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Khorsand F, Hamali H, Qasemi-Panahi B, Tohidkia M. The Effects of Supplementation of the Freezing Extender with Silymarin on the Quality Parameters of Frozen-Thawed Arabian Stallion Sperm: A Preliminary Evaluation. Biopreserv Biobank 2024. [PMID: 38905135 DOI: 10.1089/bio.2023.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024] Open
Abstract
This study evaluated the effects of supplementation of the freezing extender with different concentrations of silymarin on the quality of frozen-thawed Arabian stallion spermatozoa. Semen samples from three stallions (1, 2, and 3) were suspended in the freezing extender without or with silymarin (0, 25 μg/mL, 50 μg/mL, 75 μg/mL, and 100 μg/mL) and cryopreserved in 0.5 mL straws. After 1 month of storage, the frozen semen samples in straws were thawed and evaluated in terms of viability, mitochondrial membrane potential, kinematic parameters, total and progressive motility, plasma membrane integrity, lipid peroxidation, and DNA fragmentation. The findings indicated that 25-100 μg/mL of silymarin significantly improved viability and mitochondrial membrane potential while reducing the stallion sperm lipid peroxidation, DNA fragmentation, and apoptosis compared with the control group (p < 0.05). Silymarin concentrations of 75 μg/mL and 100 μg/mL significantly increased progressive motility and plasma membrane integrity (p < 0.05). Based on our findings, it can be inferred that silymarin exhibited a dose-dependent enhancement in the frozen-thawed Arabian stallion sperm quality. The most favorable outcomes were observed when 100 μg/mL silymarin was used.
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Affiliation(s)
- Farzaneh Khorsand
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Hossein Hamali
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Babak Qasemi-Panahi
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mohammadreza Tohidkia
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, University of Tabriz, Tabriz, Iran
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2
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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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3
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Favaudon V, Labarbe R, Limoli CL. Model studies of the role of oxygen in the FLASH effect. Med Phys 2022; 49:2068-2081. [PMID: 34407219 PMCID: PMC8854455 DOI: 10.1002/mp.15129] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
Current radiotherapy facilities are standardized to deliver dose rates around 0.1-0.4 Gy/s in 2 Gy daily fractions, designed to deliver total accumulated doses to reach the tolerance limit of normal tissues undergoing irradiation. FLASH radiotherapy (FLASH-RT), on the other hand, relies on facilities capable of delivering ultrahigh dose rates in large doses in a single microsecond pulse, or in a few pulses given over a very short time sequence. For example, most studies to date have implemented 4-6 MeV electrons with intra-pulse dose rates in the range 106 -107 Gy/s. The proposed dependence of the FLASH effect on oxygen tension has stimulated several theoretical models based on three different hypotheses: (i) Radiation-induced transient oxygen depletion; (ii) cell-specific differences in the ability to detoxify and/or recover from injury caused by reactive oxygen species; (iii) self-annihilation of radicals by bimolecular recombination. This article focuses on the observations supporting or refuting these models in the frame of the chemical-biological bases of the impact of oxygen on the radiation response of cell free, in vitro and in vivo model systems.
