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Li Y, Hecht SS. Metabolic Activation and DNA Interactions of Carcinogenic N-Nitrosamines to Which Humans Are Commonly Exposed. Int J Mol Sci 2022; 23:ijms23094559. [PMID: 35562949 PMCID: PMC9105260 DOI: 10.3390/ijms23094559] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Carcinogenic N-nitrosamine contamination in certain drugs has recently caused great concern and the attention of regulatory agencies. These carcinogens-widely detectable in relatively low levels in food, water, cosmetics, and drugs-are well-established and powerful animal carcinogens. The electrophiles resulting from the cytochrome P450-mediated metabolism of N-nitrosamines can readily react with DNA and form covalent addition products (DNA adducts) that play a central role in carcinogenesis if not repaired. In this review, we aim to provide a comprehensive and updated review of progress on the metabolic activation and DNA interactions of 10 carcinogenic N-nitrosamines to which humans are commonly exposed. Certain DNA adducts such as O6-methylguanine with established miscoding properties play central roles in the cancer induction process, whereas others have been linked to the high incidence of certain types of cancers. We hope the data summarized here will help researchers gain a better understanding of the bioactivation and DNA interactions of these 10 carcinogenic N-nitrosamines and facilitate further research on their toxicologic and carcinogenic properties.
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Affiliation(s)
- Yupeng Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: ; Tel.: +1-612-624-8187
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
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2
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Synthesis of a new alkynylated deoxyadenosine phosphoramidite for the click reaction-mediated DNA labeling. MENDELEEV COMMUNICATIONS 2019. [DOI: 10.1016/j.mencom.2019.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Wang P, Leng J, Wang Y. DNA replication studies of N-nitroso compound-induced O 6-alkyl-2'-deoxyguanosine lesions in Escherichia coli. J Biol Chem 2019; 294:3899-3908. [PMID: 30655287 DOI: 10.1074/jbc.ra118.007358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/16/2019] [Indexed: 12/30/2022] Open
Abstract
N-Nitroso compounds (NOCs) are common DNA-alkylating agents, are abundantly present in food and tobacco, and can also be generated endogenously. Metabolic activation of some NOCs can give rise to carboxymethylation and pyridyloxobutylation/pyridylhydroxybutylation of DNA, which are known to be carcinogenic and can lead to gastrointestinal and lung cancer, respectively. Herein, using the competitive replication and adduct bypass (CRAB) assay, along with MS- and NMR-based approaches, we assessed the cytotoxic and mutagenic properties of three O 6-alkyl-2'-deoxyguanosine (O 6-alkyl-dG) adducts, i.e. O 6-pyridyloxobutyl-dG (O 6-POB-dG) and O 6-pyridylhydroxybutyl-dG (O 6-PHB-dG), derived from tobacco-specific nitrosamines, and O 6-carboxymethyl-dG (O 6-CM-dG), induced by endogenous N-nitroso compounds. We also investigated two neutral analogs of O 6-CM-dG, i.e. O 6-aminocarbonylmethyl-dG (O 6-ACM-dG) and O 6-hydroxyethyl-dG (O 6-HOEt-dG). We found that, in Escherichia coli cells, these lesions mildly (O 6-POB-dG), moderately (O 6-PHB-dG), or strongly (O 6-CM-dG, O 6-ACM-dG, and O 6-HOEt-dG) impede DNA replication. The strong blockage effects of the last three lesions were attributable to the presence of hydrogen-bonding donor(s) located on the alkyl functionality of these lesions. Except for O 6-POB-dG, which also induced a low frequency of G → T transversions, all other lesions exclusively stimulated G → A transitions. SOS-induced DNA polymerases played redundant roles in bypassing all the O 6-alkyl-dG lesions investigated. DNA polymerase IV (Pol IV) and Pol V, however, were uniquely required for inducing the G → A transition for O 6-CM-dG exposure. Together, our study expands our knowledge about the recognition of important NOC-derived O 6-alkyl-dG lesions by the E. coli DNA replication machinery.
