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Halami B, Shahsavari S, Nelson Z, Prehoda L, Eriyagama DNAM, Fang S. Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid Phase Synthesis. ChemistrySelect 2018; 3:8857-8862. [PMID: 30886889 PMCID: PMC6420219 DOI: 10.1002/slct.201801484] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023]
Abstract
Nucleosides containing ester groups that are sensitive to nucleophiles were incorporated into oligodeoxynucleotides (ODNs) through solid phase chemical synthesis. The sensitive esters are located on a purine nucleobase. They are the esters of ethyl, 2-methoxyethyl, 4-methoxyphenyl and phenyl groups, and a thioester. These esters cannot survive the deprotection and cleavage conditions used in known ODN synthesis technologies, which involve strong nucleophiles such as ammonium hydroxide and potassium methoxide (potassium carbonate in anhydrous methanol). To incorporate these sensitive groups into ODNs, the Dmoc phosphoramidites and linker were used for solid phase synthesis, which allowed ODN deprotection and cleavage to be carried out under non-nucleophilic oxidative conditions. Sixteen ODN sequences containing these groups were synthesized and characterized with MALDI MS. In addition, the synthesis and characterization of three ODNs containing a nucleophile sensitive 6-chloropurine using the same strategy are described.
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Affiliation(s)
- Bhaskar Halami
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Shahien Shahsavari
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Zack Nelson
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Lucas Prehoda
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | | | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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Chang SC, Seneviratne UI, Wu J, Tretyakova N, Essigmann JM. 1,3-Butadiene-Induced Adenine DNA Adducts Are Genotoxic but Only Weakly Mutagenic When Replicated in Escherichia coli of Various Repair and Replication Backgrounds. Chem Res Toxicol 2017; 30:1230-1239. [PMID: 28394575 PMCID: PMC5512570 DOI: 10.1021/acs.chemrestox.7b00064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The adverse effects of the human carcinogen 1,3-butadiene (BD) are believed to be mediated by its DNA-reactive metabolites such as 3,4-epoxybut-1-ene (EB) and 1,2,3,4-diepoxybutane (DEB). The specific DNA adducts responsible for toxic and mutagenic effects of BD, however, have yet to be identified. Recent in vitro polymerase bypass studies of BD-induced adenine (BD-dA) adducts show that DEB-induced N6,N6-DHB-dA (DHB = 2,3-dihydroxybutan-1,4-diyl) and 1,N6-γ-HMHP-dA (HMHP = 2-hydroxy-3-hydroxymethylpropan-1,3-diyl) adducts block replicative DNA polymerases but are bypassed by human polymerases η and κ, leading to point mutations and deletions. In contrast, EB-induced N6-HB-dA (HB = 2-hydroxy-3-buten-1-yl) does not block DNA synthesis and is nonmutagenic. In the present study, we employed a newly established in vivo lesion-induced mutagenesis/genotoxicity assay via next-generation sequencing to evaluate the in vivo biological consequences of S-N6-HB-dA, R,R-N6,N6-DHB-dA, S,S-N6,N6-DHB-dA, and R,S-1,N6-γ-HMHP-dA. In addition, the effects of AlkB-mediated direct reversal repair, MutM and MutY catalyzed base excision repair, and DinB translesion synthesis on the BD-dA adducts in bacterial cells were investigated. BD-dA adducts showed the expected inhibition of DNA replication in vivo but were not substantively mutagenic in any of the genetic environments investigated. This result is in contrast with previous in vitro observations and opens the possibility that E. coli repair and bypass systems other than the ones studied here are able to minimize the mutagenic properties of BD-dA adducts.
