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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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Biswas PK, Chakraborty S. Targeted DNA oxidation and trajectory of radical DNA using DFT based QM/MM dynamics. Nucleic Acids Res 2019; 47:2757-2765. [PMID: 30773597 PMCID: PMC6451130 DOI: 10.1093/nar/gkz089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/27/2019] [Accepted: 02/04/2019] [Indexed: 01/06/2023] Open
Abstract
Molecular insight into electronic rearrangements and structural trajectories arising from oxidative damages to DNA backbone is of crucial importance in understanding the effect of ionizing radiation, developing DNA biosensors and designing effective DNA cleaving molecules. Employing a Density Functional Theory based multi-scale Quantum-Mechanical-Molecular-Mechanical (QM/MM) simulation and a suitable partitioning of the Hamiltonian on solvated nucleotide, and single-, and double-stranded DNA, we mimic hydrogen transfer reactions from the backbone by OH radicals and report structural trajectories arising from on-the-fly electronic charge- and spin-density redistribution in these three different structural topologies of DNA. Trajectories reveal that H4′ abstraction can disrupt the deoxyribose moiety through the formation of C4′=O4′ ketone and a π-bond with base at C1′-N9 in a nucleotide versus only partial ketone formation in single- and double-stranded DNA, where the orientation of the base is topologically restrained. However, H5′ abstraction can lead DNA cleavage at 5′ end through the formation of C5′=O5′ ketone and breakage of P-O5′ bond. Results demonstrate that structural damages from oxidative reactions are restrained by base stacking and base-pair hydrogen bonding. The methodology can be suitably used to study targeted DNA and RNA damages from radicals and radiomimetic drugs to design DNA cleaving molecules for chemotherapy.
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Affiliation(s)
- Pradip K Biswas
- Laboratory of Computational Biophysics and Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174, USA
| | - Sandipan Chakraborty
- Laboratory of Computational Biophysics and Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174, USA
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3
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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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4
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Amato NJ, Zhai Q, Navarro DC, Niedernhofer LJ, Wang Y. In vivo detection and replication studies of α-anomeric lesions of 2'-deoxyribonucleosides. Nucleic Acids Res 2015. [PMID: 26202973 PMCID: PMC4787794 DOI: 10.1093/nar/gkv725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA damage, arising from endogenous metabolism or exposure to environmental agents, may perturb the transmission of genetic information by blocking DNA replication and/or inducing mutations, which contribute to the development of cancer and likely other human diseases. Hydroxyl radical attack on the C1′, C3′ and C4′ of 2-deoxyribose can give rise to epimeric 2-deoxyribose lesions, for which the in vivo occurrence and biological consequences remain largely unexplored. Through independent chemical syntheses of all three epimeric lesions of 2′-deoxyguanosine (dG) and liquid chromatography-tandem mass spectrometry analysis, we demonstrated unambiguously the presence of substantial levels of the α-anomer of dG (α-dG) in calf thymus DNA and in DNA isolated from mouse pancreatic tissues. We further assessed quantitatively the impact of all four α-dN lesions on DNA replication in Escherichia coli by employing a shuttle-vector method. We found that, without SOS induction, all α-dN lesions except α-dA strongly blocked DNA replication and, while replication across α-dA was error-free, replicative bypass of α-dC and α-dG yielded mainly C→A and G→A mutations. In addition, SOS induction could lead to markedly elevated bypass efficiencies for the four α-dN lesions, abolished the G→A mutation for α-dG, pronouncedly reduced the C→A mutation for α-dC and triggered T→A mutation for α-dT. The preferential misincorporation of dTMP opposite the α-dNs could be attributed to the unique base-pairing properties of the nucleobases elicited by the inversion of the configuration of the N-glycosidic linkage. Our results also revealed that Pol V played a major role in bypassing α-dC, α-dG and α-dT in vivo. The abundance of α-dG in mammalian tissue and the impact of the α-dNs on DNA replication demonstrate for the first time the biological significance of this family of DNA lesions.
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Affiliation(s)
- Nicholas J Amato
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Qianqian Zhai
- Department of Chemistry, University of California, Riverside, CA 92521, USA Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Diana C Navarro
- Department of Metabolism and Aging, The Scripps Research Institute Florida, FL 33458, USA
| | - Laura J Niedernhofer
- Department of Metabolism and Aging, The Scripps Research Institute Florida, FL 33458, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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5
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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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6
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Synthesis of 4′-C-Ethynyl-β-D-ribo-pentofuranosyl Pyrimidines. Biosci Biotechnol Biochem 2014; 63:736-42. [DOI: 10.1271/bbb.63.736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Amato NJ, Wang Y. Epimeric 2-deoxyribose lesions: Products from the improper chemical repair of 2-deoxyribose radicals. Chem Res Toxicol 2014; 27:470-9. [PMID: 24517165 PMCID: PMC4002128 DOI: 10.1021/tx400430g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Genomic
integrity is constantly challenged by DNA damaging agents
such as reactive oxygen species (ROS). Consequently, DNA damage can
compromise the fidelity and efficiency of essential DNA metabolic
processes, including replication and transcription, which may contribute
significantly to the etiology of many human diseases. Here, we review
one family of DNA lesions, the epimeric 2-deoxyribose lesions, which
arise from the improper chemical repair of the 2-deoxyribose radicals.
