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Abstract
The eukaryotic global genomic nucleotide excision repair (GG-NER) pathway is the major mechanism that removes most bulky and some nonbulky lesions from cellular DNA. There is growing evidence that certain DNA lesions are repaired slowly or are entirely resistant to repair in cells, tissues, and in cell extract model assay systems. It is well established that the eukaryotic DNA lesion-sensing proteins do not detect the damaged nucleotide, but recognize the distortions/destabilizations in the native DNA structure caused by the damaged nucleotides. In this article, the nature of the structural features of certain bulky DNA lesions that render them resistant to NER, or cause them to be repaired slowly, is compared to that of those that are good-to-excellent NER substrates. Understanding the structural features that distinguish NER-resistant DNA lesions from good NER substrates may be useful for interpreting the biological significance of biomarkers of exposure of human populations to genotoxic environmental chemicals. NER-resistant lesions can survive to replication and cause mutations that can initiate cancer and other diseases. Furthermore, NER diminishes the efficacy of certain chemotherapeutic drugs, and the design of more potent pharmaceuticals that resist repair can be advanced through a better understanding of the structural properties of DNA lesions that engender repair-resistance.
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Affiliation(s)
- Nicholas E. Geacintov
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| | - Suse Broyde
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
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Toxicology of DNA Adducts Formed Upon Human Exposure to Carcinogens. ADVANCES IN MOLECULAR TOXICOLOGY 2016. [DOI: 10.1016/b978-0-12-804700-2.00007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Kowal EA, Wickramaratne S, Kotapati S, Turo M, Tretyakova N, Stone MP. Major groove orientation of the (2S)-N(6)-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA adduct induced by 1,2-epoxy-3-butene. Chem Res Toxicol 2014; 27:1675-86. [PMID: 25238403 PMCID: PMC4203389 DOI: 10.1021/tx500159w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 02/08/2023]
Abstract
1,3-Butadiene (BD) is an environmental and occupational toxicant classified as a human carcinogen. It is oxidized by cytochrome P450 monooxygenases to 1,2-epoxy-3-butene (EB), which alkylates DNA. BD exposures lead to large numbers of mutations at A:T base pairs even though alkylation of guanines is more prevalent, suggesting that one or more adenine adducts of BD play a role in BD-mediated genotoxicity. However, the etiology of BD-mediated genotoxicity at adenine remains poorly understood. EB alkylates the N(6) exocyclic nitrogen of adenine to form N(6)-(hydroxy-3-buten-1-yl)-2'-dA ((2S)-N(6)-HB-dA) adducts ( Tretyakova , N. , Lin , Y. , Sangaiah , R. , Upton , P. B. , and Swenberg , J. A. ( 1997 ) Carcinogenesis 18 , 137 - 147 ). The structure of the (2S)-N(6)-HB-dA adduct has been determined in the 5'-d(C(1)G(2)G(3)A(4)C(5)Y(6)A(7)G(8)A(9)A(10)G(11))-3':5'-d(C(12)T(13)T(14)C(15)T(16)T(17)G(18)T(19) C(20)C(21)G(22))-3' duplex [Y = (2S)-N(6)-HB-dA] containing codon 61 (underlined) of the human N-ras protooncogene, from NMR spectroscopy. The (2S)-N(6)-HB-dA adduct was positioned in the major groove, such that the butadiene moiety was oriented in the 3' direction. At the Cα carbon, the methylene protons of the modified nucleobase Y(6) faced the 5' direction, which placed the Cβ carbon in the 3' direction. The Cβ hydroxyl group faced toward the solvent, as did carbons Cγ and Cδ. The Cβ hydroxyl group did not form hydrogen bonds with either T(16) O(4) or T(17) O(4). The (2S)-N(6)-HB-dA nucleoside maintained the anti conformation about the glycosyl bond, and the modified base retained Watson-Crick base pairing with the complementary base (T(17)). The adduct perturbed stacking interactions at base pairs C(5):G(18), Y(6):T(17), and A(7):T(16) such that the Y(6) base did not stack with its 5' neighbor C(5), but it did with its 3' neighbor A(7). The complementary thymine T(17) stacked well with both 5' and 3' neighbors T(16) and G(18). The presence of the (2S)-N(6)-HB-dA resulted in a 5 °C reduction in the Tm of the duplex, which is attributed to less favorable stacking interactions and adduct accommodation in the major groove.