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Affiliation(s)
- Shiou-chi Chang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Uthpala I. Seneviratne
- Department of Medicinal Chemistry, and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
| | - Jie Wu
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
| | - John M. Essigmann
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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Liu LY, Zheng J, Kong C, An J, Yu YX, Zhang XY, Elfarra AA. Characterization of the Major Purine and Pyrimidine Adducts Formed after Incubations of 1-Chloro-3-buten-2-one with Single-/Double-Stranded DNA and Human Cells. Chem Res Toxicol 2016; 30:552-563. [PMID: 27977153 DOI: 10.1021/acs.chemrestox.6b00282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have previously shown that 1-chloro-3-buten-2-one (CBO), a potential reactive metabolite of 1,3-butadiene (BD), exhibits potent cytotoxicity and genotoxicity that have been attributed in part to its reactivity toward DNA. In an effort to identify the DNA adducts of CBO, we characterized the CBO reactions with 2'-deoxyguanosine (dG), 2'-deoxycytidine (dC), and 2'-deoxyadenosine (dA) under in vitro physiological conditions (pH 7.4, 37 °C). In the present study, we investigated the CBO reaction with 2'-deoxythymidine (dT) and compared the rate constants of the reactions of CBO with dA, dC, dG, and dT at both individual- and mixed-nucleosides levels. We also investigated the reactions of CBO with single- and double-stranded DNA using HPLC with UV detection after adducts were released by either acid or enzymatic hydrolysis of DNA. Consistent with the results from the nucleoside reactions and the rate constant experiments, 1,N6-(1-hydroxy-1-chloromethylpropan-1,3-diyl)adenine (A-2D) was identified as the major DNA adduct detected after acid hydrolysis, followed by N7-(4-chloro-3-oxobutyl)guanine (CG-2H) and a small amount of 1,N6-(1-hydroxy-1-hydroxymethylpropan-1,3-diyl)adenine (A-1D). After enzymatic hydrolysis, 1,N6-(1-hydroxy-1-hydroxymethylpropan-1,3-diyl)-2'-dexoyadenosine (dA-1), 3,N4-(1-hydroxy-1-hydroxymethylpropan-1,3-diyl)-2'-deoxycytidine (dC-1/2), and 1,N2-(3-hydroxy-3-hydroxymethylpropan-1,3-diyl)-2'-dexoyguanosine (CG-1) were detected, with dA-1 being the major product, followed by dC-1/2. When a nontoxic concentration of CBO (1 μM) was incubated with HepG2 cells, no adducts could be detected by LC-MS. However, pretreatment of cells with l-buthionine sulfoximine to deplete GSH levels allowed A-2D to be consistently detected in cellular DNA. These results may contribute to a better understanding of the role of the DNA adducts in CBO genotoxicity and mutagenicity. It also suggests that A-2D could be developed as a biomarker of CBO formation after BD exposure in vivo.
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Affiliation(s)
- Ling-Yan Liu
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University , Shanghai 200444, China
| | - Jin Zheng
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University , Shanghai 200444, China
| | - Cong Kong
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai 200090, China
| | - Jing An
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University , Shanghai 200444, China
| | - Ying-Xin Yu
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University , Shanghai 200444, China
| | - Xin-Yu Zhang
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University , Shanghai 200444, China
| | - Adnan A Elfarra
- Department of Comparative Biosciences and the Molecular and Environmental Toxicology Center, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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Wickramaratne S, Banda DM, Ji S, Manlove AH, Malayappan B, Nuñez NN, Samson L, Campbell C, David SS, Tretyakova N. Base Excision Repair of N 6-Deoxyadenosine Adducts of 1,3-Butadiene. Biochemistry 2016; 55:6070-6081. [PMID: 27552084 DOI: 10.1021/acs.biochem.6b00553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The important industrial and environmental carcinogen 1,3-butadiene (BD) forms a range of adenine adducts in DNA, including N6-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine (N6-HB-dA), 1,N6-(2-hydroxy-3-hydroxymethylpropan-1,3-diyl)-2'-deoxyadenosine (1,N6-HMHP-dA), and N6,N6-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine (N6,N6-DHB-dA). If not removed prior to DNA replication, these lesions can contribute to A → T and A → G mutations commonly observed following exposure to BD and its metabolites. In this study, base excision repair of BD-induced 2'-deoxyadenosine (BD-dA) lesions was investigated. Synthetic DNA duplexes containing site-specific and stereospecific (S)-N6-HB-dA, (R,S)-1,N6-HMHP-dA, and (R,R)-N6,N6-DHB-dA adducts were prepared by a postoligomerization strategy. Incision assays with nuclear extracts from human fibrosarcoma (HT1080) cells have revealed that BD-dA adducts were recognized and cleaved by a BER mechanism, with the relative excision efficiency decreasing in the following order: (S)-N6-HB-dA > (R,R)-N6,N6-DHB-dA > (R,S)-1,N6-HMHP-dA. The extent of strand cleavage at the adduct site was decreased in the presence of BER inhibitor methoxyamine and by competitor duplexes containing known BER substrates. Similar strand cleavage assays conducted using several eukaryotic DNA glycosylases/lyases (AAG, Mutyh, hNEIL1, and hOGG1) have failed to observe correct incision products at the BD-dA lesion sites, suggesting that a different BER enzyme may be involved in the removal of BD-dA adducts in human cells.