Unlike most other DNA lesions, the epimeric 2-deoxyribose lesions
are indistinguishable from their corresponding unmodified nucleosides
in both molecular mass and chemical reactivity. We placed our emphasis
of discussion on the formation of these lesions, their impact on the
structure and stability of duplex DNA, their biological consequences,
their potential therapeutic relevance, and future research directions
about these modified nucleosides.
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Affiliation(s)
- Nicholas J Amato
- Department of Chemistry, University of California , 900 University Avenue, Riverside, California 92521, United States
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8
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Bartoli G, Marcantoni E, Marcolini M, Sambri L. Applications of CeCl(3) as an environmental friendly promoter in organic chemistry. Chem Rev 2011; 110:6104-43. [PMID: 20731375 DOI: 10.1021/cr100084g] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Giuseppe Bartoli
- Department of Organic Chemistry A. Mangini, University of Bologna, viale Risorgimento 4, I-40156 Bologna, Italy
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9
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Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
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10
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Fate of DNA Sugar Radicals. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1872-0854(10)04004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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11
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Huang H, Greenberg MM. Synthesis and analysis of oligonucleotides containing abasic site analogues. J Org Chem 2008; 73:2695-703. [PMID: 18324835 DOI: 10.1021/jo702614p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.
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Affiliation(s)
- Haidong Huang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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12
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Chowdhury G, Junnotula V, Daniels JS, Greenberg MM, Gates KS. DNA strand damage product analysis provides evidence that the tumor cell-specific cytotoxin tirapazamine produces hydroxyl radical and acts as a surrogate for O(2). J Am Chem Soc 2007; 129:12870-7. [PMID: 17900117 PMCID: PMC2821206 DOI: 10.1021/ja074432m] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The compound 3-amino-1,2,4-benzotriazine 1,4-dioxide (tirapazamine, TPZ) is a clinically promising anticancer agent that selectively kills the oxygen-poor (hypoxic) cells found in solid tumors. It has long been known that, under hypoxic conditions, TPZ causes DNA strand damage that is initiated by the abstraction of hydrogen atoms from the deoxyribose phosphate backbone of duplex DNA, but exact chemical mechanisms underlying this process remain unclear. Here we describe detailed characterization of sugar-derived products arising from TPZ-mediated strand damage. We find that the action of TPZ on duplex DNA under hypoxic conditions generates 5-methylene-2-furanone (6), oligonucleotide 3'-phosphoglycolates (7), malondialdehyde equivalents (8 or 9), and furfural (10). These results provide evidence that TPZ-mediated strand damage arises via hydrogen atom abstraction from both the most hindered (C1') and least hindered (C4' and C5') positions of the deoxyribose sugars in the double helix. The products observed are identical to those produced by hydroxyl radical. Additional experiments were conducted to better understand the chemical pathways by which TPZ generates the observed DNA-damage products. Consistent with previous work showing that TPZ can substitute for molecular oxygen in DNA damage reactions, it is found that, under anaerobic conditions, reaction of TPZ with a discrete, photogenerated C1'-radical in a DNA 2'-oligodeoxynucleotide cleanly generates the 2-deoxyribonolactone lesion (5) that serves as the precursor to 5-methylene-2-furanone (6). Overall, the results provide insight regarding the chemical structure of the DNA lesions that confront cellular repair, transcription, and replication machinery following exposure to TPZ and offer new information relevant to the chemical mechanisms underlying TPZ-mediated strand cleavage.
