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Robert G, Wagner JR, Cadet J. Oxidatively generated tandem DNA modifications by pyrimidinyl and 2-deoxyribosyl peroxyl radicals. Free Radic Biol Med 2023; 196:22-36. [PMID: 36603668 DOI: 10.1016/j.freeradbiomed.2022.12.104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]
Abstract
Molecular oxygen sensitizes DNA to damage induced by ionizing radiation, Fenton-like reactions, and other free radical-mediated reactions. It rapidly converts carbon-centered radicals within DNA into peroxyl radicals, giving rise to a plethora of oxidized products consisting of nucleobase and 2-deoxyribose modifications, strand breaks and abasic sites. The mechanism of formation of single oxidation products has been extensively studied and reviewed. However, much evidence shows that reactive peroxyl radicals can propagate damage to vicinal components in DNA strands. These intramolecular reactions lead to the dual alteration of two adjacent nucleotides, designated as tandem or double lesions. Herein, current knowledge about the formation and biological implications of oxidatively generated DNA tandem lesions is reviewed. Thus far, most reported tandem lesions have been shown to arise from peroxyl radicals initially generated at pyrimidine bases, notably thymine, followed by reaction with 5'-flanking bases, especially guanine, although contiguous thymine lesions have also been characterized. Proper biomolecular processing is impaired by several tandem lesions making them refractory to base excision repair and potentially more mutagenic.
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Affiliation(s)
- Gabriel Robert
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada.
| | - Jean Cadet
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada.
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2
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Cadet J, Angelov D, Wagner JR. Hydroxyl radical is predominantly involved in oxidatively generated base damage to cellular DNA exposed to ionizing radiation. Int J Radiat Biol 2022; 98:1-7. [PMID: 35475423 DOI: 10.1080/09553002.2022.2067363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 12/28/2022]
Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule LBMC, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University Health Campus, Balçova, Izmir, Turkey
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Canada
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3
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Wagner JR, Madugundu GS, Cadet J. Ozone-Induced DNA Damage: A Pandora's Box of Oxidatively Modified DNA Bases. Chem Res Toxicol 2021; 34:80-90. [PMID: 33417438 DOI: 10.1021/acs.chemrestox.0c00342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ozone is a major component of air pollution and carries potentially mutagenic and harmful affects to health. The oxidation of isolated calf thymus DNA (CT-DNA) led to the nearly quantitative loss of normal DNA 2'-deoxyribonucleosides in the following order: T > G > C ≫ A. The major modification of pyrimidines (T, C, and 5-methylcytosine (5mC)) was the corresponding 5-hydroxyhydantoin derivative after complete digestion of DNA to its component 2'-deoxyribonucleosides. The oxidation of 5mC was 2.5-fold more susceptible than C considering the relative mole fraction of 5mC to C in CT-DNA. Other common oxidation products of pyrimidines (e.g., 5,6-dihydroxy-5,6-dihydropyrimidines, the so-called pyrimidine 5,6-glycols) were formed with a lower yield than 5-hydroxyhydantoin derivatives. In addition, several common oxidation products of G were observed (e.g., 8-oxo-7,8-dihydroguanine (8oxoG)) albeit with relatively minor yields. The sum of individual products was notably less than the loss of 2'-deoxyribonucleosides from which they were derived. In a search for additional products, we discovered the formation of pyrimidine ring fragments, predominantly N-formamide and N-urea, which were measured as a dinucleotide next to a nonmodified nucleotide upon partial digestion of oxidized DNA. Interestingly, the latter fragments were also observed in dinucleotides containing 8oxoG, indicating the formation of tandem lesions during ozonolysis of DNA. The oxidation of DNA upon exposure to ozone can be explained by reactions of an intermediate ozonide. These studies underline the complexity of ozone-induced DNA damage and provide valuable information to assess the formation of this damage in cellular DNA.
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Affiliation(s)
- J Richard Wagner
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, 3001 12e avenue Nord, Sherbrooke, Québec, Canada J1H 5N4
| | - Guru S Madugundu
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, 3001 12e avenue Nord, Sherbrooke, Québec, Canada J1H 5N4
| | - Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, 3001 12e avenue Nord, Sherbrooke, Québec, Canada J1H 5N4
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4
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A theoretical study towards understanding the origin of DNA oxidation products. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Wang SD, Zhang RB, Cadet J. Enhanced reactivity of the pyrimidine peroxyl radical towards the C–H bond in duplex DNA – a theoretical study. Org Biomol Chem 2020; 18:3536-3543. [DOI: 10.1039/d0ob00302f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The peroxyl radical exhibits a much stronger reactivity towards C1′–H1′ in duplex DNA with respect to single-stranded DNA.