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Affiliation(s)
- Susith Wickramaratne
- Masonic Cancer Center and Departments of Chemistry and Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Douglas M Banda
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Shaofei Ji
- Masonic Cancer Center and Departments of Chemistry and Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Bhaskar Malayappan
- Masonic Cancer Center and Departments of Chemistry and Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Nicole N Nuñez
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Leona Samson
- Division of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Sheila S David
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Natalia Tretyakova
- Masonic Cancer Center and Departments of Chemistry and Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
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Kotapati S, Wickramaratne S, Esades A, Boldry EJ, Quirk Dorr D, Pence MG, Guengerich FP, Tretyakova NY. Polymerase Bypass of N(6)-Deoxyadenosine Adducts Derived from Epoxide Metabolites of 1,3-Butadiene. Chem Res Toxicol 2015; 28:1496-507. [PMID: 26098310 DOI: 10.1021/acs.chemrestox.5b00166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
N(6)-(2-Hydroxy-3-buten-1-yl)-2'-deoxyadenosine (N(6)-HB-dA I) and N(6),N(6)-(2,3-dihydroxybutan-1,4-diyl)-2'-deoxyadenosine (N(6),N(6)-DHB-dA) are exocyclic DNA adducts formed upon alkylation of the N(6) position of adenine in DNA by epoxide metabolites of 1,3-butadiene (BD), a common industrial and environmental chemical classified as a human and animal carcinogen. Since the N(6)-H atom of adenine is required for Watson-Crick hydrogen bonding with thymine, N(6)-alkylation can prevent adenine from normal pairing with thymine, potentially compromising the accuracy of DNA replication. To evaluate the ability of BD-derived N(6)-alkyladenine lesions to induce mutations, synthetic oligodeoxynucleotides containing site-specific (S)-N(6)-HB-dA I and (R,R)-N(6),N(6)-DHB-dA adducts were subjected to in vitro translesion synthesis in the presence of human DNA polymerases β, η, ι, and κ. While (S)-N(6)-HB-dA I was readily bypassed by all four enzymes, only polymerases η and κ were able to carry out DNA synthesis past (R,R)-N(6),N(6)-DHB-dA. Steady-state kinetic analyses indicated that all four DNA polymerases preferentially incorporated the correct base (T) opposite (S)-N(6)-HB-dA I. In contrast, hPol β was completely blocked by (R,R)-N(6),N(6)-DHB-dA, while hPol η and κ inserted A, G, C, or T opposite the adduct with similar frequency. HPLC-ESI-MS/MS analysis of primer extension products confirmed that while translesion synthesis past (S)-N(6)-HB-dA I was mostly error-free, replication of DNA containing (R,R)-N(6),N(6)-DHB-dA induced significant numbers of A, C, and G insertions and small deletions. These results indicate that singly substituted (S)-N(6)-HB-dA I lesions are not miscoding, but that exocyclic (R,R)-N(6),N(6)-DHB-dA adducts are strongly mispairing, probably due to their inability to form stable Watson-Crick pairs with dT.
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Affiliation(s)
- Srikanth Kotapati
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Susith Wickramaratne
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Amanda Esades
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Emily J Boldry
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Danae Quirk Dorr
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew G Pence
- ‡Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - F Peter Guengerich
- ‡Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Natalia Y Tretyakova
- †Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Wickramaratne S, Seiler CL, Tretyakova NY. Synthesis of DNA Oligodeoxynucleotides Containing Site-Specific 1,3-Butadiene-Deoxyadenosine Lesions. ACTA ACUST UNITED AC 2015; 61:4.61.1-4.61.22. [PMID: 26344227 DOI: 10.1002/0471142700.nc0461s61] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Post-oligomerization synthesis is a useful technique for preparing site-specifically modified DNA oligomers. This approach involves site-specific incorporation of inherently reactive halogenated nucleobases into DNA strands using standard solid-phase synthesis, followed by post-oligomerization nucleophilic aromatic substitution (SNAr) reactions with carcinogen-derived synthons. In these reactions, the inherent reactivities of DNA and carcinogen-derived species are reversed: the modified DNA nucleobase acts as an electrophile, while the carcinogen-derived species acts as a nucleophile. In the present protocol, we describe the use of the post-oligomerization approach to prepare DNA strands containing site- and stereospecific N6-adenine and N1,N6-adenine adducts induced by epoxide metabolites of the known human and animal carcinogen 1,3-butadiene (BD). The resulting oligomers containing site-specific, structurally defined DNA adducts can be used in structural and biological studies to reveal the roles of specific BD adducts in carcinogenesis and mutagenesis.