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Affiliation(s)
- Vincent Favaudon
- Institut Curie, Inserm U 1021- CNRS UMR 3347, University Paris-Saclay, PSL Research University, Centre Universitaire, 91405 Orsay Cedex, France
- Corresponding author:
| | - Rudi Labarbe
- Ion Beam Applications S.A. (IBA), Louvain-la-Neuve, Belgium
| | - Charles L. Limoli
- Dept. of Radiation Oncology, Medical Sciences I, B146B, Irvine, California 92697-2695, USA
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Abdelhady AM, Hirano Y, Onizuka K, Okamura H, Komatsu Y, Nagatsugi F. Synthesis of Crosslinked 2'-OMe RNA Duplexes Using 2-Amino-6-Vinylpurine and Their Application for Effective Inhibition of miRNA Function. Curr Protoc 2022; 2:e386. [PMID: 35316581 DOI: 10.1002/cpz1.386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Crosslinking reactions to nucleic acids are an effective way to prepare stable complexes formed by covalent bonding. We demonstrated that fully 2'-O-methylated (2'-OMe) RNAs having a 2-amino-6-vinylpurine (AVP) exhibited an efficient crosslinking to uracil in the target RNA. Recently, we reported the preparation of crosslinked 2'-OMe RNA duplexes using AVP and the anti-miRNA oligonucleotides (AMOs) containing crosslinked duplexes at the terminal positions. These AMOs exhibited efficient microRNA (miRNA) inhibition at very low concentrations. In this article, we describe the chemical synthesis of 2'-OMe oligonucleotides containing AVP and preparation of the AMOs bearing crosslinked 2'-OMe RNA duplexes using AVP. In addition, we describe in detail the miRNA inhibition assay using these AMOs. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of phosphoramidite of 2-amino-6-vinylguanosine derivative Basic Protocol 2: Synthesis of AVP-2'-OMe RNA Basic Protocol 3: Evaluation of the crosslink reactivity of CFO containing AVP to the 2'-OMe RNA and preparation of AMOs containing crosslinked duplex Basic Protocol 4: miRNA inhibition assays.
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Affiliation(s)
- Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Sendai, Miyagi, Japan
| | - Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
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5
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Tavakoli A, Min JH. Photochemical modifications for DNA/RNA oligonucleotides. RSC Adv 2022; 12:6484-6507. [PMID: 35424630 PMCID: PMC8982246 DOI: 10.1039/d1ra05951c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022] Open
Abstract
Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.
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Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
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6
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Peng H, Jie J, Mortimer IP, Ma Z, Su H, Greenberg MM. Reactivity and DNA Damage by Independently Generated 2'-Deoxycytidin- N4-yl Radical. J Am Chem Soc 2021; 143:14738-14747. [PMID: 34467764 DOI: 10.1021/jacs.1c06425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Oxidative stress produces a variety of radicals in DNA, including pyrimidine nucleobase radicals. The nitrogen-centered DNA radical 2'-deoxycytidin-N4-yl radical (dC·) plays a role in DNA damage mediated by one electron oxidants, such as HOCl and ionizing radiation. However, the reactivity of dC· is not well understood. To reduce this knowledge gap, we photochemically generated dC· from a nitrophenyl oxime nucleoside and within chemically synthesized oligonucleotides from the same precursor. dC· formation is confirmed by transient UV-absorption spectroscopy in laser flash photolysis (LFP) experiments. LFP and duplex DNA cleavage experiments indicate that dC· oxidizes dG. Transient formation of the dG radical cation (dG+•) is observed in LFP experiments. Oxidation of the opposing dG in DNA results in hole transfer when the opposing dG is part of a dGGG sequence. The sequence dependence is attributed to a competition between rapid proton transfer from dG+• to the opposing dC anion formed and hole transfer. Enhanced hole transfer when less acidic O6-methyl-2'-deoxyguanosine is opposite dC· supports this proposal. dC· produces tandem lesions in sequences containing thymidine at the 5'-position by abstracting a hydrogen atom from the thymine methyl group. The corresponding thymidine peroxyl radical completes tandem lesion formation by reacting with the 5'-adjacent nucleotide. As dC· is reduced to dC, its role in the process is traceless and is only detectable because of the ability to independently generate it from a stable precursor. These experiments reveal that dC· oxidizes neighboring nucleotides, resulting in deleterious tandem lesions and hole transfer in appropriate sequences.