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Affiliation(s)
- Pengcheng Wang
- From the Department of Chemistry, University of California, Riverside, California 92521-0403 and.,the Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, China
| | - Jiapeng Leng
- From the Department of Chemistry, University of California, Riverside, California 92521-0403 and
| | - Yinsheng Wang
- From the Department of Chemistry, University of California, Riverside, California 92521-0403 and
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Wu J, Wang P, Li L, Williams NL, Ji D, Zahurancik WJ, You C, Wang J, Suo Z, Wang Y. Replication studies of carboxymethylated DNA lesions in human cells. Nucleic Acids Res 2017; 45:7276-7284. [PMID: 28531304 PMCID: PMC5499590 DOI: 10.1093/nar/gkx442] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/04/2017] [Indexed: 12/11/2022] Open
Abstract
Metabolic activation of some N-nitroso compounds (NOCs), an important class of DNA damaging agents, can induce the carboxymethylation of nucleobases in DNA. Very little was previously known about how the carboxymethylated DNA lesions perturb DNA replication in human cells. Here, we investigated the effects of five carboxymethylated DNA lesions, i.e. O6-CMdG, N6-CMdA, N4-CMdC, N3-CMdT and O4-CMdT on the efficiency and fidelity of DNA replication in HEK293T human embryonic kidney cells. We found that, while neither N6-CMdA nor N4-CMdC blocked DNA replication or induced mutations, N3-CMdT, O4-CMdT and O6-CMdG moderately blocked DNA replication and induced substantial frequencies of T→A (81%), T→C (68%) and G→A (6.4%) mutations, respectively. In addition, our results revealed that CRISPR-Cas9-mediated depletion of Pol η resulted in significant drops in bypass efficiencies of N4-CMdC and N3-CMdT. Diminution in bypass efficiencies was also observed for N6-CMdA and O6-CMdG upon depletion of Pol κ, and for O6-CMdG upon removal of Pol ζ. Together, our study provided molecular-level insights into the impacts of the carboxymethylated DNA lesions on DNA replication in human cells, revealed the roles of individual translesion synthesis DNA polymerases in bypassing these lesions, and suggested the contributions of O6-CMdG, N3-CMdT and O4-CMdT to the mutations found in p53 gene of human gastrointestinal cancers.
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Affiliation(s)
- Jun Wu
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Lin Li
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Nicole L Williams
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Debin Ji
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Walter J Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Changjun You
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Jianshuang Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA.,Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
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5
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Sedgeman CA, Su Y, Guengerich FP. Formation of S-[2-(N 6-Deoxyadenosinyl)ethyl]glutathione in DNA and Replication Past the Adduct by Translesion DNA Polymerases. Chem Res Toxicol 2017; 30:1188-1196. [PMID: 28395138 DOI: 10.1021/acs.chemrestox.7b00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
1,2-Dibromoethane (DBE, ethylene dibromide) is a potent carcinogen due at least in part to its DNA cross-linking effects. DBE cross-links glutathione (GSH) to DNA, notably to sites on 2'-deoxyadenosine and 2'-deoxyguanosine ( Cmarik , J. L. , et al. ( 1991 ) J. Biol. Chem. 267 , 6672 - 6679 ). Adduction at the N6 position of 2'-deoxyadenosine (dA) had not been detected, but this is a site for the linkage of O6-alkylguanine DNA alkyltransferase ( Chowdhury , G. , et al. ( 2013 ) Angew. Chem. Int. Ed. 52 , 12879 - 12882 ). We identified and quantified a new adduct, S-[2-(N6-deoxyadenosinyl)ethyl]GSH, in calf thymus DNA using LC-MS/MS. Replication studies were performed in duplex oligonucleotides containing this adduct with human DNA polymerases (hPols) η, ι, and κ, as well as with Sulfolobus solfataricus Dpo4, Escherichia coli polymerase I Klenow fragment, and bacteriophage T7 polymerase. hPols η and ι, Dpo4, and Klenow fragment were able to bypass the adduct with only slight impedance; hPol η and ι showed increased misincorporation opposite the adduct compared to that of unmodified 2'-deoxyadenosine. LC-MS/MS analysis of full-length primer extension products by hPol η confirmed the incorporation of dC opposite S-[2-(N6-deoxyadenosinyl)ethyl]GSH and also showed the production of a -1 frameshift. These results reveal the significance of N6-dA GSH-DBE adducts in blocking replication, as well as producing mutations, by human translesion synthesis DNA polymerases.