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Affiliation(s)
- Ewa A. Kowal
- Department
of Chemistry, Center in Molecular Toxicology, Vanderbilt Ingram Cancer
Center, and Center for Structural Biology, Vanderbilt University, 2201 West End Avenue, Nashville, Tennessee 37235, United States
| | - Susith Wickramaratne
- Department
of Medicinal Chemistry, Masonic Cancer Center, and Department of Chemistry, University of Minnesota, Minneapolis Minnesota 55455, United States
| | - Srikanth Kotapati
- Department
of Medicinal Chemistry, Masonic Cancer Center, and Department of Chemistry, University of Minnesota, Minneapolis Minnesota 55455, United States
| | - Michael Turo
- Department
of Chemistry, Center in Molecular Toxicology, Vanderbilt Ingram Cancer
Center, and Center for Structural Biology, Vanderbilt University, 2201 West End Avenue, Nashville, Tennessee 37235, United States
| | - Natalia Tretyakova
- Department
of Medicinal Chemistry, Masonic Cancer Center, and Department of Chemistry, University of Minnesota, Minneapolis Minnesota 55455, United States
| | - Michael P. Stone
- Department
of Chemistry, Center in Molecular Toxicology, Vanderbilt Ingram Cancer
Center, and Center for Structural Biology, Vanderbilt University, 2201 West End Avenue, Nashville, Tennessee 37235, United States
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Kowal EA, Seneviratne U, Wickramaratne S, Doherty KE, Cao X, Tretyakova N, Stone MP. Structures of exocyclic R,R- and S,S-N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine adducts induced by 1,2,3,4-diepoxybutane. Chem Res Toxicol 2014; 27:805-17. [PMID: 24741991 PMCID: PMC4027948 DOI: 10.1021/tx400472p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
1,3-Butadiene (BD) is an industrial and environmental chemical present in urban air and cigarette smoke, and is classified as a human carcinogen. It is oxidized by cytochrome P450 to form 1,2,3,4-diepoxybutane (DEB); DEB bis-alkylates the N(6) position of adenine in DNA. Two enantiomers of bis-N(6)-dA adducts of DEB have been identified: R,R-N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine (R,R-DHB-dA), and S,S-N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine (S,S-DHB-dA) [ Seneviratne , U. , Antsypovich , S. , Dorr , D. Q. , Dissanayake , T. , Kotapati , S. , and Tretyakova , N. ( 2010 ) Chem. Res. Toxicol. 23 , 1556 -1567 ]. Herein, the R,R-DHB-dA and S,S-DHB-dA adducts have been incorporated into the 5'-d(C(1)G(2)G(3)A(4)C(5)X(6)A(7)G(8)A(9)A(10)G(11))-3':5'-d(C(12)T(13)T(14)C(15)T(16)T(17)G(18)T(19)C(20)C(21)G(22))-3' duplex [X(6) = R,R-DHB-dA (R(6)) or S,S-DHB-dA (S(6))]. The structures of the duplexes were determined by molecular dynamics calculations, which were restrained by experimental distances obtained from NMR data. Both the R,R- and S,S-DHB-dA adducts are positioned in the major groove of DNA. In both instances, the bulky 3,4-dihydroxypyrrolidine rings are accommodated by an out-of-plane rotation about the C6-N(6) bond of the bis-alkylated adenine. In both instances, the directionality of the dihydroxypyrrolidine ring is evidenced by the pattern of NOEs between the 3,4-dihydroxypyrrolidine protons and DNA. Also in both instances, the anti conformation of the glycosyl bond is maintained, which combined with the out-of-plane rotation about the C6-N(6) bond, allows the complementary thymine, T(17), to remain stacked within the duplex, and form one hydrogen bond with the modified base, between the imine nitrogen of the modified base and the T(17) N3H imino proton. The loss of the second Watson-Crick hydrogen bonding interaction at the lesion sites correlates with the lower thermal stabilities of the R,R- and S,S-DHB-dA duplexes, as compared to the corresponding unmodified duplex. The reduced base stacking at the adduct sites may also contribute to the thermal instability.