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Affiliation(s)
- Haihui Peng
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ifor P Mortimer
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Zehan Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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7
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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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8
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Wardman P. Radiotherapy Using High-Intensity Pulsed Radiation Beams (FLASH): A Radiation-Chemical Perspective. Radiat Res 2020; 194:607-617. [DOI: 10.1667/rade-19-00016] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 11/03/2022]
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9
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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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10
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Peña FJ, O’Flaherty C, Ortiz Rodríguez JM, Martín Cano FE, Gaitskell-Phillips GL, Gil MC, Ortega Ferrusola C. Redox Regulation and Oxidative Stress: The Particular Case of the Stallion Spermatozoa. Antioxidants (Basel) 2019; 8:antiox8110567. [PMID: 31752408 PMCID: PMC6912273 DOI: 10.3390/antiox8110567] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023] Open
Abstract
Redox regulation and oxidative stress have become areas of major interest in spermatology. Alteration of redox homeostasis is recognized as a significant cause of male factor infertility and is behind the damage that spermatozoa experience after freezing and thawing or conservation in a liquid state. While for a long time, oxidative stress was just considered an overproduction of reactive oxygen species, nowadays it is considered as a consequence of redox deregulation. Many essential aspects of spermatozoa functionality are redox regulated, with reversible oxidation of thiols in cysteine residues of key proteins acting as an “on–off” switch controlling sperm function. However, if deregulation occurs, these residues may experience irreversible oxidation and oxidative stress, leading to malfunction and ultimately death of the spermatozoa. Stallion spermatozoa are “professional producers” of reactive oxygen species due to their intense mitochondrial activity, and thus sophisticated systems to control redox homeostasis are also characteristic of the spermatozoa in the horse. As a result, and combined with the fact that embryos can easily be collected in this species, horses are a good model for the study of redox biology in the spermatozoa and its impact on the embryo.
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Affiliation(s)
- Fernando J. Peña
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, 10003 Cáceres, Spain; (J.M.O.R.); (F.E.M.C.); (G.L.G.-P.); (M.C.G.); (C.O.F.)
- Correspondence: ; Tel.: +34-927-257-167
| | - Cristian O’Flaherty
- Departments of Surgery (Urology Division) and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montréal, QC H4A 3J1, Canada;
| | - José M. Ortiz Rodríguez
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, 10003 Cáceres, Spain; (J.M.O.R.); (F.E.M.C.); (G.L.G.-P.); (M.C.G.); (C.O.F.)
| | - Francisco E. Martín Cano
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, 10003 Cáceres, Spain; (J.M.O.R.); (F.E.M.C.); (G.L.G.-P.); (M.C.G.); (C.O.F.)
| | - Gemma L. Gaitskell-Phillips
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, 10003 Cáceres, Spain; (J.M.O.R.); (F.E.M.C.); (G.L.G.-P.); (M.C.G.); (C.O.F.)
| | - María C. Gil
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, 10003 Cáceres, Spain; (J.M.O.R.); (F.E.M.C.); (G.L.G.-P.); (M.C.G.); (C.O.F.)
| | - Cristina Ortega Ferrusola
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, 10003 Cáceres, Spain; (J.M.O.R.); (F.E.M.C.); (G.L.G.-P.); (M.C.G.); (C.O.F.)
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11
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Abstract
If the genome contains outlier sequences extraordinarily sensitive to environmental agents, these would be sentinels for monitoring personal carcinogen exposure and might drive direct changes in cell physiology rather than acting through rare mutations. New methods, adductSeq and freqSeq, provided statistical resolution to quantify rare lesions at single-base resolution across the genome. Primary human melanocytes, but not fibroblasts, carried spontaneous apurinic sites and TG sequence lesions more frequent than ultraviolet (UV)-induced cyclobutane pyrimidine dimers (CPDs). UV exposure revealed hyperhotspots acquiring CPDs up to 170-fold more frequently than the genomic average; these sites were more prevalent in melanocytes. Hyperhotspots were disproportionately located near genes, particularly for RNA-binding proteins, with the most-recurrent hyperhotspots at a fixed position within 2 motifs. One motif occurs at ETS family transcription factor binding sites, known to be UV targets and now shown to be among the most sensitive in the genome, and at sites of mTOR/5' terminal oligopyrimidine-tract translation regulation. The second occurs at A2-15TTCTY, which developed "dark CPDs" long after UV exposure, repaired CPDs slowly, and had accumulated CPDs prior to the experiment. Motif locations active as hyperhotspots differed between cell types. Melanocyte CPD hyperhotspots aligned precisely with recurrent UV signature mutations in individual gene promoters of melanomas and with known cancer drivers. At sunburn levels of UV exposure, every cell would have a hyperhotspot CPD in each of the ∼20 targeted cell pathways, letting hyperhotspots act as epigenetic marks that create phenome instability; high prevalence favors cooccurring mutations, which would allow tumor evolution to use weak drivers.