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Affiliation(s)
- Shu-dong Wang
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Ru-bo Zhang
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie
- Faculté de Médecine
- Université de Sherbrooke
- Sherbrooke
- Canada JIH 5N4
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6
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Robert G, Wagner JR. Tandem Lesions Arising from 5-(Uracilyl)methyl Peroxyl Radical Addition to Guanine: Product Analysis and Mechanistic Studies. Chem Res Toxicol 2019; 33:565-575. [PMID: 31820932 DOI: 10.1021/acs.chemrestox.9b00407] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of hydroxyl radical (HO•) with thymine in DNA generates 5-(uracilyl)-methyl radicals (T•) and the corresponding methylperoxyl radical (TOO•) in the presence of O2, which in turn propagates damage by reacting with a vicinal nucleobase. This leads to so-called double or tandem lesions. Because methyl oxidation products of thymine are major products, we investigated the reactivity of TOO• using a photolabile precursor: 5-(phenylthiomethyl)uracil (TSPh). The precursor was prepared and incorporated into a DNA trinucleotide: 5'-d(GpTSPhpA)-3' (G-TSPh-A). Upon photolysis, the resulting products were characterized by LC-MS/MS. Thereby, we identified four tandem lesions involving GpT, which include either 2,6-diamino-4-hydroxy-5-formamidopyrimidine (fapyG) or 8-oxo-7,8-dihydroguanine (oxoG) in tandem with either 5-formyluracil (fU) or 5-hydroxymethyluracil (hmU). The formation of these tandem lesions is explained by initial addition of TOO• to the C8 of guanine moiety, giving an N7-guanine cross-linked radical. The latter radical undergoes either reduction to an 7,8-saturated endoperoxide or oxidation to an 7,8-unsaturated endoperoxide, which transform into fapyG-fU-A and oxoG-fU-A, respectively. This is supported by the effect of a reducing (dithiothreitol) and oxidizing agent (Fe3+) on product formation. This study expands the repertoire of tandem lesions that can occur at GpT sequences and underlines the importance of redox environment.
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Affiliation(s)
- Gabriel Robert
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé , Université de Sherbrooke , Sherbrooke , Québec J1H 5N4 , Canada
| | - J Richard Wagner
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé , Université de Sherbrooke , Sherbrooke , Québec J1H 5N4 , Canada.,Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé , Université de Sherbrooke , Sherbrooke , Québec J1H 5N4 , Canada
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7
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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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8
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Wang S, Ding J, Liu P, Xie S, Xie D, Zhang M, Cheng F. Theoretical studies on the purine radical induced purine-purine type intrastrand cross-links. Org Biomol Chem 2019; 17:892-897. [PMID: 30629064 DOI: 10.1039/c8ob02882f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
At the density functional theory (DFT) level, addition reactions between the guanine-8-yl radical and its 3'/5' neighboring purine deoxynucleosides forming the purine-purine type intrastrand cross-links were studied. It is found that addition of the guanine-8-yl radical to the C8 site of its 5' neighboring deoxyguanosine or deoxyadenosine is a two-step reaction consisting of a structurally relatively unfavourable conformational transformation step, while the corresponding 3' C8 addition is straightforward and kinetically more efficient. The 3' C8 preference of the guanine-8-yl radical additions indicates the existence of an obvious sequence effect, which is completely opposite to that observed in the formation of pyrimidine radicals induced DNA intrastrand cross-links. The detrimental effects from steric hindrance and stabilizing weak interactions make these addition reactions markedly suppressed in double stranded DNA. This work broadens our knowledge about the possible types of DNA intrastrand cross-links.
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Affiliation(s)
- Shoushan Wang
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials, School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan 523808, People's Republic of China.