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Affiliation(s)
- Susith Wickramaratne
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Christopher L Seiler
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
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7
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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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Petrova KV, Millsap AD, Stec DF, Rizzo CJ. Characterization of the deoxyguanosine-lysine cross-link of methylglyoxal. Chem Res Toxicol 2014; 27:1019-29. [PMID: 24801980 PMCID: PMC4060920 DOI: 10.1021/tx500068v] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methylglyoxal is a mutagenic bis-electrophile that is produced endogenously from carbohydrate precursors. Methylglyoxal has been reported to induce DNA-protein cross-links (DPCs) in vitro and in cultured cells. Previous work suggests that these cross-links are formed between guanine and either lysine or cysteine side chains. However, the chemical nature of the methylglyoxal induced DPC have not been determined. We have examined the reaction of methylglyoxal, deoxyguanosine (dGuo), and Nα-acetyllysine (AcLys) and determined the structure of the cross-link to be the N2-ethyl-1-carboxamide with the lysine side chain amino group (1). The cross-link was identified by mass spectrometry and the structure confirmed by comparison to a synthetic sample. Further, the cross-link between methylglyoxal, dGuo, and a peptide (AcAVAGKAGAR) was also characterized. The mechanism of cross-link formation is likely to involve an Amadori rearrangement.
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Affiliation(s)
- Katya V Petrova
- Departments of Chemistry and Biochemistry, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University , 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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Kotapati S, Maddukuri L, Wickramaratne S, Seneviratne U, Goggin M, Pence MG, Villalta P, Guengerich FP, Marnett L, Tretyakova N. Translesion synthesis across 1,N6-(2-hydroxy-3-hydroxymethylpropan-1,3-diyl)-2'-deoxyadenosine (1,N6-γ-HMHP-dA) adducts by human and archebacterial DNA polymerases. J Biol Chem 2012; 287:38800-11. [PMID: 22977231 DOI: 10.1074/jbc.m112.396788] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The 1,N(6)-(2-hydroxy-3-hydroxymethylpropan-1,3-diyl)-2'-deoxyadenosine (1,N(6)-γ-HMHP-dA) adducts are formed upon bifunctional alkylation of adenine nucleobases in DNA by 1,2,3,4-diepoxybutane, the putative ultimate carcinogenic metabolite of 1,3-butadiene. The presence of a substituted 1,N(6)-propano group on 1,N(6)-γ-HMHP-dA is expected to block the Watson-Crick base pairing of the adducted adenine with thymine, potentially contributing to mutagenesis. In this study, the enzymology of replication past site-specific 1,N(6)-γ-HMHP-dA lesions in the presence of human DNA polymerases (hpols) β, η, κ, and ι and archebacterial polymerase Dpo4 was investigated. Run-on gel analysis with all four dNTPs revealed that hpol η, κ, and Dpo4 were able to copy the modified template. In contrast, hpol ι inserted a single base opposite 1,N(6)-γ-HMHP-dA but was unable to extend beyond the damaged site, and a complete replication block was observed with hpol β. Single nucleotide incorporation experiments indicated that although hpol η, κ, and Dpo4 incorporated the correct nucleotide (dTMP) opposite the lesion, dGMP and dAMP were inserted with a comparable frequency. HPLC-ESI-MS/MS analysis of primer extension products confirmed the ability of bypass polymerases to insert dTMP, dAMP, or dGMP opposite 1,N(6)-γ-HMHP-dA and detected large amounts of -1 and -2 deletion products. Taken together, these results indicate that hpol η and κ enzymes bypass 1,N(6)-γ-HMHP-dA lesions in an error-prone fashion, potentially contributing to A→T and A→C transversions and frameshift mutations observed in cells following treatment with 1,2,3,4-diepoxybutane.
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Affiliation(s)
- Srikanth Kotapati
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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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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