1
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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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Yokoyama K, Li D, Pang H. Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems. ACS BIO & MED CHEM AU 2022; 2:94-108. [PMID: 35480226 PMCID: PMC9026282 DOI: 10.1021/acsbiomedchemau.1c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 01/31/2023]
Abstract
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MoaA is one of the
most conserved radical S-adenosyl-l-methionine
(SAM) enzymes, and is found in most organisms in
all three kingdoms of life. MoaA contributes to the biosynthesis of
molybdenum cofactor (Moco), a redox enzyme cofactor used in various
enzymes such as purine and sulfur catabolism in humans and anaerobic
respiration in bacteria. Unlike many other cofactors, in most organisms,
Moco cannot be taken up as a nutrient and requires de novo biosynthesis.
Consequently, Moco biosynthesis has been linked to several human health
problems, such as human Moco deficiency disease and bacterial infections.
Despite
the medical and biological significance, the biosynthetic mechanism
of Moco’s characteristic pyranopterin structure remained elusive
for more than two decades. This transformation requires the actions
of the MoaA radical SAM enzyme and another protein, MoaC. Recently,
MoaA and MoaC functions were elucidated as a radical SAM GTP 3′,8-cyclase
and cyclic pyranopterin monophosphate (cPMP) synthase, respectively.
This finding resolved the key mystery in the field and revealed new
opportunities in studying the enzymology and chemical biology of MoaA
and MoaC to elucidate novel mechanisms in enzyme catalysis or to address
unsolved questions in Moco-related human health problems. Here, we
summarize the recent progress in the functional and mechanistic studies
of MoaA and MoaC and discuss the field’s future directions.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Di Li
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Haoran Pang
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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3
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Pang H, Lilla EA, Zhang P, Zhang D, Shields TP, Scott LG, Yang W, Yokoyama K. Mechanism of Rate Acceleration of Radical C-C Bond Formation Reaction by a Radical SAM GTP 3',8-Cyclase. J Am Chem Soc 2020; 142:9314-9326. [PMID: 32348669 DOI: 10.1021/jacs.0c01200] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
While the number of characterized radical S-adenosyl-l-methionine (SAM) enzymes is increasing, the roles of these enzymes in radical catalysis remain largely ambiguous. In radical SAM enzymes, the slow radical initiation step kinetically masks the subsequent steps, making it impossible to study the kinetics of radical chemistry. Due to this kinetic masking, it is unknown whether the subsequent radical reactions require rate acceleration by the enzyme active site. Here, we report the first evidence that a radical SAM enzyme MoaA accelerates the radical-mediated C-C bond formation. MoaA catalyzes an unprecedented 3',8-cyclization of GTP into 3',8-cyclo-7,8-dihydro-GTP (3',8-cH2GTP) during the molybdenum cofactor (Moco) biosynthesis. Through a series of EPR and biochemical characterizations, we found that MoaA catalyzes a shunt pathway in which an on-pathway intermediate, GTP C-3' radical, abstracts H-4' atom from (4'R)-5'-deoxyadenosine (5'-dA) to transiently generate 5'-deoxyadenos-4'-yl radical (5'-dA-C4'•) that is subsequently reduced stereospecifically to yield (4'S)-5'-dA. Detailed kinetic characterization of the shunt and the main pathways provided the comprehensive view of MoaA kinetics and determined the rate of the on-pathway 3',8-cyclization step as 2.7 ± 0.7 s-1. Together with DFT calculations, this observation suggested that the 3',8-cyclization by MoaA is accelerated by 6-9 orders of magnitude. Further experimental and theoretical characterizations suggested that the rate acceleration is achieved mainly by constraining the triphosphate and guanine base positions while leaving the ribose flexible, and a transition state stabilization through H-bond and electrostatic interactions with the positively charged R17 residue. This is the first evidence for rate acceleration of radical reactions by a radical SAM enzyme and provides insights into the mechanism by which radical SAM enzymes accelerate radical chemistry.