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Affiliation(s)
- Goutam Chowdhury
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Venkatraman Junnotula
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - J. Scott Daniels
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Marc M. Greenberg
- Johns Hopkins University Department of Chemistry 3400 N. Charles St. Baltimore, MD 21218
| | - Kent S. Gates
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
- To whom correspondence should be addressed: ; phone: (573) 882-6763; FAX: (573) 882-2754
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13
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Greenberg MM. Elucidating DNA damage and repair processes by independently generating reactive and metastable intermediates. Org Biomol Chem 2006; 5:18-30. [PMID: 17164902 DOI: 10.1039/b612729k] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA damage is a double-edged sword. The modifications produced in the biopolymer are associated with aging, and give rise to a variety of diseases, including cancer. DNA is also the target of anti-tumor agents and the most generally used nonsurgical treatment of cancer, ionizing radiation. Agents that damage DNA produce a variety of radicals. Elucidating the chemistry of individual DNA radicals is challenging due to the availability of multiple reactive pathways and complexities inherent with carrying out mechanistic studies on a heterogeneous polymer. The ability to independently generate radicals and their metastable products at defined sites in DNA has greatly facilitated understanding this biologically important chemistry.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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14
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15
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Lahoud G, Fancher J, Grosu S, Cavanaugh B, Bryant-Friedrich A. Automated synthesis, characterization, and structural analysis of oligonucleotide C-3'-radical precursors. Bioorg Med Chem 2005; 14:2581-8. [PMID: 16338139 DOI: 10.1016/j.bmc.2005.11.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Revised: 11/19/2005] [Accepted: 11/21/2005] [Indexed: 11/16/2022]
Abstract
C-3'-Acyl-3'-xylothymidine-containing oligonucleotides have been designed and synthesized for their use as radical precursors in the study of oxidative DNA damage initiated by a C-3'-radical. These oligomers were efficiently obtained using automated DNA synthesis techniques based on H-phosphonate chemistry. CD spectra and melting curves of the synthesized oligonucleotides were compared to those of their unmodified and xylomodified counterparts. The conformational analysis and hybridization studies indicate that the combination of the photolabile acyl group and the inversion of configuration at the sugar has no profound effect on the overall conformation of C-3'-acyl-2'-deoxy-3'-xylonucleotides as compared to their natural analogues. These systems should provide excellent tools for the elucidation of DNA damage processes.
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Affiliation(s)
- Georges Lahoud
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
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16
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Zhang Q, Wang Y. Independent generation of the 5-hydroxy-5,6-dihydrothymidin-6-yl radical and its reactivity in dinucleoside monophosphates. J Am Chem Soc 2005; 126:13287-97. [PMID: 15479083 DOI: 10.1021/ja048492t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxyl radical is a major reactive oxygen species produced by gamma-radiolysis of water or Fenton reaction. It attacks pyrimidine bases and gives the 5-hydroxy-5,6-dihydropyrimidin-6-yl radical as the major product. Here we report the synthesis of all four stereoisomers of 5-hydroxy-6-phenylthio-5,6-dihydrothymidine (T*), which, upon 254 nm UV irradiation, give rise to the 5-hydroxy-5,6-dihydrothymidin-6-yl radical (I). We also incorporated the photolabile radical precursors into dinucleoside monophosphates d(GT*) and d(TT*) and characterized major products resulting from the 254-nm irradiation of these dinucleoside monophosphates. Our results showed that, under anaerobic conditions, the most abundant product emanating from the 254-nm irradiation of d(GT*) and d(TT*) is an abasic site lesion. Products with the thymine portion being modified to thymine glycol and 5-hydroxy-5,6-dihydrothymine were also observed. In addition, we demonstrated that radical I can attack the C8 carbon atom of its 5' neighboring guanine and give rise to a novel cross-link lesion. Moreover, LC-MS/MS results showed that gamma-radiation of d(GT) under anaerobic condition yielded the same type of cross-link lesions.
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Affiliation(s)
- Qibin Zhang
- Department of Chemistry-027, University of California at Riverside, Riverside, California 92521-0403, USA
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17
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Bryant-Friedrich AC. Generation of a C-3'-thymidinyl radical in single-stranded oligonucleotides under anaerobic conditions. Org Lett 2005; 6:2329-32. [PMID: 15228271 DOI: 10.1021/ol0493453] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A C-3'-thymidinyl radical has been photochemically generated site-specifically in DNA oligonucleotides. A nucleoside H-phosphonate bearing a C-3' acetyl group was incorporated into DNA oligomers using a hand-coupling technique. When nucleotides containing the modified monomer were photolyzed (> or =320 nm) in the presence of a hydrogen atom donor, reduction products were detected by RP-HPLC and MALDI-ToF MS analysis.
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18
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Kim J, Weledji YN, Greenberg MM. Independent generation and characterization of a C2'-oxidized abasic site in chemically synthesized oligonucleotides. J Org Chem 2004; 69:6100-4. [PMID: 15373495 DOI: 10.1021/jo049033d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abasic lesions, which are formed endogenously and as a consequence of exogenous agents, are lethal and mutagenic. Hydrogen atom abstraction from C2' in DNA under aerobic conditions produces an oxidized abasic lesion (C2-AP), along with other forms of DNA damage. The effects of C2-AP on DNA structure and function are not well understood. A method for the solid-phase synthesis of oligonucleotides containing C2-AP lesions is reported. The lesion is released via periodate oxidation of a triol containing a vicinal diol. The triol is introduced via a phosphoramidite that is compatible with standard oligonucleotide synthesis and deprotection conditions. UV-melting studies indicate that the C2-AP lesion has a comparable effect on the thermal stability of duplex DNA as other abasic lesions. The C2-AP lesion is rapidly cleaved by piperidine at 90 degrees C. However, cleavage by NaOH (0.1 M, 37 degrees C) shows that C2-AP is considerably less labile (t(1/2) = 3.3 +/- 0.2 h) than other abasic lesions.
