ionization states of the reactants. The present work has confirmed that the initial 1O2 addition represents the rate-limiting step for the oxidative transformations of 9MG. All of the downstream steps are exothermic with respect to the starting reactants. The C5-cross-linking of 9MOGOX with LysNH2 significantly suppressed the formation of spiroiminodihydantoin (9MSp) resulting from the C5-water addition. The latter became dominant only at the low concentration (∼1 mM) of LysNH2.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States.,Ph.D. Program in Chemistry , The Graduate Center of the City University of New York , 365 5th Avenue , New York , New York 10016 , United States
| | - Midas Tsai
- Department of Natural Sciences , LaGuardia Community College , 31-10 Thomson Avenue , Long Island City , New York 11101 , United States
| | - Wenjing Zhou
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States
| | - Wenchao Lu
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States.,Ph.D. Program in Chemistry , The Graduate Center of the City University of New York , 365 5th Avenue , New York , New York 10016 , United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry , Queens College of the City University of New York , 65-30 Kissena Blvd. , Queens , New York 11367 , United States.,Ph.D. Program in Chemistry , The Graduate Center of the City University of New York , 365 5th Avenue , New York , New York 10016 , United States
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16
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Hognon C, Gebus A, Barone G, Monari A. Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes. Antioxidants (Basel) 2019; 8:antiox8090337. [PMID: 31443537 PMCID: PMC6770428 DOI: 10.3390/antiox8090337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 01/23/2023] Open
Abstract
By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channel and that (ii) the electrostatic interactions of the DNA sequence with the aforementioned cations are fundamental to the maintenance of the global quadruplex structure.
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Affiliation(s)
- Cecilia Hognon
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Adrien Gebus
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France
| | - Giampaolo Barone
- Department of Biological, Chenical and Pharmaceutical Sciences and Technologies, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
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17
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Thapa B, Hebert SP, Munk BH, Burrows CJ, Schlegel HB. Computational Study of the Formation of C8, C5, and C4 Guanine:Lysine Adducts via Oxidation of Guanine by Sulfate Radical Anion. J Phys Chem A 2019; 123:5150-5163. [DOI: 10.1021/acs.jpca.9b03598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Sebastien P. Hebert
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Barbara H. Munk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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18
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Di Mascio P, Martinez GR, Miyamoto S, Ronsein GE, Medeiros MHG, Cadet J. Singlet Molecular Oxygen Reactions with Nucleic Acids, Lipids, and Proteins. Chem Rev 2019; 119:2043-2086. [DOI: 10.1021/acs.chemrev.8b00554] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Glaucia R. Martinez
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, 81531-990 Curitiba, PR, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Graziella E. Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Marisa H. G. Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4 Québec, Canada
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19
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Hebert SP, Schlegel HB. Computational Study of the pH-Dependent Competition between Carbonate and Thymine Addition to the Guanine Radical. Chem Res Toxicol 2019; 32:195-210. [PMID: 30592213 DOI: 10.1021/acs.chemrestox.8b00302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
When oligonucleotides are oxidized by carbonate radical, thymine and carbonate can add to guanine radical, yielding either a guanine-thymine cross-link product (G∧T) or 8-oxo-7,8-dehydroguanine (8oxoG) and its further oxidation products such as spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). The ratio of thymine addition to carbonate addition depends strongly on the pH. Details of the mechanism have been explored by density functional calculations using the ωB97XD/6-31+G(d,p) level of theory with the SMD implicit solvation method, augmented with a few explicit waters. Free energies of intermediates and transition states in aqueous solution have been calculated along the pathways for addition of thymine, CO32-/HCO3- and carbonate radical to guanine radical. The pH dependence was examined by using appropriate explicit proton donors/acceptors as computational models for buffers at pH 2.5, 7, and 10. Deprotonation of thymine is required for nucleophilic addition at C8 of guanine radical, and thus is favored at higher pH. The barrier for carbonate radical addition is lower than for bicarbonate or carbonate dianion addition; however, for low concentrations of carbonate radical, the reaction may proceed by addition of bicarbonate/carbonate dianion to guanine radical. Thymine and bicarbonate/carbonate dianion addition are followed by oxidation by O2, loss of a proton from C8 and decarboxylation of the carbonate adduct. At pH 2.5, guanine radical cation can be formed by oxidization with sulfate radical. Water addition to guanine radical cation is the preferred path for forming 8oxoG at pH 2.5.