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Affiliation(s)
- Haoran Pang
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Edward A Lilla
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Du Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Thomas P Shields
- Cassia, LLC, 3030 Bunker Hill Street, Suite 214, San Diego, California 92109, United States
| | - Lincoln G Scott
- Cassia, LLC, 3030 Bunker Hill Street, Suite 214, San Diego, California 92109, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
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4
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Bedi MF, Li W, Gutwald T, Bryant-Friedrich AC. Synthesis of damaged DNA containing the oxidative lesion 3'-oxothymidine. Bioorg Med Chem 2017; 25:5598-5602. [PMID: 28927804 DOI: 10.1016/j.bmc.2017.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/16/2022]
Abstract
Oxidative events that take place during regular oxygen metabolism can lead to the formation of organic or inorganic radicals. The interaction of these radicals with macromolecules in the organism and with DNA in particular is suspected to lead to apoptosis, DNA lesions and cell damage. Independent generation of DNA lesions resulting from oxidative damage is used to promote the study of their effects on biological systems. An efficient synthesis of oligodeoxyribonucleotides (ODNs) containing the oxidative damage lesion 3'-oxothymidine has been accomplished via incorporation of C3'-hydroxymethyl thymidine as its corresponding 5'-phosphoramidite. Through oxidative cleavage using sodium periodate in aqueous solution, the lesion of interest is easily generated. Due to its inherent instability it cannot be directly isolated, but must be generated in situ. 3'-Oxothymidine is a demonstrated damage product formed upon generation of the C3'-thymidinyl radical in ODN.
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Affiliation(s)
- Mel F Bedi
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801 W. Bancroft St., Toledo, OH, United States
| | - Weiye Li
- Department of Medicinal Chemistry and Pharmacognosy, The University of Illinois Chicago, 1601 Parkview Ave. Rm A301, Rockford, IL 61107, United States
| | - Taylor Gutwald
- Chicago College of Pharmacy, Midwestern University, Chicago, 555 31st Street, Downers Grove, IL 60515, United States
| | - Amanda C Bryant-Friedrich
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801 W. Bancroft St., Toledo, OH, United States.
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5
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Wang P, Amato NJ, Wang Y. Cytotoxic and Mutagenic Properties of C3'-Epimeric Lesions of 2'-Deoxyribonucleosides in Escherichia coli Cells. Biochemistry 2017. [PMID: 28650656 DOI: 10.1021/acs.biochem.7b00146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactive oxygen species (ROS), resulting from endogenous metabolism and/or environmental exposure, can induce damage to the 2-deoxyribose moiety in DNA. Specifically, a hydrogen atom from each of the five carbon atoms in 2-deoxyribose can be abstracted by hydroxyl radical, and improper chemical repair of the ensuing radicals formed at the C1', C3', and C4' positions can lead to the stereochemical inversion at these sites to yield epimeric 2-deoxyribose lesions. Although ROS-induced single-nucleobase lesions have been well studied, the biological consequences of the C3'-epimeric lesions of 2'-deoxynucleosides, i.e., 2'-deoxyxylonucleosides (dxN), have not been comprehensively investigated. Herein, we assessed the impact of dxN lesions on the efficiency and fidelity of DNA replication in Escherichia coli cells by conducting a competitive replication and adduct bypass assay with single-stranded M13 phage containing a site-specifically incorporated dxN. Our results revealed that, of the four dxN lesions, only dxG constituted a strong impediment to DNA replication, and intriguingly, dxT and dxC conferred replication bypass efficiencies higher than those of the unmodified counterparts. In addition, the three SOS-induced DNA polymerases (Pol II, Pol IV, and Pol V) did not play any appreciable role in bypassing these lesions. Among the four dxNs, only dxA directed a moderate frequency of dCMP misincorporation. These results provided important insights into the impact of the C3'-epimeric lesions on DNA replication in E. coli cells.
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Affiliation(s)
- Pengcheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Nicholas J Amato
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
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6
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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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7
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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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8
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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
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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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9
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Amato NJ, Bryant-Friedrich AC. The impact of structure on oxidatively generated DNA damage products resulting from the C3'-thymidinyl radical. Chembiochem 2012; 14:187-90. [PMID: 23280951 DOI: 10.1002/cbic.201200723] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Indexed: 11/05/2022]
Abstract
What's the damage? Trapping the C3'-thymidinyl radical in biologically significant architectures delivers both the repaired oligomer and 1-(2'-deoxy-β-D-threo-pentofuranosyl)thymidine-containing substrates. The stereoselectivity of the reduction was found to be dependent upon the DNA structure.
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Affiliation(s)
- Nicholas J Amato
- Department of Chemistry, The University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606-3390, USA
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10
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Al-Oudat B, Salyer A, Trabbic K, Bryant-Friedrich A. 3'-Modified oligodeoxyribonucleotides for the study of 2-deoxyribose damage in DNA. Bioorg Med Chem Lett 2012; 23:854-9. [PMID: 23265876 DOI: 10.1016/j.bmcl.2012.11.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/09/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
Abstract
Well-defined substrates for the study of oxidative processes are important for the elucidation of the role of DNA damage in the etiology of diseases such as cancer. We have synthesized 3'-modified oligodeoxyribonucleotides (ODNs) using 5'→3' 'reverse' DNA synthesis for the study of 2-deoxyribose oxidative damage to DNA. The modified monomers designed for these studies all share a common feature, they lack the naturally occurring 3'-hydroxyl group found in 2-deoxyribonucleosides. Modified H-phosphonates containing 3'-phenyl selenides as well as saturated and unsaturated sugars were obtained and incorporated in ODNs. These ODNs were used to investigate the fate of C3'-dideoxyribonucleotide radicals in DNA.