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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: 216] [Impact Index Per Article: 36.0] [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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10
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Wang S, Zhang M, Liu P, Xie S, Cheng F, Wang L. DNA intrastrand cross-links induced by the purine-type deoxyguanosine-8-yl radical: a DFT study. Phys Chem Chem Phys 2018; 19:16621-16628. [PMID: 28617503 DOI: 10.1039/c7cp02725g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Currently, all known DNA intrastrand cross-links are found to be induced by pyrimidine-type radicals; however, whether or not purine-type radicals are able to cause DNA intrastrand cross-links remains unclear. In the present study, probable additions of the highly reactive deoxyguanosine-8-yl radical to its 3'/5' neighboring pyrimidine nucleotides in four model compounds, 5'-G˙T-3', 5'-TG˙-3', 5'-G˙C-3', and 5'-CG˙-3', were studied using density functional theory (DFT) methods. In single-stranded DNA, the deoxyguanosine-8-yl radical is preferred to efficiently attack the C5 site of its 3' neighboring deoxythymidine or deoxycytidine, forming the G[8-5]T or G[8-5]C intrastrand cross-link rather than the C6 site forming the G[8-6]T or G[8-6]C intrastrand cross-link. The four corresponding sequence isomers, namely T[5-8]G, T[6-8]G, C[5-8]G, and C[6-8]G, formed by additions of deoxyguanosine-8-yl radical to its 5' neighboring pyrimidine nucleotides are predicted to be formed inefficiently. In double-stranded DNA, considering the detrimental effects of stabilizing weak interactions on related structural adjustments required in each addition reaction path, relatively lower reaction yields are suggested for the G[8-5]T and G[8-5]C intrastrand cross-links, while the formation of the other six intrastrand cross-links becomes quite difficult. All calculations definitely demonstrate that, in addition to pyrimidine-type radicals, the purine-type deoxyguanosine-8-yl radical is able to attack its 3'/5' neighboring pyrimidine nucleotides forming several DNA intrastrand cross-links.
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Affiliation(s)
- Shoushan Wang
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials, School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan 523808, People's Republic of China.
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11
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Zhao S, Eriksson LA, Zhang RB. Theoretical Insights on the Inefficiency of RNA Oxidative Damage under Aerobic Conditions. J Phys Chem A 2017; 122:431-438. [PMID: 29206039 DOI: 10.1021/acs.jpca.7b10711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oxidative damage to RNA has been linked to change or loss of RNA function and development of many human age-related diseases. However, knowledge on the nature of RNA oxidative damage is relatively limited. In this study, oxidative damage to RNA is investigated under anaerobic and aerobic conditions by exploring the properties and reactions of 5-hydroxyl-2'-uridin-6-yl and its peroxyl diastereoisomers in the RNA strand, respectively. Selective addition of OH to the nucleic base from the 5'-end is studied at the molecular level for the first time, explaining the large number of the 5S-isomer available for further reactions. Our results provide clear evidence that the efficiency of C2'-H2' bond activation in the peroxyl isomers is lower than in the carbon radical species. An exception is observed for the isomer cis-(5S,6R)-A1, whose internucleotidyl H2'-abstraction barrier is far smaller than that in the corresponding C6-yl radical. However, analysis of the equilibrium species distribution reveals that the amount of cis-(5S,6R)-A1 is very small among the peroxyl diastereoisomers, and hence the resulting products from direct strand scission should be a less important component in RNA oxidative damage. The species with maximum distribution is the cis-(5S,6R)-B1 isomer, which is derived from cis-(5S,6R)-A1 and has a moderate intranucleotidyl H2'-abstraction barrier. More importantly, the reaction is mildly exothermic. These results show that the main fraction of the intranucleotidyl H2'-abstraction intermediates can be formed from the cis-(5S,6R)-B1 isomer. The absolute reduction potentials, the hydrogen atom binding energies, and the key structural parameters of the C6-peroxyl species are used to understand the diverse reactivity of the cis-(5S,6R) diastereoisomers toward the C2'-H2' bonds activation. The present study shows that in addition to the selectivity of the OH radical addition, there is a strong correlation between the conformation of the modified uracil base and its reactivity in RNA oxidative damage.