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Affiliation(s)
- Jaeseung Kim
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA
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19
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Greenberg MM, Weledji YN, Kim J, Bales BC. Repair of oxidized abasic sites by exonuclease III, endonuclease IV, and endonuclease III. Biochemistry 2004; 43:8178-83. [PMID: 15209514 DOI: 10.1021/bi0496236] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Deoxyribonolactone (L) and the C4'-oxidized abasic site (C4-AP) are produced by a variety of DNA-damaging agents. If not repaired, these lesions can be mutagenic. Exonuclease III and endonuclease IV are the major enzymes in E. coli responsible for 5'-incision of abasic sites (APs), the first steps in AP repair. Endonuclease III efficiently excises AP lesions via intermediate Schiff-base formation. Incision of L and C4-AP lesions by exonuclease III and endonuclease IV was determined under steady-state conditions using oligonucleotide duplexes containing the lesions at defined sites. An abasic lesion (AP) in an otherwise identical DNA sequence was incised by exonuclease III or endonuclease IV approximately 6-fold more efficiently than either of the oxidized abasic sites (L, C4-AP). Endonuclease IV incision efficiency of 2-deoxyribonolactone or C4-AP was independent of whether the lesion was opposite dA or dG. 2-Deoxyribonolactone is known to cross-link to endonuclease III (Hashimoto, M. (2001) J. Am. Chem. Soc. 123, 3161.). However, the C4-AP lesion is efficiently excised by endonuclease III. Oxidized abasic site repair by endonuclease IV and endonuclease III (C4-AP only) is approximately 100-fold less efficient than repair by exonuclease III. These results suggest that the first step of C4-AP and L oxidized abasic site repair will be the same as that of regular AP lesions in E. coli.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA.
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20
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Kroeger KM, Jiang YL, Kow YW, Goodman MF, Greenberg MM. Mutagenic effects of 2-deoxyribonolactone in Escherichia coli. An abasic lesion that disobeys the A-rule. Biochemistry 2004; 43:6723-33. [PMID: 15157106 DOI: 10.1021/bi049813g] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Abasic sites are often referred to as noninstructive lesions. The C1'-oxidized abasic site (2-deoxyribonolactone, L) is produced by several DNA damaging agents, including gamma-radiolysis and the neocarzinostatin chromophore (NCS). The effects of a C1'-oxidized abasic site incorporated at a defined site in single-stranded plasmid were examined in SOS polymerase-proficient and -deficient Escherichia coli. For comparison, experiments utilizing plasmids containing an abasic site (AP) were carried out side by side. In contrast to plasmid containing AP, dA and dG were incorporated most often when plasmid containing L was replicated. The ratio of dG:dA incorporation depended upon local sequence and varied from 0.9 to 2.2. High levels of translesion incorporation of dA are consistent with previous observations that treatment of DNA with the neocarzinostatin chromophore resulted in large amounts of G.C --> A.T transitions [Povirk and Goldberg (1986) Nucleic Acids Res. 14, 1417] and support the proposal that L is the source of these mutations. Both abasic lesions were 100% lethal in triple knockout cells lacking pol II, pol IV, and pol V. Analysis of translesion synthesis in repair-deficient cells revealed that pol V played a significant role in replication of L and AP. Significant levels of -1 frameshifts were formed in 5'-d(CL) sequences in the presence of pol V and were the exclusive product in pol V-deficient cells. Frameshift products were not formed when the nucleotide on the 5'-side of L was either dT or dG. Deleting pol II or pol IV had only modest effects on replication of L-containing plasmid but significantly decreased the amount of -1 frameshift product formed from an AP lesion. Experiments carried out side by side using otherwise identical plasmids containing an AP site illustrate the distinct properties of these two abasic lesions and that neither should be thought of as noninstructive.
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Affiliation(s)
- Kelly M Kroeger
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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21
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Vivekananda S, Sadílek M, Chen X, Adams LE, Turecek F. Modeling deoxyribose radicals by neutralization-reionization mass spectrometry. Part 2. Preparation, dissociations, and energetics of 3-hydroxyoxolan-3-yl radical and cation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1068-1079. [PMID: 15234365 DOI: 10.1016/j.jasms.2004.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 03/29/2004] [Accepted: 03/29/2004] [Indexed: 05/24/2023]
Abstract
The title radical (1) is generated in the gas-phase by collisional neutralization of carbonyl-protonated oxolan-3-one. A 1.5% fraction of 1 does not dissociate and is detected following reionization as survivor ions. The major dissociation of 1 (approximately 56%) occurs as loss of the hydroxyl H atom forming oxolan-3-one (2). The competing ring cleavages by O[bond]C-2 and C-4[bond]C-5 bond dissociations combined account for approximately 42% of dissociation and result in the formation of formaldehyde and 2-hydroxyallyl radical. Additional ring-cleavage dissociations of 1 resulting in the formation of C(2)H(3)O and C(2)H(4)O cannot be explained as occurring competitively on the doublet ground (X) electronic state of 1, but are energetically accessible from the A and higher electronic states accessed by vertical electron transfer. Exothermic protonation of 2 also produces 3-oxo-(1H)-oxolanium cation (3(+)) which upon collisional neutralization gives hypervalent 3-oxo-(1H)-oxolanium radical (3). The latter dissociates spontaneously by ring opening and expulsion of hydroxy radical. Experiment and calculations suggest that carbohydrate radicals incorporating the 3-hydroxyoxolan-3-yl motif will prefer ring-cleavage dissociations at low internal energies or upon photoexcitation by absorbing light at approximately 590 and approximately 400 nm.