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Affiliation(s)
- Buthina Al-Oudat
- Department of Medicinal Chemistry and Pharmacognosy, Jordan University of Science and Technology, Irbid 22110, Jordan
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11
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Belostotskii AM, Genizi E, Hassner A. Essential reactive intermediates in nucleoside chemistry: cyclonucleoside cations. Org Biomol Chem 2012; 10:6624-8. [PMID: 22805739 DOI: 10.1039/c2ob25868d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DFT-based modeling as well as experimental examination of model keto nucleosides have revealed that high susceptibility of these compounds to acids is due to formation of intermediate cyclonucleoside cations of low energy. Theoretically established chemical structures of these previously overlooked intermediates explain the reaction courses for a cluster of nucleoside reactions.
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12
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Audat SAS, Love CT, Al-Oudat BAS, Bryant-Friedrich AC. Synthesis of C3' modified nucleosides for selective generation of the C3'-deoxy-3'-thymidinyl radical: a proposed intermediate in LEE induced DNA damage. J Org Chem 2012; 77:3829-37. [PMID: 22468713 DOI: 10.1021/jo300045m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA damage pathways induced by low-energy electrons (LEEs) are believed to involve the formation of 2-deoxyribose radicals. These radicals, formed at the C3' and C5' positions of nucleotides, are the result of cleavage of the C-O phosphodiester bond through transfer of LEEs to the phosphate group of DNA oligomers from the nucleobases. A considerable amount of information has been obtained to illuminate the identity of the unmodified oligonucleotide products formed through this process. There exists, however, a paucity of information as to the nature of the modified lesions formed from degradation of these sugar radicals. To determine the identity of the damage products formed via the 2',3'-dideoxy-C3'-thymidinyl radical (C3'(dephos) sugar radical), phenyl selenide and acyl modified sugar and nucleoside derivatives have been synthesized, and their suitability as photochemical precursors of the radical of interest has been evaluated. Upon photochemical activation of C3'-derivatized nucleosides in the presence of the hydrogen atom donor tributyltin hydride, 2',3'-dideoxythymidine is formed indicating the selective generation of the C3'(dephos) sugar radical. These precursors will make the identification and quantification of products of DNA damage derived from radicals generated by LEEs possible.
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Affiliation(s)
- Suaad A S Audat
- Department of Medicinal and Biological Chemistry, The University of Toledo, 2801 W. Bancroft Street, Toledo, Ohio 43606, USA
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13
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Zaidi R, Bryant-Friedrich AC. The effect of reductant levels on the formation of damage lesions derived from a 2-deoxyribose radical in ssDNA. Radiat Res 2012; 177:565-72. [PMID: 22463681 DOI: 10.1667/rr2733.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Thiols play a major role in the outcome of oxidative damage to DNA when it is initiated through cellular exposure to ionizing radiation. DNA radicals formed under aerobic conditions are converted to peroxyl radicals through trapping by oxygen at a diffusion-controlled rate. As a primary source of cellular reductant, thiols are responsible for the conversion of these DNA-derived peroxyl radicals to their corresponding hydrogen peroxides and subsequent strand breaks. Through the use of modified nucleotides, which act as precursors to nucleic acid radicals, we have investigated the effect of varying amounts of the cellular thiol glutathione (GSH) on the distribution of damage products produced from a 2-deoxyribose radical in DNA: the C3'-thymidinyl radical. The C3'-thymidinyl radical results from the abstraction of a hydrogen atom from the C3'-position of DNA oligomers at a thymidine residue, and is known to deliver several DNA damage lesions including the 3'-phosphoglycolaldehyde, 3'-phosphoglycolate and a 5'-aldehyde. Here we show that the level of GSH present has an impact on the level of production of these C3'-thymidinyl radical derived damage products.