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Affiliation(s)
- Shuang Zhao
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology , South Street No. 5, Zhongguancun, Haidian District, Beijing 100081, China
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg , Box 462, 405 30 Göteborg, Sweden
| | - Ru-Bo Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology , South Street No. 5, Zhongguancun, Haidian District, Beijing 100081, China
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12
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Cadet J, Davies KJA, Medeiros MH, Di Mascio P, Wagner JR. Formation and repair of oxidatively generated damage in cellular DNA. Free Radic Biol Med 2017; 107:13-34. [PMID: 28057600 PMCID: PMC5457722 DOI: 10.1016/j.freeradbiomed.2016.12.049] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/27/2016] [Accepted: 12/31/2016] [Indexed: 12/18/2022]
Abstract
In this review article, emphasis is placed on the critical survey of available data concerning modified nucleobase and 2-deoxyribose products that have been identified in cellular DNA following exposure to a wide variety of oxidizing species and agents including, hydroxyl radical, one-electron oxidants, singlet oxygen, hypochlorous acid and ten-eleven translocation enzymes. In addition, information is provided about the generation of secondary oxidation products of 8-oxo-7,8-dihydroguanine and nucleobase addition products with reactive aldehydes arising from the decomposition of lipid peroxides. It is worth noting that the different classes of oxidatively generated DNA damage that consist of single lesions, intra- and interstrand cross-links were unambiguously assigned and quantitatively detected on the basis of accurate measurements involving in most cases high performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. The reported data clearly show that the frequency of DNA lesions generated upon severe oxidizing conditions, including exposure to ionizing radiation is low, at best a few modifications per 106 normal bases. Application of accurate analytical measurement methods has also allowed the determination of repair kinetics of several well-defined lesions in cellular DNA that however concerns so far only a restricted number of cases.
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Affiliation(s)
- Jean Cadet
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4.
| | - Kelvin J A Davies
- Leonard Davis School of Gerontology of the Ethel Percy Andrus Gerontology Center, The University of Southern California, Los Angeles, CA 90089-0191, United States; Division of Molecular & Computational Biology, Department of Biological Sciences of the Dornsife College of Letters, Arts, and Sciences, The University of Southern California, Los Angeles, CA 90089-0191, United States
| | - Marisa Hg Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508 000 São Paulo, SP, Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508 000 São Paulo, SP, Brazil
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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13
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Abstract
Nucleobase radicals are major products of the reactions between nucleic acids and hydroxyl radical, which is produced via the indirect effect of ionizing radiation. The nucleobase radicals also result from hydration of cation radicals that are produced via the direct effect of ionizing radiation. The role that nucleobase radicals play in strand scission has been investigated indirectly using ionizing radiation to generate them. More recently, the reactivity of nucleobase radicals resulting from formal hydrogen atom or hydroxyl radical addition to pyrimidines has been studied by independently generating the reactive intermediates via UV-photolysis of synthetic precursors. This approach has provided control over where the reactive intermediates are produced within biopolymers and facilitated studying their reactivity. The contributions to our understanding of pyrimidine nucleobase radical reactivity by this approach are summarized.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
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14
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Zhao S, Zhang RB. Alternative role of cisplatin in DNA damage – theoretical studies on the influence of excess electrons on the cisplatin–DNA complex. RSC Adv 2016. [DOI: 10.1039/c6ra17919c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Interaction of excess electrons with cisplatin–DNA generates highly reactive Pt-containing species towards C–H abstraction, which strongly contributes to DNA damage.
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Affiliation(s)
- Shuang Zhao
- School of Chemistry
- Beijing Institute of Technology
- Beijing
- China
| | - Ru-bo Zhang
- School of Chemistry
- Beijing Institute of Technology
- Beijing
- China
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15
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Zhao S, Zhang RB, Li ZS. A new understanding towards the reactivity of DNA peroxy radicals. Phys Chem Chem Phys 2016; 18:23763-8. [DOI: 10.1039/c6cp04720c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
New radical reaction paths for the formation of DNA oxidation products are suggested, which are strongly different from the previously suggested paths with the tetraoxide intermediate.
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Affiliation(s)
- Shuang Zhao
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
| | - Ru-bo Zhang
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
| | - Ze-sheng Li
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
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16
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Nikitaki Z, Hellweg CE, Georgakilas AG, Ravanat JL. Stress-induced DNA damage biomarkers: applications and limitations. Front Chem 2015; 3:35. [PMID: 26082923 PMCID: PMC4451417 DOI: 10.3389/fchem.2015.00035] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/07/2015] [Indexed: 11/13/2022] Open
Abstract
A variety of environmental stresses like chemicals, UV and ionizing radiation and organism's endogenous processes such as replication stress and metabolism can lead to the generation of reactive oxygen and nitrogen species (ROS/RNS) that can attack cellular vital components like DNA, proteins and lipid membranes. Among them, much attention has been focused on DNA since DNA damage plays a role in several biological disorders and aging processes. Thus, DNA damage can be used as a biomarker in a reliable and accurate way to quantify for example radiation exposure and can indicate its possible long term effects and cancer risk. Based on the type of DNA lesions detected one can hypothesize on the most probable mechanisms involved in the formation of these lesions for example in the case of UV and ionizing radiation (e.g., X- or α-, γ-rays, energetic ions, neutrons). In this review we describe the most accepted chemical pathways for DNA damage induction and the different types of DNA lesions, i.e., single, complex DNA lesions etc. that can be used as DNA damage biomarkers. We critically compare DNA damage detection methods and their limitations. In addition, we suggest the use of DNA repair gene products as biomarkes for identification of different types of stresses i.e., radiation, oxidative, or replication stress, based on bioinformatic approaches and meta-analysis of literature data.