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12
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Peña FJ, Ortiz Rodriguez JM, Gil MC, Ortega Ferrusola C. Flow cytometry analysis of spermatozoa: Is it time for flow spermetry? Reprod Domest Anim 2018; 53 Suppl 2:37-45. [DOI: 10.1111/rda.13261] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Fernando J. Peña
- Laboratory of Equine Reproduction and Spermatology; University of Extremadura; Cáceres Spain
| | - Jose M. Ortiz Rodriguez
- Laboratory of Equine Reproduction and Spermatology; University of Extremadura; Cáceres Spain
| | - María C. Gil
- Laboratory of Equine Reproduction and Spermatology; University of Extremadura; Cáceres Spain
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13
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Zheng L, Greenberg MM. Traceless Tandem Lesion Formation in DNA from a Nitrogen-Centered Purine Radical. J Am Chem Soc 2018; 140:6400-6407. [PMID: 29738242 DOI: 10.1021/jacs.8b02828] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nitrogen-centered nucleoside radicals are commonly produced reactive intermediates in DNA exposed to γ-radiolysis and oxidants, but their reactivity is not well understood. Examination of the reactivity of independently generated 2'-deoxyadenosin- N6-yl radical (dA•) reveals that it is an initiator of tandem lesions, an important form of DNA damage that is a hallmark of γ-radiolysis. dA• yields O2-dependent tandem lesions by abstracting a hydrogen atom from the C5-methyl group of a 5'-adjacent thymidine to form 5-(2'-deoxyuridinyl)methyl radical (T•). The subsequently formed thymidine peroxyl radical adds to the 5'-adjacent dG, ultimately producing a 5'-OxodGuo-fdU tandem lesion. Importantly, the initial hydrogen abstraction repairs dA• to form dA. Thus, the involvement of dA• in tandem lesion formation is traceless by product analysis. The tandem lesion structure, as well as the proposed mechanism, are supported by LC-MS/MS, isotopic labeling, chemical reactivity experiments, and independent generation of T•. Tandem lesion formation efficiency is dependent on the ease of ionization of the 5'-flanking sequence, and the yields are >27% in the 5'-d(GGGT) flanking sequence. The traceless involvement of dA• in tandem lesion formation may be general for nitrogen-centered radicals in nucleic acids, and presents a new pathway for forming a deleterious form of DNA damage.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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14
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Fleming AM, Burrows CJ. 8-Oxo-7,8-dihydro-2'-deoxyguanosine and abasic site tandem lesions are oxidation prone yielding hydantoin products that strongly destabilize duplex DNA. Org Biomol Chem 2018; 15:8341-8353. [PMID: 28936535 DOI: 10.1039/c7ob02096a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In DNA, 2'-deoxyguanosine (dG) is susceptible to oxidative modification by reactive oxygen species (ROS) yielding many products, one of which is 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG). Interestingly, dOG is stable but much more labile toward oxidation than dG, furnishing 5-guanidinohydantoin-2'-deoxyribose (dGh) that is favored in the duplex context or spiroiminodihydantoin-2'-deoxyribose (dSp) that is favored in the oxidation of single-stranded contexts. Previously, exposure of DNA to ionizing radiation found ∼50% of the dOG exists as a tandem lesion with an adjacent formamide site. The present work explored oxidation of dOG in a tandem lesion with a THF abasic site analog (F) that models the formamide on either the 5' or 3' side. When dOG was in a tandem lesion, both dGh and dSp were observed as oxidation products. The 5' versus 3' side in which F resided influenced the stereochemistry of the dSp formed. Further, tandem lesions with dOG were found to be up to two orders of magnitude more reactive to oxidation than dOG in an intact duplex. When dOG is in a tandem lesion it is up to fivefold more prone to formation of spermine cross-links during oxidation compared to dOG in an intact duplex. Lastly, dOG, dGh, and each dSp diastereomer were synthesized as part of a tandem lesion in a duplex DNA to establish that dOG tandem lesions decrease the thermal stability by 12-13 °C, while dGh or either dSp diastereomer in a tandem lesion decrease the stability by >20 °C. The biological consequences of these results are 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, USA.