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Affiliation(s)
- Sebastien P Hebert
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - H Bernhard Schlegel
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
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20
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Cadet J, Douki T. Formation of UV-induced DNA damage contributing to skin cancer development. Photochem Photobiol Sci 2018; 17:1816-1841. [PMID: 29405222 DOI: 10.1039/c7pp00395a] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UV-induced DNA damage plays a key role in the initiation phase of skin cancer. When left unrepaired or when damaged cells are not eliminated by apoptosis, DNA lesions express their mutagneic properties, leading to the activation of proto-oncogene or the inactivation of tumor suppression genes. The chemical nature and the amount of DNA damage strongly depend on the wavelength of the incident photons. The most energetic part of the solar spectrum at the Earth's surface (UVB, 280-320 nm) leads to the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (64PPs). Less energetic but 20-times more intense UVA (320-400 nm) also induces the formation of CPDs together with a wide variety of oxidatively generated lesions such as single strand breaks and oxidized bases. Among those, 8-oxo-7,8-dihydroguanine (8-oxoGua) is the most frequent since it can be produced by several mechanisms. Data available on the respective yield of DNA photoproducts in cells and skin show that exposure to sunlight mostly induces pyrimidine dimers, which explains the mutational signature found in skin tumors, with lower amounts of 8-oxoGua and strand breaks. The present review aims at describing the basic photochemistry of DNA and discussing the quantitative formation of the different UV-induced DNA lesions reported in the literature. Additional information on mutagenesis, repair and photoprotection is briefly provided.
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Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, 3001 12e Avenue Nord, Université de Sherbrooke, Sherbrooke, Québec JIH 5N4, Canada.
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21
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Lu W, Sun Y, Tsai M, Zhou W, Liu J. Singlet O 2 Oxidation of a Deprotonated Guanine-Cytosine Base Pair and Its Entangling with Intra-Base-Pair Proton Transfer. Chemphyschem 2018; 19:2645-2654. [PMID: 30047606 DOI: 10.1002/cphc.201800643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Indexed: 12/24/2022]
Abstract
We report an experimental and computational study on the 1 O2 oxidation of gas-phase deprotonated guanine-cytosine base pair [G ⋅ C-H]- that is composed of 9HG ⋅ [C-H]- and 7HG ⋅ [C-H]- (pairing 9H- or 7H-guanine with N1-deprotonated cytosine), and 9HG ⋅ [C-H]- _PT and 7HG ⋅ [C-H]- _PT (formed by intra-base-pair proton transfer from the N1 of guanine to the N3 of [C-H]- ). The conformer-averaged reaction product ions and cross section were measured over a center-of-mass collision energy range from 0.1 to 0.5 eV using a guided-ion-beam tandem mass spectrometer. To explore conformation-specific reactivity, collision dynamics of 1 O2 with each of the four [G ⋅ C-H]- conformers was simulated at B3LYP/6-31G(d). Trajectories showed that the 1 O2 oxidation of the base pair entangles with intra-base-pair proton transfer, and prefers to occur in a collision when the base pair adopts a proton-transferred structure; trajectories also indicate that the 9HG-containing base pair favors stepwise formation of 4,8-endoperoxide of guanine, whereas the 7HG-containing base pair prefers concerted formation of guanine 5,8-endoperoxide. Using trajectory results as a guide, potential energy surfaces (PESs) along all possible reaction pathways were established using the approximately spin-projected ωB97XD/6-311++G(d,p)//B3LYP/6-311++G(d,p) method. PESs have not only rationalized trajectory findings but provided more accurate energetics and indicated that the proton-transferred base-pair conformers have lower activation barriers for oxidation than their non-proton-transferred counterparts.
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Affiliation(s)
- Wenchao Lu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, the, Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
| | - Yan Sun
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, the, Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY, 11101, USA
| | - Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, the, Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
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22
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Mettra B, Liao YY, Gallavardin T, Armagnat C, Pitrat D, Baldeck P, Le Bahers T, Monnereau C, Andraud C. A combined theoretical and experimental investigation on the influence of the bromine substitution pattern on the photophysics of conjugated organic chromophores. Phys Chem Chem Phys 2018; 20:3768-3783. [DOI: 10.1039/c7cp06535c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-photon photosensitizers with heavy atom substituents were synthesized and evaluated through a combined photophysical and computational study.