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22
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Greenberg MM, Weledji YN, Kroeger KM, Kim J, Goodman MF. In vitro effects of a C4'-oxidized abasic site on DNA polymerases. Biochemistry 2004; 43:2656-63. [PMID: 14992603 DOI: 10.1021/bi036028f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxidative damage to DNA produces abasic sites resulting from the formal hydrolysis of the nucleotides' glycosidic bonds, along with a variety of oxidized abasic sites. The C4'-oxidized abasic site (C4-AP) is produced by several DNA-damaging agents. This lesion accounts for approximately 40% of the DNA damage produced by bleomycin. The effect of a C4'-oxidized abasic site incorporated at a defined site in a template was examined on Klenow fragments with and without 3' --> 5' exonuclease activity. Both enzymes preferentially incorporated dA > dG >> dC, T opposite C4-AP. Neither enzyme is able to extend the primer past the lesion. Experiments with regular AP sites in an otherwise identical template indicate that Klenow does not differentiate between these two disparate abasic sites. Extension of the primer by alternative polymerases pol II, pol II exo(-), pol IV, and pol V was examined. Pol II exo(-) was most efficient. Qualitative translesion synthesis experiments showed that pol II exo(-) preferentially incorporates T opposite C4-AP, followed in order by dG, dA, and dC. Thymidine incorporation opposite C4'-AP is distinct from the pol II exonuclease interaction with a regular AP site in an otherwise identical template. These in vitro experiments suggest that bypass polymerases may play a crucial role in survival of cells in which C4-AP is produced, and unlike a typical AP site, the C4-AP lesion may not follow the "A-rule". The interaction between bypass polymerases and a C4-AP lesion could explain the high levels of G:C --> T:A transversions in cells treated with bleomycin.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA.
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23
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Kumamoto H, Murasaki M, Haraguchi K, Anamura A, Tanaka H. Nucleophilic addition of benzenethiol to 1',2'-unsaturated nucleosides: 1'-C-phenylthio-2'-deoxynucleosides as anomeric radical precursors. J Org Chem 2002; 67:6124-30. [PMID: 12182652 DOI: 10.1021/jo0201934] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The addition reaction of benzenethiol to the glycal portion of 1',2'-unsaturated uridine proceeds efficiently in the presence of Et(3)N. The mechanism involves nucleophilic attack of thiolate at the anomeric position in the rate-determining step, wherein conjugation between the nucleobase and the glycal portion is crucial. The derivative having a methyl group either at the 2'- or 6-position did not undergo this addition reaction, due to their sterically prohibited coplanarity. The 1',2'-unsaturated derivatives of thymine and adenine can also be used as substrates for this addition reaction. It was also shown that the resulting 1'-C-phenylthio-2'-deoxynucleosides serve as precursors for radical-mediated C-C bond formation at the anomeric position.
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Affiliation(s)
- Hiroki Kumamoto
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan.
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24
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Roupioz Y, Lhomme J, Kotera M. Chemistry of the 2-deoxyribonolactone lesion in oligonucleotides: cleavage kinetics and products analysis. J Am Chem Soc 2002; 124:9129-35. [PMID: 12149017 DOI: 10.1021/ja025688p] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deoxyribonolactone in DNA is an oxidized abasic site damage that is produced by a variety of physical and chemical agents such as gamma-irradiation and ene-diyne antibiotics. The extent and biological significance of the lesion are poorly documented due to the high lability of the damaged DNA. The chemistry of degradation of deoxyribonolactone-containing DNA was investigated using oligonucleotides of different length (5-, 11-, 23-, 34-mers) in which the lactone was photochemically generated, as already reported, from oligonucleotide precursors containing a photoactive nitroindole residue. The procedure was successfully extended to double-strand synthesis by irradiation of the preformed duplex in which one strand contained the nitroindole residue. The degradation kinetics were investigated as a function of pH, temperature, length, and ionic strength. The cleavage fragments resulting from beta- and delta-eliminations were isolated and identified by (1)H NMR. It was found that the lesion is extremely sensitive to pH and temperature while slightly dependent upon ionic strength, length, and sequence. The cleavage rates for the beta- and delta-elimination steps are of the same order of magnitude. The deoxyribonolactone site leads to greater instability of DNA than the "regular" deoxyribose abasic site.