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Affiliation(s)
- Carl A Sedgeman
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - Yan Su
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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Yu Y, Wang J, Wang P, Wang Y. Quantification of Azaserine-Induced Carboxymethylated and Methylated DNA Lesions in Cells by Nanoflow Liquid Chromatography-Nanoelectrospray Ionization Tandem Mass Spectrometry Coupled with the Stable Isotope-Dilution Method. Anal Chem 2016; 88:8036-42. [PMID: 27441891 PMCID: PMC5038140 DOI: 10.1021/acs.analchem.6b01349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Humans are exposed to N-nitroso compounds through environmental exposure and endogenous metabolism. Some N-nitroso compounds can be metabolically activated to yield diazoacetate, which is known to induce DNA carboxymethylation. DNA lesion measurement remains one of the core tasks in toxicology and in evaluating human health risks associated with carcinogen exposure. In this study, we developed a highly sensitive nanoflow liquid chromatography-nanoelectrospray ionization-multistage tandem mass spectrometry (nLC-nESI-MS(3)) method for the simultaneous quantification of O(6)-carboxymethyl-2'-deoxyguanosine (O(6)-CMdG), O(6)-methyl-2'-deoxyguanosine (O(6)-MedG), and N(6)-carboxymethyl-2'-deoxyadenosine (N(6)-CMdA). We were able to measure the levels of these three lesions with the use of low-microgram quantities of DNA from cultured human skin fibroblasts and human colorectal carcinoma cells treated with azaserine, a DNA carboxymethylating agent. Our results revealed that the levels of O(6)-CMdG and O(6)-MedG increased when the dose of azaserine was increased from 0 to 450 μM. We, however, did not observe an apparent dose-dependent induction of N(6)-CMdA, suggesting the presence of repair mechanism(s) for the rapid clearance of this lesion in cells. This is the first report about the application of nLC-nESI-MS(3) technique for the simultaneous quantification of O(6)-CMdG, O(6)-MedG, and N(6)-CMdA. The method reported here will be useful for future investigations about the repair of the carboxymethylated DNA lesions and about the implications of these lesions in carcinogenesis.
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Affiliation(s)
- Yang Yu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Jianshuang Wang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
- Department of Chemistry, University of California, Riverside, California 92521, United States
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You C, Wang P, Nay SL, Wang J, Dai X, O’Connor TR, Wang Y. Roles of Aag, Alkbh2, and Alkbh3 in the Repair of Carboxymethylated and Ethylated Thymidine Lesions. ACS Chem Biol 2016; 11:1332-8. [PMID: 26930515 DOI: 10.1021/acschembio.6b00085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Environmental and endogenous genotoxic agents can result in a variety of alkylated and carboxymethylated DNA lesions, including N3-ethylthymidine (N3-EtdT), O(2)-EtdT, and O(4)-EtdT as well as N3-carboxymethylthymidine (N3-CMdT) and O(4)-CMdT. By using nonreplicative double-stranded vectors harboring a site-specifically incorporated DNA lesion, we assessed the potential roles of alkyladenine DNA glycosylase (Aag); alkylation repair protein B homologue 2 (Alkbh2); or Alkbh3 in modulating the effects of N3-EtdT, O(2)-EtdT, O(4)-EtdT, N3-CMdT, or O(4)-CMdT on DNA transcription in mammalian cells. We found that the depletion of Aag did not significantly change the transcriptional inhibitory or mutagenic properties of all five examined lesions, suggesting a negligible role of Aag in the repair of these DNA adducts in mammalian cells. In addition, our results revealed that N3-EtdT, but not other lesions, could be repaired by Alkbh2 and Alkbh3 in mammalian cells. Furthermore, we demonstrated the direct reversal of N3-EtdT by purified human Alkbh2 protein in vitro. These findings provided important new insights into the repair of the carboxymethylated and alkylated thymidine lesions in mammalian cells.