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Affiliation(s)
- B. Mettra
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - Y. Y. Liao
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - T. Gallavardin
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - C. Armagnat
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - D. Pitrat
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - P. Baldeck
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - T. Le Bahers
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - C. Monnereau
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
| | - C. Andraud
- Univ Lyon
- Ens de Lyon
- CNRS UMR 5182
- Université Lyon 1
- Laboratoire de Chimie
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23
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Lu W, Sun Y, Zhou W, Liu J. pH-Dependent Singlet O2 Oxidation Kinetics of Guanine and 9-Methylguanine: An Online Mass Spectrometry and Spectroscopy Study Combined with Theoretical Exploration. J Phys Chem B 2017; 122:40-53. [DOI: 10.1021/acs.jpcb.7b09515] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wenchao Lu
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Yan Sun
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Wenjing Zhou
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
| | - Jianbo Liu
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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24
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Šebera J, Hattori Y, Sato D, Reha D, Nencka R, Kohno T, Kojima C, Tanaka Y, Sychrovský V. The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine. Nucleic Acids Res 2017; 45:5231-5242. [PMID: 28334993 PMCID: PMC5435939 DOI: 10.1093/nar/gkx157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/24/2017] [Indexed: 12/14/2022] Open
Abstract
The excision of 8-oxoguanine (oxoG) by the human 8-oxoguanine DNA glycosylase 1 (hOGG1) base-excision repair enzyme was studied by using the QM/MM (M06-2X/6-31G(d,p):OPLS2005) calculation method and nuclear magnetic resonance (NMR) spectroscopy. The calculated glycosylase reaction included excision of the oxoG base, formation of Lys249-ribose enzyme–substrate covalent adduct and formation of a Schiff base. The formation of a Schiff base with ΔG# = 17.7 kcal/mol was the rate-limiting step of the reaction. The excision of the oxoG base with ΔG# = 16.1 kcal/mol proceeded via substitution of the C1΄-N9 N-glycosidic bond with an H-N9 bond where the negative charge on the oxoG base and the positive charge on the ribose were compensated in a concerted manner by NH3+(Lys249) and CO2−(Asp268), respectively. The effect of Asp268 on the oxoG excision was demonstrated with 1H NMR for WT hOGG1 and the hOGG1(D268N) mutant: the excision of oxoG was notably suppressed when Asp268 was mutated to Asn. The loss of the base-excision function was rationalized with QM/MM calculations and Asp268 was confirmed as the electrostatic stabilizer of ribose oxocarbenium through the initial base-excision step of DNA repair. The NMR experiments and QM/MM calculations consistently illustrated the base-excision reaction operated by hOGG1.
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Affiliation(s)
- Jakub Šebera
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 166 10 Praha, Czech Republic
| | - Yoshikazu Hattori
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama-Boji 180, Yamashiro-cho, Tokushima 770 8514, Japan
| | - Daichi Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980 8578, Japan
| | - David Reha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Zámek 136, 373 33 Nové Hrady, Czech Republic
| | - Radim Nencka
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 166 10 Praha, Czech Republic
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104 0045, Japan
| | - Chojiro Kojima
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240 8501, Japan
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama-Boji 180, Yamashiro-cho, Tokushima 770 8514, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980 8578, Japan
| | - Vladimír Sychrovský
- The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha, Czech Republic.,Department of Electrotechnology, Electrical Engineering Czech Technical University, Technická 2, 166 27 Praha, Czech Republic
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25
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Grüber R, Aranda J, Bellili A, Tuñón I, Dumont E. Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA. Phys Chem Chem Phys 2017; 19:14695-14701. [PMID: 28537602 DOI: 10.1039/c6cp07966k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol-1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol-1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.
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Affiliation(s)
- R Grüber
- Univ. Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
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Fleming AM, Burrows CJ. Formation and processing of DNA damage substrates for the hNEIL enzymes. Free Radic Biol Med 2017; 107:35-52. [PMID: 27880870 PMCID: PMC5438787 DOI: 10.1016/j.freeradbiomed.2016.11.030] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022]
Abstract
Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed. The major G base oxidation products are 8-oxo-7,8-dihydroguanine (OG), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), spiroiminodihydantoin (Sp), and 5-guanidinohydantoin (Gh). The yields of these products show dependency on the oxidant and the reaction context that includes nucleoside, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and G-quadruplex DNA (G4-DNA) structures. Upon formation of these products in cells, they are recognized by the DNA glycosylases in the base excision repair (BER) pathway. This review focuses on initiation of BER by the mammalian Nei-like1-3 (NEIL1-3) glycosylases for removal of 2Ih, Sp, and Gh. The unique ability of the human NEILs to initiate removal of the hydantoins in ssDNA, bulge-DNA, bubble-DNA, dsDNA, and G4-DNA is outlined. Additionally, when Gh exists in a G4 DNA found in a gene promoter, NEIL-mediated repair is modulated by the plasticity of the G4-DNA structure provided by additional G-runs flanking the sequence. On the basis of these observations and cellular studies from the literature, the interplay between DNA oxidation and BER to alter gene expression is discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States.