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Affiliation(s)
- Rehana Zaidi
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4401, USA
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14
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Chan W, Chen B, Wang L, Taghizadeh K, Demott MS, Dedon PC. Quantification of the 2-deoxyribonolactone and nucleoside 5'-aldehyde products of 2-deoxyribose oxidation in DNA and cells by isotope-dilution gas chromatography mass spectrometry: differential effects of gamma-radiation and Fe2+-EDTA. J Am Chem Soc 2010; 132:6145-53. [PMID: 20377226 DOI: 10.1021/ja910928n] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The oxidation of 2-deoxyribose in DNA has emerged as a critical determinant of the cellular toxicity of oxidative damage to DNA, with oxidation of each carbon producing a unique spectrum of electrophilic products. We have developed and validated an isotope-dilution gas chromatography-coupled mass spectrometry (GC-MS) method for the rigorous quantification of two major 2-deoxyribose oxidation products: the 2-deoxyribonolactone abasic site of 1'-oxidation and the nucleoside 5'-aldehyde of 5'-oxidation chemistry. The method entails elimination of these products as 5-methylene-2(5H)-furanone (5MF) and furfural, respectively, followed by derivatization with pentafluorophenylhydrazine (PFPH), addition of isotopically labeled PFPH derivatives as internal standards, extraction of the derivatives, and quantification by GC-MS analysis. The precision and accuracy of the method were validated with oligodeoxynucleotides containing the 2-deoxyribonolactone and nucleoside 5'-aldehyde lesions. Further, the well-defined 2-deoxyribose oxidation chemistry of the enediyne antibiotics, neocarzinostatin and calicheamicin gamma(1)(I), was exploited in control studies, with neocarzinostatin producing 10 2-deoxyribonolactone and 300 nucleoside 5'-aldehyde per 10(6) nt per microM in accord with its established minor 1'- and major 5'-oxidation chemistry. Calicheamicin unexpectedly caused 1'-oxidation at a low level of 10 2-deoxyribonolactone per 10(6) nt per microM in addition to the expected predominance of 5'-oxidation at 560 nucleoside 5'-aldehyde per 10(6) nt per microM. The two hydroxyl radical-mediated DNA oxidants, gamma-radiation and Fe(2+)-EDTA, produced nucleoside 5'-aldehyde at a frequency of 57 per 10(6) nt per Gy (G-value 74 nmol/J) and 3.5 per 10(6) nt per microM, respectively, which amounted to 40% and 35%, respectively, of total 2-deoxyribose oxidation as measured by a plasmid nicking assay. However, gamma-radiation and Fe(2+)-EDTA produced different proportions of 2-deoxyribonolactone at 7% and 24% of total 2-deoxyribose oxidation, respectively, with frequencies of 10 lesions per 10(6) nt per Gy (G-value, 13 nmol/J) and 2.4 lesions per 10(6) nt per microM. Studies in TK6 human lymphoblastoid cells, in which the analytical data were corrected for losses sustained during DNA isolation, revealed background levels of 2-deoxyribonolactone and nucleoside 5'-aldehyde of 9.7 and 73 lesions per 10(6) nt, respectively. Gamma-irradiation of the cells caused increases of 0.045 and 0.22 lesions per 10(6) nt per Gy, respectively, which represents a approximately 250-fold quenching effect of the cellular environment similar to that observed in previous studies. The proportions of the various 2-deoxyribose oxidation products generated by gamma-radiation are similar for purified DNA and cells. These results are consistent with solvent exposure as a major determinant of hydroxyl radical reactivity with 2-deoxyribose in DNA, but the large differences between gamma-radiation and Fe(2+)-EDTA suggest that factors other than hydroxyl radical reactivity govern DNA oxidation chemistry.
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Affiliation(s)
- Wan Chan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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15
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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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16
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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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17
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Affiliation(s)
- Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, NE47-277, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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18
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Lahoud GA, Hitt AL, Bryant-Friedrich AC. Aerobic fate of the C-3'-thymidinyl radical in single-stranded DNA. Chem Res Toxicol 2007; 19:1630-6. [PMID: 17173376 DOI: 10.1021/tx060174f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxidative events that target the sugar-phosphate backbone of DNA can lead to reactive fragments that interfere with DNA repair, transcription and translation by the formation of cross-links and adducts of proteins and nucleobases. Here we report the formation of several such lesions through the aerobic degradation of an independently generated C-3'-thymidinyl radical in 2'-deoxyoligonucleotides. Individual fragments were identified by independent synthesis and comparison of retention times in high-performance liquid chromatography (HPLC) and/or matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) along with gel electrophoresis. The formation of this reactive intermediate in the presence of oxygen was found to produce 3'-phosphoglycolaldehyde (3'-PGA) as well as 3'-ketoenolether (3'-KEE), 3'-phosphoglycolate (3'-PG), and 5'-aldehyde terminated oligonucleotide fragments. Additionally, a significant outcome of C-3'-thymidinyl radical formation in DNA oligomers is a strand break resulting in one 3'- and two 5'-phosphate-terminated oligomers. These results suggest the involvement of several sugar derived reactive species upon C-3'-radical initiated scission of single-stranded DNA under aerobic conditions. The electrophilic nature of several of these products as well as their formation through a single oxidative event can make the presence of a C-3'-DNA radical more detrimental to the cell than products derived from more frequently occurring DNA sugar radicals.
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Affiliation(s)
- Georges A Lahoud
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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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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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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