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Affiliation(s)
- Yoann Roupioz
- Chimie Bioorganique, L.E.D.S.S., Associé au CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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25
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Lenox HJ, McCoy CP, Sheppard TL. Site-specific generation of deoxyribonolactone lesions in DNA oligonucleotides. Org Lett 2001; 3:2415-8. [PMID: 11463330 DOI: 10.1021/ol016255e] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] An efficient method for the site-specific generation of 2-deoxyribonolactone oxidative DNA damage lesions from a "photocaged" nucleoside analogue was developed. A nucleoside phosphoramidite bearing a C-1' nitrobenzyl cyanohydrin was prepared and incorporated into DNA oligonucleotides using automated DNA synthesis. The caged analogue, which was stable in aqueous solution, was converted to the 2-deoxyribonolactone lesion by UV irradiation. DNA containing the caged analogue and the deoxyribonolactone site were characterized by electrospray mass spectrometry (ES-MS).
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Affiliation(s)
- H J Lenox
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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26
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Tallman KA, Greenberg MM. Oxygen-dependent DNA damage amplification involving 5,6-dihydrothymidin-5-yl in a structurally minimal system. J Am Chem Soc 2001; 123:5181-7. [PMID: 11457379 DOI: 10.1021/ja010180s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5,6-Dihydrothymidin-5-yl (1) was independently generated in a dinucleotide from a phenyl selenide precursor (4). Under free radical chain propagation conditions, the products resulting from hydrogen atom donation and radical-pair reaction are the major observed products in the absence of O(2). The stereoselectivity of the trapping process is dependent on the structure of the hydrogen atom donor. No evidence for internucleotidyl hydrogen atom abstraction by 1 was detected. The tandem lesion (17) resulting from hydrogen atom abstraction from the C1' position of the adjacent 2'-deoxyuridine by the peroxyl radical derived from 1 (3) is observed under aerobic conditions. The structure of this product is confirmed by independent synthesis and its transformation into a second independently synthesized product (24). Internucleotidyl hydrogen atom abstraction is effected selectively by the 5S-diastereomer of the peroxyl radical. The formation of dinucleotide 17 provides further support for the novel O(2)-dependent DNA damage amplification mechanism involving 1 reported previously (Greenberg, M. M.; et al. J. Am. Chem. Soc. 1997, 119, 1828).
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Affiliation(s)
- K A Tallman
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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27
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Praly JP. Structure of anomeric glycosyl radicals and their transformations under reductive conditions. Adv Carbohydr Chem Biochem 2001; 56:65-151. [PMID: 11039110 DOI: 10.1016/s0065-2318(01)56003-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- J P Praly
- Unité Mixte de Recherche CNRS-Université Claude-Bernard no. 5622, ESCPE-Lyon, Villeurbanne, France
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28
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Kotera M, Roupioz Y, Defrancq E, Bourdat AG, Garcia J, Coulombeau C, Lhomme J. The 7-nitroindole nucleoside as a photochemical precursor of 2'-deoxyribonolactone: access to DNA fragments containing this oxidative abasic lesion. Chemistry 2000; 6:4163-9. [PMID: 11128280 DOI: 10.1002/1521-3765(20001117)6:22<4163::aid-chem4163>3.0.co;2-k] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
On the basis of molecular modeling studies, the 7-nitroindole nucleoside 1 was selected as a suitable photochemical precursor for photochemical generation of the C1' deoxyribosyl radical under irradiation, which led to 2'-deoxyribonolactone. The nitro-indole nucleoside derivatives 1a and 1b were prepared and their conformation was determined by X-ray crystallography and NMR spectroscopy. The photoreaction of these nucleosides gave the corresponding deoxyribonolactone derivatives efficiently, with release of 7-nitrosoindole. This reaction was successfully applied to synthesis of oligonucleotides containing the deoxyribonolactone lesion.
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Affiliation(s)
- M Kotera
- LEDSS, Chimie Bioorganique, UMR CNRS 5616, Université Joseph Fourier, Grenoble, France.