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Affiliation(s)
- Zacharenia Nikitaki
- DNA Damage and Repair Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens Athens, Greece
| | - Christine E Hellweg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine Köln, Germany
| | - Alexandros G Georgakilas
- DNA Damage and Repair Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens Athens, Greece
| | - Jean-Luc Ravanat
- Laboratoire des Lésions des Acides Nucléiques, Institut des Nanosciences et Cryogénie, Service de Chimie Inorgranique et Biologique, Université Grenoble Alpes Grenoble, France ; CEA, Institut des Nanosciences et Cryogénie, Service de Chimie Inorgranique et Biologique Grenoble, France
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17
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Cerón-Carrasco JP, Requena A, Zúñiga J, Jacquemin D. Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair. Front Chem 2015; 3:13. [PMID: 25798437 PMCID: PMC4351615 DOI: 10.3389/fchem.2015.00013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/16/2015] [Indexed: 12/04/2022] Open
Abstract
We investigate the attack of the nitrogen dioxide radical (NO•2) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO•2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO•2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.
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Affiliation(s)
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - Denis Jacquemin
- Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR Centre National de la Recherche Scientifique, Université de Nantes Nantes, France ; Institut Universitaire de France Paris, France
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Garrec J, Dumont E. Are dinucleoside monophosphates relevant models for the study of DNA intrastrand cross-link lesions? The example of g[8-5m]T. Chem Res Toxicol 2014; 27:1133-41. [PMID: 24911289 DOI: 10.1021/tx4004616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxidatively generated tandem lesions such as G[8-5m]T pose a potent threat to genome integrity. Direct experimental studies of the kinetics and thermodynamics of a specific lesion within DNA are very challenging, mostly due to the variety of products that can be formed in oxidative conditions. Dinucleoside monophosphates (DM) involving only the reactive nucleobases in water represent appealing alternative models on which most physical chemistry and structural techniques can be applied. However, it is not yet clear how relevant these models are. Here, we present QM/MM MD simulations of the cyclization step involved in the formation of G[8-5m]T from the guanine-thymine (GpT) DM in water, with the aim of comparing our results to our previous investigation of the same reaction in DNA ( Garrec , J. , Patel , C. , Rothlisberger , U. , and Dumont , E. ( 2012 ) J. Am. Chem. Soc. 134 , 2111 - 2119 ). We show that, despite the different levels of preorganization of the two systems, the corresponding reactions share many energetic and structural characteristics. The main difference lies in the angle between the G and T bases, which is slightly higher in the transition state (TS) and product of the reaction in water than in the reaction in DNA. This effect is due to the Watson-Crick H-bonds, which are absent in the {GpT+water} system and restrain the relative positioning of the reactive nucleobases in DNA. However, since the lesion is accommodated easily in the DNA macromolecule, the induced energetic penalty is relatively small. The high similarity between the two reactions strongly supports the use of GpT in water as a model of the corresponding reaction in DNA.
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Affiliation(s)
- Julian Garrec
- CNRS, Théorie-Modélisation-Simulation, SRSMC, Vandoeuvre-lès-Nancy F-54506, France
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19
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Ravanat JL, Breton J, Douki T, Gasparutto D, Grand A, Rachidi W, Sauvaigo S. Radiation-mediated formation of complex damage to DNA: a chemical aspect overview. Br J Radiol 2014; 87:20130715. [PMID: 24472775 DOI: 10.1259/bjr.20130715] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
During the last three decades, a considerable amount of work has been undertaken to determine the nature, the mechanism of formation and the biological consequences of radiation-induced DNA lesions. Most of the information was obtained via the development of chemical approaches, including theoretical, analytical and organic synthesis methods. Since it is not possible to present all the results obtained in this review article, we will focus on recent data dealing with the formation of complex DNA lesions produced by a single oxidation event, as these lesions may play a significant role in cellular responses to ionizing radiation and also to other sources of oxidative stress. Through the description of specific results, the contribution of different chemical disciplines in the assessment of the structure, the identification of the mechanism of formation and the biological impacts in terms of repair and mutagenicity of these complex radiation-induced DNA lesions will be highlighted.