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Affiliation(s)
- Changjun You
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Pengcheng Wang
- Environmental
Toxicology Graduate Program, University of California, Riverside, California, United States
| | - Stephanie L. Nay
- Department
of Cancer Biology, Beckman Research Institute, Duarte, California, United States
| | - Jianshuang Wang
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Xiaoxia Dai
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Timothy R. O’Connor
- Department
of Cancer Biology, Beckman Research Institute, Duarte, California, United States
| | - Yinsheng Wang
- Department
of Chemistry, University of California, Riverside, California, United States
- Environmental
Toxicology Graduate Program, University of California, Riverside, California, United States
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8
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Fu L, Amato NJ, Wang P, McGowan SJ, Niedernhofer LJ, Wang Y. Simultaneous Quantification of Methylated Cytidine and Adenosine in Cellular and Tissue RNA by Nano-Flow Liquid Chromatography-Tandem Mass Spectrometry Coupled with the Stable Isotope-Dilution Method. Anal Chem 2015; 87:7653-9. [PMID: 26158405 DOI: 10.1021/acs.analchem.5b00951] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The rising interest in understanding the functions, regulation, and maintenance of the epitranscriptome calls for robust and accurate analytical methods for the identification and quantification of post-transcriptionally modified nucleosides in RNA. Monomethylations of cytidine and adenosine are common post-transcriptional modifications in RNA. Herein, we developed an LC-MS/MS/MS coupled with the stable isotope-dilution method for the sensitive and accurate quantifications of 5-methylcytidine (m(5)C), 2'-O-methylcytidine (Cm), N(6)-methyladenosine (m(6)A), and 2'-O-methyladenosine (Am) in RNA isolated from mammalian cells and tissues. Our results showed that the distributions of m(5)C, Cm and Am are tissue-specific. In addition, the 2'-O-methylated ribonucleosides (Cm and Am) are present at higher levels than the corresponding methylated nucleobase products (m(5)C and m(6)A) in total RNA isolated from mouse brain, pancreas, and spleen but not mouse heart. We also found that the levels of m(5)C, Cm, and Am are significantly lower (by 6.5-43-fold) in mRNA than in total RNA isolated from HEK293T cells, whereas the level of m(6)A was slightly higher (by 1.6-fold) in mRNA than in total RNA. The availability of this analytical method, in combination with genetic manipulation, may facilitate the future discovery of proteins involved in the maintenance and regulation of these RNA modifications.
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Affiliation(s)
| | | | | | - Sara J McGowan
- §Department of Metabolism and Aging, Scripps Florida, Jupiter, Florida 33458, United States
| | - Laura J Niedernhofer
- §Department of Metabolism and Aging, Scripps Florida, Jupiter, Florida 33458, United States
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You C, Wang J, Dai X, Wang Y. Transcriptional inhibition and mutagenesis induced by N-nitroso compound-derived carboxymethylated thymidine adducts in DNA. Nucleic Acids Res 2015; 43:1012-8. [PMID: 25572317 PMCID: PMC4333421 DOI: 10.1093/nar/gku1391] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
N-nitroso compounds represent a common type of environmental and endogenous DNA-damaging agents. After metabolic activation, many N-nitroso compounds are converted into a diazoacetate intermediate that can react with nucleobases to give carboxymethylated DNA adducts such as N3-carboxymethylthymidine (N3-CMdT) and O4-carboxymethylthymidine (O4-CMdT). In this study, we constructed non-replicative plasmids carrying a single N3-CMdT or O4-CMdT, site-specifically positioned in the transcribed strand, to investigate how these lesions compromise the flow of genetic information during transcription. Our results revealed that both N3-CMdT and O4-CMdT substantially inhibited DNA transcription mediated by T7 RNA polymerase or human RNA polymerase II in vitro and in human cells. In addition, we found that N3-CMdT and O4-CMdT were miscoding lesions and predominantly directed the misinsertion of uridine and guanosine, respectively. Our results also suggested that these carboxymethylated thymidine lesions may constitute efficient substrates for transcription-coupled nucleotide excision repair in human cells. These findings provided important new insights into the biological consequences of the carboxymethylated DNA lesions in living cells.
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Affiliation(s)
- Changjun You
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Jianshuang Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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10
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Trantakis IA, Bolisetty S, Mezzenga R, Sturla SJ. Reversible aggregation of DNA-decorated gold nanoparticles controlled by molecular recognition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10824-10830. [PMID: 23883185 DOI: 10.1021/la401211u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The programmable assembly of functional nanomaterials has been extensively addressed; however, their selective reversible assembly in response to an external stimulus has been more difficult to realize. The specificity and programmable interactions of DNA have been exploited for the rational self-assembly of DNA-conjugated nanoparticles, and here we demonstrate the sequence-controlled disaggregation of DNA-modified gold nanoparticles simply by employing two complementary oligonucleotides. Target oligonucleotides with perfectly matching sequence enabled dissociation of aggregated nanoparticles, whereas oligonucleotides differing by one nucleotide did not cause disassembly of the aggregated nanoparticles. Physical aspects of this process were characterized by UV-vis absorption, light scattering, and transmission electron microscopy. This strategy for programmed disassembly of gold nanoparticles in response to biological stimuli demonstrates a fundamentally important concept anticipated to be useful for diverse applications involving molecular recognition.