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Affiliation(s)
- Ewa A Kowal
- Department of Chemistry, Center in Molecular Toxicology, and Center for Structural Biology, Stevenson Science Center, Vanderbilt University , 2201 West End Avenue, Nashville, Tennessee 37235, United States
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Kuska MS, Witham AA, Sproviero M, Manderville RA, Majdi Yazdi M, Sharma P, Wetmore SD. Structural Influence of C8-Phenoxy-Guanine in the NarI Recognition DNA Sequence. Chem Res Toxicol 2013; 26:1397-408. [DOI: 10.1021/tx400252g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Michael S. Kuska
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Aaron A. Witham
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Michael Sproviero
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Mohadeseh Majdi Yazdi
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Purshotam Sharma
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
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Stone MP, Huang H, Brown KL, Shanmugam G. Chemistry and structural biology of DNA damage and biological consequences. Chem Biodivers 2011; 8:1571-615. [PMID: 21922653 PMCID: PMC3714022 DOI: 10.1002/cbdv.201100033] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The formation of adducts by the reaction of chemicals with DNA is a critical step for the initiation of carcinogenesis. The structural analysis of various DNA adducts reveals that conformational and chemical rearrangements and interconversions are a common theme. Conformational changes are modulated both by the nature of adduct and the base sequences neighboring the lesion sites. Equilibria between conformational states may modulate both DNA repair and error-prone replication past these adducts. Likewise, chemical rearrangements of initially formed DNA adducts are also modulated both by the nature of adducts and the base sequences neighboring the lesion sites. In this review, we focus on DNA damage caused by a number of environmental and endogenous agents, and biological consequences.
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Affiliation(s)
- Michael P Stone
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37235, USA.
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Satterwhite JE, Pugh AM, Danell AS, Hvastkovs EG. Electrochemical detection of anti-benzo[a]pyrene diol epoxide DNA damage on TP53 codon 273 oligomers. Anal Chem 2011; 83:3327-35. [PMID: 21428456 DOI: 10.1021/ac103091v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA damage from (+/-)-anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE) at a hotspot TP53 gene sequence was electrochemically detected. BPDE was exposed to gold electrode immobilized double-stranded DNA oligomers followed by voltammetric measurements in the presence of redox-active C(12)H(25)V(2+)C(6)H(12)V(2+)C(12)H(25) (V(2+) = 4,4'-bipyridyl or viologen, C12-viologen). Square wave voltammograms from BPDE-exposed DNA-modified electrodes showed the emergence of a C12-viologen-DNA complex at -0.37 V versus Ag/AgCl. The peak current intensity of this redox wave was dependent on both BPDE concentration and exposure time. Controls with alternate xenobiotics and DNA sequences showed this redox wave to be primarily due to BPDE damage at the wild-type DNA sequence. The detection limit was determined to be approximately 170 nM BPDE. Mass spectrometry and UV thermal melting experiments provided insight into the BPDE reaction and mirrored the sensor results. This report demonstrates that an electrochemical hybridization sensor can be used to detect sequence-related xenobiotic DNA damage.
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Affiliation(s)
- Jennifer E Satterwhite
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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El Ashry ESH, Nadeem S, Shah MR, Kilany YE. Recent Advances in the Dimroth Rearrangement. ADVANCES IN HETEROCYCLIC CHEMISTRY 2010. [DOI: 10.1016/s0065-2725(10)01005-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Delaney JC, Essigmann JM. Biological properties of single chemical-DNA adducts: a twenty year perspective. Chem Res Toxicol 2008; 21:232-52. [PMID: 18072751 PMCID: PMC2821157 DOI: 10.1021/tx700292a] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The genome and its nucleotide precursor pool are under sustained attack by radiation, reactive oxygen and nitrogen species, chemical carcinogens, hydrolytic reactions, and certain drugs. As a result, a large and heterogeneous population of damaged nucleotides forms in all cells. Some of the lesions are repaired, but for those that remain, there can be serious biological consequences. For example, lesions that form in DNA can lead to altered gene expression, mutation, and death. This perspective examines systems developed over the past 20 years to study the biological properties of single DNA lesions.