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Affiliation(s)
- J-L Ravanat
- Laboratoire Lésions des Acides Nucléiques, Université Joseph Fourier/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France
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20
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Cadet J, Wagner JR. Oxidatively generated base damage to cellular DNA by hydroxyl radical and one-electron oxidants: similarities and differences. Arch Biochem Biophys 2014; 557:47-54. [PMID: 24820329 DOI: 10.1016/j.abb.2014.05.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 01/05/2023]
Abstract
Hydroxyl radical (OH) and one-electron oxidants that may be endogenously formed through oxidative metabolism, phagocytosis, inflammation and pathological conditions constitute the main sources of oxidatively generated damage to cellular DNA. It is worth mentioning that exposure of cells to exogenous physical agents (UV light, high intensity UV laser, ionizing radiation) and chemicals may also induce oxidatively generated damage to DNA. Emphasis is placed in this short review article on the mechanistic aspects of OH and one-electron oxidant-mediated formation of single and more complex damage (tandem lesions, intra- and interstrand cross-links, DNA-protein cross-links) in cellular DNA arising from one radical hit. This concerns DNA modifications that have been accurately measured using suitable analytical methods such as high performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Evidence is provided that OH and one-electron oxidants after generating neutral radicals and base radical cations respectively may partly induce common degradation pathways. In addition, selective oxidative reactions giving rise to specific degradation products of OH and one-electron oxidation reactions that can be used as representative biomarkers of these oxidants have been identified.
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Affiliation(s)
- Jean Cadet
- Institut Nanosciences et Cryogénie, CEA/Grenoble, F-38054 Grenoble Cedex 9, France; Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada.
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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21
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Abstract
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Nucleobase radicals are a major family
of reactive species produced
in DNA as a result of oxidative stress. Two such radicals, 5-hydroxy-5,6-dihydrothymidin-6-yl
radical (1) and 5,6-dihydrouridin-6-yl radical (5), were independently generated within chemically synthesized
oligonucleotides from photochemical precursors. Neither nucleobase
radical produces direct strand breaks or alkali-labile lesions in
single or double stranded DNA. The respective peroxyl radicals, resulting
from O2 trapping, add to 5′-adjacent nucleobases,
with a preference for dG. Distal dG’s are also oxidatively
damaged by the peroxyl radicals. Experiments using a variety of sequences
indicate that distal damage occurs via covalent modification of the
5′-adjacent dG, but there is no evidence for electron transfer
by the nucleobase peroxyl radicals.
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Affiliation(s)
- Joanna Maria N San Pedro
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles St., Baltimore, Maryland 21218, United States
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Cerón-Carrasco JP, Jacquemin D, Dumont E. Impact of DNA Environment on the Intrastrand Cross-Link Lesions: Hydrogen Atom Release as the Last Step of Formation of G[8-5m]T. J Phys Chem B 2013; 117:16397-404. [DOI: 10.1021/jp408947u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- José Pedro Cerón-Carrasco
- Departamento
de Quı́mica Fı́sica, Universidad de Murcia, 30100 Murcia, Spain
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes, 2 Rue de la Houssinière, 44322 Nantes, Cedex 3, France
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes, 2 Rue de la Houssinière, 44322 Nantes, Cedex 3, France
- Institut Universitaire de France, 103 bd St Michel, 75005 Paris, Cedex 5, France
| | - Elise Dumont
- Laboratoire de Chimie, UMR 5182 CNRS, École Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon, Cedex 07, France
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Patel C, Dršata T, Lankaš F, Dumont E. Structure, Dynamics, and Interactions of a C4′-Oxidized Abasic Site in DNA: A Concomitant Strand Scission Reverses Affinities. Biochemistry 2013; 52:8115-25. [DOI: 10.1021/bi401268q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chandan Patel
- Laboratoire
de Chimie, UMR 5182 CNRS, École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Tomàš Dršata
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Filip Lankaš
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Elise Dumont
- Laboratoire
de Chimie, UMR 5182 CNRS, École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France
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