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29
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Chatgilialoglu C, Ferreri C, Bazzanini R, Guerra M, Choi SY, Emanuel CJ, Horner JH, Newcomb M. Models of DNA C1‘ Radicals. Structural, Spectral, and Chemical Properties of the Thyminylmethyl Radical and the 2‘-Deoxyuridin-1‘-yl Radical. J Am Chem Soc 2000. [DOI: 10.1021/ja001783r] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chryssostomos Chatgilialoglu
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Carla Ferreri
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Rita Bazzanini
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Maurizio Guerra
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Seung-Yong Choi
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Calvin J. Emanuel
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - John H. Horner
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Martin Newcomb
- Contribution from the I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy, Dipartimento di Chimica Organica e Biologica, Università di Napoli “Federico II”, Via Mezzocannone 16, I-80134 Napoli, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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30
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Anderson AS, Hwang JT, Greenberg MM. Independent generation and reactivity of 2-deoxy-5-methyleneuridin-5-yl, a significant reactive intermediate produced from thymidine as a result of oxidative stress. J Org Chem 2000; 65:4648-54. [PMID: 10959870 DOI: 10.1021/jo000271s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2'-Deoxy-5-methyleneuridin-5-yl (1) is produced in a variety of DNA damage processes and is believed to result in the formation of lesions that are mutagenic and refractory to enzymatic repair. 2'-Deoxy-5-methyleneuridin-5-yl (1) was independently generated under anaerobic conditions via Norrish Type I photocleavage during Pyrex filtered photolysis of the benzyl ketone 7. The radical (1) exhibits behavior consistent with that of a resonance-stabilized radical. The KIE for hydrogen atom transfer from t-BuSH was found to be 7.3 +/- 1.7. Competition studies between radical recombination and hydrogen atom donors (2,5-dimethyltetrahydrofuran, kTrap = 46.1 +/- 15.4 M(-1) s(-1); propan-2-ol, kTrap = 13.6 +/- 3.5 M(-1) s(-1)) chosen to mimic the carbohydrate components of 2'-deoxyribonucleotides suggest that 2'-deoxy-5-methyleneuridin-5-yl (1) may be able to transfer damage from the nucleobase to the deoxyribose of an adjacent nucleotide in DNA under hypoxic conditions.
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Affiliation(s)
- A S Anderson
- Department of Chemistry, Colorado State University Fort Collins, 80523, USA
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31
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Synthesis of a 1′-α-phenylselenouridine derivative as a synthetic precursor for various 1′-modified nucleosides, via enolization at the 1′-position of 3′,5′-O-TIPDS-2′-ketouridine. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)00432-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Chattopadhyay A, Dhotare B, Hassarajani S. (R)-2,3-Cyclohexylideneglyceraldehyde: A Potential Intermediate for Convenient Synthesis of 2-C-Branched 2-Deoxypentofuranoses. J Org Chem 1999; 64:6874-6878. [PMID: 11674698 DOI: 10.1021/jo982130k] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Chattopadhyay
- Bio-organic Division, Bhabha Atomic Research Centre, Mumbai 400085, India
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33
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Kittaka A, Asakura T, Kuze T, Tanaka H, Yamada N, Nakamura KT, Miyasaka T. Cyclization Reactions of Nucleoside Anomeric Radical with Olefin Tethered on Base: Factors That Induce Anomeric Stereochemistry. J Org Chem 1999. [DOI: 10.1021/jo990611d] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Atsushi Kittaka
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Takashi Asakura
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Tetsuya Kuze
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Hiromichi Tanaka
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Naoki Yamada
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Kazuo T. Nakamura
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Tadashi Miyasaka
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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34
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Hwang JT, Greenberg MM. Kinetics and Stereoselectivity of Thiol Trapping of Deoxyuridin-1‘-yl in Biopolymers and Their Relationship to the Formation of Premutagenic α-Deoxynucleotides. J Am Chem Soc 1999. [DOI: 10.1021/ja990152y] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae-Taeg Hwang
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Marc M. Greenberg
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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35
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Kittaka A, Kato H, Tanaka H, Nonaka Y, Amano M, Nakamura KT, Miyasaka T. Face selective 6,1′-(1-oxo)ethano bridge formation of uracil nucleosides under hypoiodite reaction conditions. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00232-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Emanuel CJ, Newcomb M, Ferreri C, Chatgilialoglu C. Kinetics of 2‘-Deoxyuridin-1‘-yl Radical Reactions. J Am Chem Soc 1999. [DOI: 10.1021/ja9839872] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Calvin J. Emanuel
- Department of Chemistry, Wayne State University Detroit, Michigan 48202 Dipartimento di Chimica Organica e Biologica Università di Napoli “Federico II” Via Mezzocannone 16, I-80134 Napoli, Italy I.Co.C.E.A., Consiglio Nazionale delle Ricerche Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Martin Newcomb
- Department of Chemistry, Wayne State University Detroit, Michigan 48202 Dipartimento di Chimica Organica e Biologica Università di Napoli “Federico II” Via Mezzocannone 16, I-80134 Napoli, Italy I.Co.C.E.A., Consiglio Nazionale delle Ricerche Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Carla Ferreri
- Department of Chemistry, Wayne State University Detroit, Michigan 48202 Dipartimento di Chimica Organica e Biologica Università di Napoli “Federico II” Via Mezzocannone 16, I-80134 Napoli, Italy I.Co.C.E.A., Consiglio Nazionale delle Ricerche Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Department of Chemistry, Wayne State University Detroit, Michigan 48202 Dipartimento di Chimica Organica e Biologica Università di Napoli “Federico II” Via Mezzocannone 16, I-80134 Napoli, Italy I.Co.C.E.A., Consiglio Nazionale delle Ricerche Via P. Gobetti 101, I-40129 Bologna, Italy
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37
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Daniels JS, Gates KS, Tronche C, Greenberg MM. Direct evidence for bimodal DNA damage induced by tirapazamine. Chem Res Toxicol 1998; 11:1254-7. [PMID: 9815184 DOI: 10.1021/tx980184j] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability of tirapazamine (1, 3-amino-1,2,4-benzotriazine 1, 4-dioxide, SR4233) to fix DNA radical lesions is demonstrated by studying the reaction between the antitumor drug and an oligonucleotide radical that is independently produced at a defined site within a biopolymer. Using beta-mercaptoethanol as a competitor, it was determined that tirapazamine traps a C1'-nucleotide radical with a rate constant of approximately 2 x 10(8) M-1 s-1. Product and isotopic labeling studies suggest that tirapazamine reacts with the radical via covalent adduct formation, resulting primarily from reaction at the N-oxide oxygen. Intermediate covalent adducts could not be observed, but are postulated to decompose to the alkaline labile 2'-deoxyribonolactone lesion. These experiments affirm recent proposals suggesting that tirapazamine can serve as a surrogate for O2 in converting DNA radicals into toxic strand damage events.