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15
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Zheng L, Greenberg MM. DNA Damage Emanating From a Neutral Purine Radical Reveals the Sequence Dependent Convergence of the Direct and Indirect Effects of γ-Radiolysis. J Am Chem Soc 2017; 139:17751-17754. [PMID: 29190086 DOI: 10.1021/jacs.7b10942] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleobase radicals are the major intermediates generated by the direct (e.g., dA•+) and indirect (e.g., dA•) effects of γ-radiolysis. dA• was independently generated in DNA for the first time. The dA•+/dA• equilibrium, and consequently the reactivity in DNA, is significantly shifted toward the radical cation by a flanking dA. Tandem lesions emanating from dA• are the major products when the reactive intermediate is flanked by a 5'-dGT. In contrast, when dA• is flanked by dA, the increased dA•+ pKa results in DNA damage arising from hole transfer. This is the first demonstration that sequence effects lead to the intersection of the direct and indirect effects of ionizing radiation.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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16
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Zheng L, Lin L, Qu K, Adhikary A, Sevilla MD, Greenberg MM. Independent Photochemical Generation and Reactivity of Nitrogen-Centered Purine Nucleoside Radicals from Hydrazines. Org Lett 2017; 19:6444-6447. [PMID: 29125775 DOI: 10.1021/acs.orglett.7b03368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Photochemical precursors that produce dA• and dG(N2-H)• are needed to investigate their reactivity. The synthesis of two 1,1-diphenylhydrazines (1, 2) and their use as photochemical sources of dA• and dG(N2-H)• is presented. Trapping studies indicate production of these radicals with good fidelity, and 1 was incorporated into an oligonucleotide via solid-phase synthesis. Cyclic voltammetric studies show that reduction potentials of 1 and 2 are lower than those of widely used "hole sinks", e.g., 8-oxodGuo and 7-deazadGuo, to investigate DNA-hole transfer processes. These molecules could be useful (a) as sources of dA• and dG(N2-H)• at specific sites in oligonucleotides and (b) as "hole sinks" for the study of DNA-hole transfer processes.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Lu Lin
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ke Qu
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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17
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Sun H, Taverna Porro ML, Greenberg MM. Independent Generation and Reactivity of Thymidine Radical Cations. J Org Chem 2017; 82:11072-11083. [PMID: 28994287 DOI: 10.1021/acs.joc.7b02017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymidine radical cation (1) is produced by ionizing radiation and has been invoked as an intermediate in electron transfer in DNA. Previous studies on its structure and reactivity have utilized thymidine as a precursor, which limits quantitative product analysis because thymidine is readily reformed from 1. In this investigation, radical cation 1 is independently generated via β-heterolysis of a pyrimidine radical generated photochemically from an aryl sulfide. Thymidine is the major product (33%) from 1 at pH 7.2. Diastereomeric mixtures of thymidine glycol and the corresponding 5-hydroxperoxides resulting from water trapping of 1 are formed. Significantly lower yields of products such as 5-formyl-2'-deoxyuridine that are ascribable to deprotonation from the C5-methyl group of 1 are observed. Independent generation of the N3-methyl analogue of 1 (NMe-1) produces considerably higher yields of products derived from water trapping, and these products are formed in much higher yields than those attributable to the C5-methyl group deprotonation in NMe-1. N3-Methyl-thymidine is, however, the major product and is produced in as high as 70% yield when the radical cation is produced in the presence of excess thiol. The effects of exogenous reagents on product distributions are consistent with the formation of diffusively free radical cations (1, NMe-1). This method should be compatible with producing radical cations at defined positions within DNA.