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Thapa B, Munk BH, Burrows CJ, Schlegel HB. Computational Study of Oxidation of Guanine by Singlet Oxygen ( 1 Δ g ) and Formation of Guanine:Lysine Cross-Links. Chemistry 2017; 23:5804-5813. [PMID: 28249102 DOI: 10.1002/chem.201700231] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/20/2022]
Abstract
Oxidation of guanine in the presence of lysine can lead to guanine-lysine cross-links. The ratio of the C4, C5 and C8 crosslinks depends on the manner of oxidation. Type II photosensitizers such as Rose Bengal and methylene blue can generate singlet oxygen, which leads to a different ratio of products than oxidation by type I photosensitizers or by one electron oxidants. Modeling reactions of singlet oxygen can be quite challenging. Reactions have been explored using CASSCF, NEVPT2, DFT, CCSD(T), and BD(T) calculations with SMD implicit solvation. The spin contamination in open-shell calculations were corrected by Yamaguchi's approximate spin projection method. The addition of singlet oxygen to guanine to form guanine endo- peroxide proceeds step-wise via a zwitterionic peroxyl intermediate. The subsequent barrier for ring closure is smaller than the initial barrier for singlet oxygen addition. Ring opening of the endoperoxide by protonation at C4-O is followed by loss of a proton from C8 and dehydration to produce 8-oxoGox . The addition of lysine (modelled by methylamine) or water across the C5=N7 double bond of 8-oxoGox is followed by acyl migration to form the final spiro products. The barrier for methylamine addition is significantly lower than for water addition and should be the dominant reaction channel. These results are in good agreement with the experimental results for the formation of guanine-lysine cross-links by oxidation by type II photosensitizers.
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Affiliation(s)
- Bishnu Thapa
- Chemistry Department, Wayne State University, Detroit, Michigan, 48202, USA
| | - Barbara H Munk
- Chemistry Department, Wayne State University, Detroit, Michigan, 48202, USA
| | - Cynthia J Burrows
- Chemistry Department, University of Utah, Salt Lake City, Utah, 84112, USA
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Sun Y, Lu W, Liu J. Exploration of the Singlet O2 Oxidation of 8-Oxoguanine by Guided-Ion Beam Scattering and Density Functional Theory: Changes of Reaction Intermediates, Energetics, and Kinetics upon Protonation/Deprotonation and Hydration. J Phys Chem B 2017; 121:956-966. [DOI: 10.1021/acs.jpcb.6b11464] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yan Sun
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Ave., New York, New York 10016, United States
| | - Wenchao Lu
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Ave., New York, New York 10016, United States
| | - Jianbo Liu
- Department
of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D.
Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Ave., New York, New York 10016, United States
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Ferreri C, Golding BT, Jahn U, Ravanat JL. COST Action CM1201 "Biomimetic Radical Chemistry": free radical chemistry successfully meets many disciplines. Free Radic Res 2016; 50:S112-S128. [PMID: 27750460 DOI: 10.1080/10715762.2016.1248961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The COST Action CM1201 "Biomimetic Radical Chemistry" has been active since December 2012 for 4 years, developing research topics organized into four working groups: WG1 - Radical Enzymes, WG2 - Models of DNA damage and consequences, WG3 - Membrane stress, signalling and defenses, and WG4 - Bio-inspired synthetic strategies. International collaborations have been established among the participating 80 research groups with brilliant interdisciplinary achievements. Free radical research with a biomimetic approach has been realized in the COST Action and are summarized in this overview by the four WG leaders.
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Affiliation(s)
- Carla Ferreri
- a ISOF, Consiglio Nazionale delle Ricerche, BioFreeRadicals Group , Bologna , Italy
| | - Bernard T Golding
- b School of Chemistry, Bedson Building, Newcastle University , Newcastle-upon-Tyne , UK
| | - Ullrich Jahn
- c Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Prague , Czech Republic
| | - Jean-Luc Ravanat
- d INAC-SCIB & CEA, INAC-SyMMES Laboratoire des Lésions des Acides Nucléiques , Université Grenoble Alpes , Grenoble , France
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