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Affiliation(s)
- J S Daniels
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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38
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39
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Pogozelski WK, Tullius TD. Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety. Chem Rev 1998; 98:1089-1108. [PMID: 11848926 DOI: 10.1021/cr960437i] [Citation(s) in RCA: 841] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wendy Knapp Pogozelski
- Department of Chemistry, State University of New York at Geneseo, Geneseo, New York 14454, and Department of Chemistry, Boston University, Boston, Massachusetts 02215
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40
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DNA damage induced via independent generation of the radical resulting from formal hydrogen atom abstraction from the C1′-position of a nucleotide. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1074-5521(98)90619-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Ossipov D, Chattopadhyaya J. Synthesis of 1′-phenazine-tethered psicofuranosyl oligonucleotides: The thermal stability and fluorescence properties of their duplexes and triplexes. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(98)00237-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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42
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Tallman KA, Tronche C, Yoo DJ, Greenberg MM. Release of Superoxide from Nucleoside Peroxyl Radicals, a Double-Edged Sword? J Am Chem Soc 1998. [DOI: 10.1021/ja973200s] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Keri A. Tallman
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Christopher Tronche
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Dong Jin Yoo
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Marc M. Greenberg
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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43
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Gimisis T, Ialongo G, Chatgilialoglu C. Generation of C-1′ radicals through a β-(acyloxy)alkyl rearrangement in modified purine and pyrimidine nucleosides. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(97)10317-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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44
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Beckwith ALJ, Crich D, Duggan PJ, Yao Q. Chemistry of beta-(Acyloxy)alkyl and beta-(Phosphatoxy)alkyl Radicals and Related Species: Radical and Radical Ionic Migrations and Fragmentations of Carbonminus signOxygen Bonds. Chem Rev 1997; 97:3273-3312. [PMID: 11851491 DOI: 10.1021/cr950207o] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Athelstan L. J. Beckwith
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia, Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, and Department of Chemistry, Monash University, Clayton, Victoria 3168, Australia
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Greenberg MM, Barvian MR, Cook GP, Goodman BK, Matray TJ, Tronche C, Venkatesan H. DNA Damage Induced via 5,6-Dihydrothymid-5-yl in Single-Stranded Oligonucleotides. J Am Chem Soc 1997. [DOI: 10.1021/ja9533510] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
The peroxy radical (ROO) is unique among reactive oxygen species implicated in the production of DNA damage in that it possesses an extremely long half-life (order of seconds) and is predicted to have a relatively greater chemical selectivity in its reactions relative to other radical intermediates. Yet no product studies of the reactions of ROO with bases, nucleosides, or DNA have appeared, and thus no meaningful predictions can be made regarding its potential involvement in the production of DNA base damage and the mutagenic process. We report here on the reaction products formed by peroxy radical with thymidine, major target of oxidative base damage. ROO reacts with thymine to yield predominantly 5-Me oxidation products. The highly mutagenic 5-(hydroperoxymethyl)-2'-deoxyuridine, 5-formyl-2'-deoxyuridine, and 5-(hydroxymethyl)-2'-deoxyuridine are produced by peroxy radical oxidation. In contrast, 5Me oxidation products are minor products of thymidine oxidation by OH, which yields predominantly saturated derivatives via addition to the 5,6 double bound. A plausible mechanistic scheme for the formation of the base oxidation products of thymidine by peroxy radicals is presented. Attach at the deoxyribose moiety resulting in oxidative depyrimidination is also found to occur, as indicated by free base release. Phosphodiester backbone cleavage resulting in single and double strand breaks is also catalyzed by peroxy radical, as demonstrated using a plasmid nicking assay.
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Affiliation(s)
- M Martini
- Department of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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Greenberg MM, Yoo DJ, Goodman BK. C1′ Acylated Derivatives of 2′-Deoxyuridine. Photolabile Precursors of 2′-Deoxyuridin-1′-yl. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708002519] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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