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Affiliation(s)
- Huabing Sun
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Marisa L Taverna Porro
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles St., Baltimore, Maryland 21218, United States
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18
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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: 205] [Impact Index Per Article: 29.3] [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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19
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Zheng L, Griesser M, Pratt DA, Greenberg MM. Aminyl Radical Generation via Tandem Norrish Type I Photocleavage, β-Fragmentation: Independent Generation and Reactivity of the 2'-Deoxyadenosin- N6-yl Radical. J Org Chem 2017; 82:3571-3580. [PMID: 28318253 DOI: 10.1021/acs.joc.7b00093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Formal hydrogen atom abstraction from the nitrogen-hydrogen bonds in purine nucleosides produces reactive intermediates that are important in nucleic acid oxidation. Herein we describe an approach for the independent generation of the purine radical resulting from hydrogen atom abstraction from the N6-amine of 2'-deoxyadenosine (dA•). The method involves sequential Norrish Type I photocleavage of a ketone (7b) and β-fragmentation of the initially formed alkyl radical (8b) to form dA• and acetone. The formation of dA• was followed by laser flash photolysis, which yields a transient with λmax ≈ 340 nm and a broader weaker absorption centered at ∼560 nm. This transient grows in at ≥2 × 105 s-1; however, computations and reactivity data suggest that β-fragmentation occurs much faster, implying the consumption of dA• as it is formed. Continuous photolysis of 7b in the presence of ferrous ion or thiophenol produces good yields of dA, whereas less reactive thiols afford lower yields presumably due to a polarity mismatch. This tandem photochemical, β-fragmentation method promises to be useful for site-specific production of dA• in nucleic acid oligomers and/or polymers and also for the production of aminyl radicals, in general.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Markus Griesser
- Department of Chemistry & Biomolecular Sciences, University of Ottawa , 10 Marie Curie Pvt., Ottawa, Canada
| | - Derek A Pratt
- Department of Chemistry & Biomolecular Sciences, University of Ottawa , 10 Marie Curie Pvt., Ottawa, Canada
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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20
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Paul R, Greenberg MM. Mechanistic Studies on RNA Strand Scission from a C2'-Radical. J Org Chem 2016; 81:9199-9205. [PMID: 27668445 DOI: 10.1021/acs.joc.6b01760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The C2'-carbon-hydrogen bond in ribonucleotides is significantly weaker than other carbohydrate carbon-hydrogen bonds in RNA or DNA. Independent generation of the C2'-uridine radical (1) in RNA oligonucleotides via Norrish type I photocleavage of a ketone-substituted nucleotide yields direct strand breaks via cleavage of the β-phosphate. The reactivity of 1 in different sequences and under a variety of conditions suggests that the rate constant for strand scission is significantly greater than 106 s-1 at pH 7.2. The initially formed C2'-radical (1) is not trapped under a variety of conditions, consistent with computational studies ( Chem.-Eur. J. 2009 , 15 , 2394 ) that suggest that the barrier to strand scission is very low and that synchronous proton transfer from the 2'-hydroxyl to the departing phosphate group facilitates cleavage. The C2'-radical could be a significant contributor to RNA strand scission by the hydroxyl radical, particularly under anaerobic conditions where 1 can be produced from nucleobase radicals.
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Affiliation(s)
- Rakesh Paul
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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21
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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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22
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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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23
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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24
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Kusano S, Ishiyama S, Lam SL, Mashima T, Katahira M, Miyamoto K, Aida M, Nagatsugi F. Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts. Nucleic Acids Res 2015; 43:7717-30. [PMID: 26245348 PMCID: PMC4652779 DOI: 10.1093/nar/gkv797] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/28/2015] [Indexed: 12/28/2022] Open
Abstract
DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to react selectively with guanine. The AOVP CFO exhibited selective crosslinking reactivity with guanine and thymine in DNA, and with guanine in RNA. These crosslinking reactions with guanine were accelerated in the presence of CoCl2, NiCl2, ZnCl2 and MnCl2. In addition, we demonstrated that the AOVP CFO was reactive toward 8-oxoguanine opposite AOVP in the duplex DNA. The structural analysis of each guanine and 8-oxoguanine adduct in the duplex DNA was investigated by high-resolution NMR. The results suggested that AOVP reacts at the N2 amine in guanine and at the N1 or N2 amines in 8-oxoguanine in the duplex DNA. This study demonstrated the first direct determination of the adduct structure in duplex DNA without enzyme digestion.