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Affiliation(s)
- James C. Delaney
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - John M. Essigmann
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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Affiliation(s)
- Mark Lukin
- Department of Pharmacological Sciences, State University of New York at Stony Brook, School of Medicine, 11794-8651, USA
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Merritt WK, Nechev LV, Scholdberg TA, Dean SM, Kiehna SE, Chang JC, Harris TM, Harris CM, Lloyd RS, Stone MP. Structure of the 1,4-bis(2'-deoxyadenosin-N6-yl)-2R,3R-butanediol cross-link arising from alkylation of the human N-ras codon 61 by butadiene diepoxide. Biochemistry 2005; 44:10081-92. [PMID: 16042385 PMCID: PMC2585418 DOI: 10.1021/bi047263g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The solution structure of the 1,4-bis(2'-deoxyadenosin-N(6)-yl)-2R,3R-butanediol cross-link arising from N(6)-dA alkylation of nearest-neighbor adenines by butadiene diepoxide (BDO(2)) was determined in the oligodeoxynucleotide 5'-d(CGGACXYGAAG)-3'.5'-d(CTTCTTGTCCG)-3'. This oligodeoxynucleotide contained codon 61 (underlined) of the human N-ras protooncogene. The cross-link was accommodated in the major groove of duplex DNA. At the 5'-side of the cross-link there was a break in Watson-Crick base pairing at base pair X(6).T(17), whereas at the 3'-side of the cross-link at base pair Y(7).T(16), base pairing was intact. Molecular dynamics calculations carried out using a simulated annealing protocol, and restrained by a combination of 338 interproton distance restraints obtained from (1)H NOESY data and 151 torsion angle restraints obtained from (1)H and (31)P COSY data, yielded ensembles of structures with good convergence. Helicoidal analysis indicated an increase in base pair opening at base pair X(6).T(17), accompanied by a shift in the phosphodiester backbone torsion angle beta P5'-O5'-C5'-C4' at nucleotide X(6). The rMD calculations predicted that the DNA helix was not significantly bent by the presence of the four-carbon cross-link. This was corroborated by gel mobility assays of multimers containing nonhydroxylated four-carbon N(6),N(6)-dA cross-links, which did not predict DNA bending. The rMD calculations suggested the presence of hydrogen bonding between the hydroxyl group located on the beta-carbon of the four-carbon cross-link and T(17) O(4), which perhaps stabilized the base pair opening at X(6).T(17) and protected the T(17) imino proton from solvent exchange. The opening of base pair X(6).T(17) altered base stacking patterns at the cross-link site and induced slight unwinding of the DNA duplex. The structural data are interpreted in terms of biochemical data suggesting that this cross-link is bypassed by a variety of DNA polymerases, yet is significantly mutagenic [Kanuri, M., Nechev, L. V., Tamura, P. J., Harris, C. M., Harris, T. M., and Lloyd, R. S. (2002) Chem. Res. Toxicol. 15, 1572-1580].
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Affiliation(s)
- W. Keither Merritt
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | | | | | - Stephen M. Dean
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Sarah E. Kiehna
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Johanna C. Chang
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Thomas M. Harris
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Constance M. Harris
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | | | - Michael P. Stone
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
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Nestmann ER, Lynch BS, Ratpan F. Perspectives on the genotoxic risk of styrene. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2005; 8:95-107. [PMID: 15804750 DOI: 10.1080/10937400590908988] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Styrene is a highly reactive monomer widely used in the plastics industry. The potential for styrene to produce genotoxic effects has been studied extensively in experimental systems. Styrene can induce sister chromatid exchanges (SCE) and chromosome aberrations (CA) in vitro under test conditions that enhance metabolism of styrene to styrene 7,8-oxide (SO)or reduce detoxification of 50 by epoxide hydrolase. The in vivo animal data indicate that styrene is not clastogenic at concentrations (doses) likely encountered by humans under ambient or occupational exposure conditions. DNA binding studies with styrene in rats and mice demonstrated no increased adducts in mice compared to rats or in mouse lung compared to liver. As a result, DNA adducts in the lungs are unlikely to be the sole explanation of the development of lung tumors in mice exposed to styrene for 2 yr. Some epidemiological studies reported that DNA and/or protein adducts and DNA strand breaks result from occupational exposure to styrene and/or 50. Results of some of these studies, how-ever, are difficult to interpret, given that the statistical significance of reported effects (SCE, CA, and micronucleus formation) was often near or at p values of .05; dose and/or temporal response relationships often were missing; confounding variables could not be excluded; and, concomitant exposures to other industrial chemicals that are potentially genotoxic may also have occurred. These studies suggest that styrene, through metabolism to SO, could be clastogenic in humans at workplace levels in excess of 125 mg/m3. However, results from controlled animal studies involving in vivo exposure to styrene alone do not show clastogenic effects at exposures of up to 1500 mg/m3/d. In any event, these studies show that there is an apparent threshold for styrene-mediated effects.
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Affiliation(s)
- E R Nestmann
- CANTOX Health Sciences International, Mississauga, Ontario, Canada.
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