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Affiliation(s)
- Ioannis A Trantakis
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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11
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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12
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Swanson AL, Wang J, Wang Y. In vitro replication studies of carboxymethylated DNA lesions with Saccharomyces cerevisiae polymerase η. Biochemistry 2011; 50:7666-73. [PMID: 21809836 DOI: 10.1021/bi2007417] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Humans are exposed to N-nitroso compounds (NOCs) both endogenously and exogenously from a number of environmental sources, and NOCs are both mutagenic and carcinogenic. After metabolic activation, some NOCs can induce carboxymethylation of nucleobases through a diazoacetate intermediate, which could give rise to p53 mutations similar to those seen in human gastrointestinal cancers. It was previously found that the growth of polymerase η-deficient human cells was inhibited by treatment with azaserine, a DNA carboxymethylation agent, suggesting the importance of this polymerase in bypassing the azaserine-induced carboxymethylated DNA lesions. In this study, we examined how carboxymethylated DNA lesions, which included N(6)-carboxymethyl-2'-deoxyadenosine (N(6)-CMdA), N(4)-carboxymethyl-2'-deoxycytidine (N(4)-CMdC), N3-carboxymethylthymidine (N3-CMdT), and O(4)-carboxymethylthymidine (O(4)-CMdT), perturbed the efficiency and fidelity of DNA replication mediated by Saccharomyces cerevisiae polymerase η (pol η). Our results from steady-state kinetic assay showed that pol η could readily bypass and extend past N(6)-CMdA and incorporated the correct nucleotides opposite the lesion and its neighboring 5'-nucleoside with high efficiency. By contrast, the polymerase could bypass N(4)-CMdC inefficiently, with substantial misincorporation of dCMP followed by dAMP, though pol η could extend past the lesion with high fidelity and efficiency when dGMP was incorporated opposite the lesion. On the other hand, yeast pol η experienced great difficulty in bypassing O(4)-CMdT and N3-CMdT, and the polymerase inserted preferentially the incorrect dGMP opposite these two DNA lesions; the extension step, nevertheless, occurred with high fidelity and efficiency when the correct dAMP was opposite the lesion, as opposed to the preferentially incorporated incorrect dGMP. These results suggest that these lesions may contribute significantly to diazoacetate-induced mutations and those in the p53 gene observed in human gastrointestinal tumors.
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Affiliation(s)
- Ashley L Swanson
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
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13
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Yuan B, Wang J, Cao H, Sun R, Wang Y. High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing. Nucleic Acids Res 2011; 39:5945-54. [PMID: 21470959 PMCID: PMC3152323 DOI: 10.1093/nar/gkr159] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Human cells are constantly exposed to environmental and endogenous agents which can induce damage to DNA. Understanding the implications of these DNA modifications in the etiology of human diseases requires the examination about how these DNA lesions block DNA replication and induce mutations in cells. All previously reported shuttle vector-based methods for investigating the cytotoxic and mutagenic properties of DNA lesions in cells have low-throughput, where plasmids containing individual lesions are transfected into cells one lesion at a time and the products from the replication of individual lesions are analyzed separately. The advent of next-generation sequencing (NGS) technology has facilitated investigators to design scientific approaches that were previously not technically feasible or affordable. In this study, we developed a new method employing NGS, together with shuttle vector technology, to have a multiplexed and quantitative assessment of how DNA lesions perturb the efficiency and accuracy of DNA replication in cells. By using this method, we examined the replication of four carboxymethylated DNA lesions and two oxidatively induced bulky DNA lesions including (5′S) diastereomers of 8,5′-cyclo-2′-deoxyguanosine (cyclo-dG) and 8,5′-cyclo-2′-deoxyadenosine (cyclo-dA) in five different strains of Escherichia coli cells. We further validated the results obtained from NGS using previously established methods. Taken together, the newly developed method provided a high-throughput and readily affordable method for assessing quantitatively how DNA lesions compromise the efficiency and fidelity of DNA replication in cells.
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Affiliation(s)
- Bifeng Yuan
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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14
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Wang J, Wang Y. Carboxymethylation of DNA Induced by N-Nitroso Compounds and Its Biological Implications. ADVANCES IN MOLECULAR TOXICOLOGY 2011. [DOI: 10.1016/b978-0-444-53864-2.00006-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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