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Affiliation(s)
- Shuhei Kusano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
| | - Shogo Ishiyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Tsukasa Mashima
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Kengo Miyamoto
- Department of Chemistry, Graduate School of Science, Hiroshima University,1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Misako Aida
- Department of Chemistry, Graduate School of Science, Hiroshima University,1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
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25
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Li M, Diao L, Liao X, Kou L, Lu W. DFT study on addition reaction mechanism of guanine-cytosine base pair with OH radical. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Minjie Li
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Ling Diao
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Xiaofei Liao
- School of Information Science and Technology; Donghua University; Shanghai 201620 China
| | - Li Kou
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Wencong Lu
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
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26
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Abstract
The uridin-2'-yl radical (1) has been proposed as an intermediate during RNA oxidation. However, its reactivity has not been thoroughly studied due to the complex conditions under which it is typically generated. The uridin-2'-yl radical was independently generated from a benzyl ketone (2a) via Norrish type I photocleavage upon irradiation at λmax = 350 nm. Dioxygen and β-mercaptoethanol are unable to compete with loss of uracil from 1 in phosphate buffer. Thiol trapping competes with uracil fragmentation in less polar solvent conditions. This is ascribed mostly to a reduction in the rate constant for uracil elimination in the less polar solvent. Hydrogen atom transfer to 1 from β-mercaptoethanol occurs exclusively from the α-face to produce arabinouridine. Mass balances range from 72 to 95%. Furthermore, the synthesis of 2a is amenable to formation of the requisite phosphoramidite for solid-phase oligonucleotide synthesis. This and the fidelity with which the urdin-2'-yl radical is generated from 2a suggest that this precursor should be useful for studying the radical's reactivity in synthetic oligonucleotides.
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Affiliation(s)
- Rakesh Paul
- Department of Chemistry, Johns
Hopkins University 3400
North Charles Street, Baltimore, Maryland 21218, United
States
| | - Marc M. Greenberg
- Department of Chemistry, Johns
Hopkins University 3400
North Charles Street, Baltimore, Maryland 21218, United
States
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27
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Madugundu GS, Cadet J, Wagner JR. Hydroxyl-radical-induced oxidation of 5-methylcytosine in isolated and cellular DNA. Nucleic Acids Res 2014; 42:7450-60. [PMID: 24852253 PMCID: PMC4066766 DOI: 10.1093/nar/gku334] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The methylation and oxidative demethylation of cytosine in CpG dinucleotides plays a critical role in the regulation of genes during cell differentiation, embryogenesis and carcinogenesis. Despite its low abundance, 5-methylcytosine (5mC) is a hotspot for mutations in mammalian cells. Here, we measured five oxidation products of 5mC together with the analogous products of cytosine and thymine in DNA exposed to ionizing radiation in oxygenated aqueous solution. The products can be divided into those that arise from hydroxyl radical (•OH) addition at the 5,6-double bond of 5mC (glycol, hydantoin and imidazolidine products) and those that arise from H-atom abstraction from the methyl group of 5mC including 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC). Based on the analysis of these products, we show that the total damage at 5mC is about 2-fold greater than that at C in identical sequences. The formation of hydantoin products of 5mC is favored, compared to analogous reactions of thymine and cytosine, which favor the formation of glycol products. The distribution of oxidation products is sequence dependent in specific ODN duplexes. In the case of 5mC, the formation of 5hmC and 5fC represents about half of the total of •OH-induced oxidation products of 5mC. Several products of thymine, cytosine, 5mC, as well as 8-oxo-7,8-dihydroguanine (8oxoG), were also estimated in irradiated cells.
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Affiliation(s)
- Guru S Madugundu
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada Institut Nanosciences & Cryogénie/DSM, CEA/Grenoble, 38054 Grenoble, France
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
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28
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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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