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Bellamri M, Yao L, Tomar R, Vartanian V, Rizzo CJ, Stone MP, Groopman JD, Lloyd RS, Turesky RJ. Mass Spectrometry-Based Method to Measure Aflatoxin B 1 DNA Adducts in Formalin-Fixed Paraffin-Embedded Tissues. Chem Res Toxicol 2024; 37:633-642. [PMID: 38498000 DOI: 10.1021/acs.chemrestox.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Aflatoxin B1 (AFB1) is a potent human liver carcinogen produced by certain molds, particularly Aspergillus flavus and Aspergillus parasiticus, which contaminate peanuts, corn, rice, cottonseed, and ground and tree nuts, principally in warm and humid climates. AFB1 undergoes bioactivation in the liver to produce AFB1-exo-8,9-epoxide, which forms the covalently bound cationic AFB1-N7-guanine (AFB1-N7-Gua) DNA adduct. This adduct is unstable and undergoes base-catalyzed opening of the guanine imidazolium ring to form two ring-opened diastereomeric 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy-aflatoxin B1 (AFB1-FapyGua) adducts. The AFB1 formamidopyrimidine (Fapy) adducts induce G → T transversion mutations and are likely responsible for the carcinogenic effects of AFB1. Quantitative liquid chromatography-mass spectrometry (LC-MS) methods have shown that AFB1-N7-Gua is eliminated in rodent and human urine, whereas ring-opened AFB1-FapyGua adducts persist in rodent liver. However, fresh frozen biopsy tissues are seldom available for biomonitoring AFB1 DNA adducts in humans, impeding research advances in this potent liver carcinogen. In contrast, formalin-fixed paraffin-embedded (FFPE) specimens used for histopathological analysis are often accessible for molecular studies. However, ensuring nucleic acid quality presents a challenge due to incomplete reversal of formalin-mediated DNA cross-links, which can preclude accurate quantitative measurements of DNA adducts. In this study, employing ion trap or high-resolution accurate Orbitrap mass spectrometry, we demonstrate that ring-opened AFB1-FapyGua adducts formed in AFB1-exposed newborn mice are stable to the formalin fixation and DNA de-cross-linking retrieval processes. The AFB1-FapyGua adducts can be detected at levels comparable to those in a match of fresh frozen liver. Orbitrap MS2 measurements can detect AFB1-FapyGua at a quantification limit of 4.0 adducts per 108 bases when only 0.8 μg of DNA is assayed on the column. Thus, our breakthrough DNA retrieval technology can be adapted to screen for AFB1 DNA adducts in FFPE human liver specimens from cohorts at risk of this potent liver carcinogen.
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Affiliation(s)
| | | | - Rachana Tomar
- Department of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Vladimir Vartanian
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Carmelo J Rizzo
- Department of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael P Stone
- Department of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John D Groopman
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
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Abstract
The combination of doxorubicin (Adriamycin) and cyclophosphamide, referred to as AC chemotherapy, is commonly used for the clinical treatment of breast and other cancers. Both agents target DNA with cyclophosphamide causing alkylation damage and doxorubicin stabilizing the topoisomerase II-DNA complex. We hypothesize a new mechanism of action whereby both agents work in concert. DNA alkylating agents, such as nitrogen mustards, increase the number of apurinic/apyrimidinic (AP) sites through deglycosylation of labile alkylated bases. Herein, we demonstrate that anthracyclines with aldehyde-reactive primary and secondary amines form covalent Schiff base adducts with AP sites in a 12-mer DNA duplex, calf thymus DNA, and MDA-MB-231 human breast cancer cells treated with nor-nitrogen mustard and the anthracycline mitoxantrone. The anthracycline-AP site conjugates are characterized and quantified by mass spectrometry after NaB(CN)H3 or NaBH4 reduction of the Schiff base. If stable, the anthracycline-AP site conjugates represent bulky adducts that may block DNA replication and contribute to the cytotoxic mechanism of therapies involving combinations of anthracyclines and DNA alkylating agents.
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Jaruga P, Tomar R, Kant M, Vartanian V, Sexton B, Rizzo CJ, Turesky RJ, Stone MP, Lloyd RS, Dizdaroglu M. Synthesis and Characterization of 15N 5-Labeled Aflatoxin B 1-Formamidopyrimidines and Aflatoxin B 1-N7-Guanine from a Partial Double-Stranded Oligodeoxynucleotide as Internal Standards for Mass Spectrometric Measurements. ACS Omega 2023; 8:14841-14854. [PMID: 37125130 PMCID: PMC10134230 DOI: 10.1021/acsomega.3c01328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Aflatoxin B1 (AFB1) exposure through contaminated food is a primary contributor to hepatocellular carcinogenesis worldwide. Hepatitis B viral infections in livers dramatically increase the carcinogenic potency of AFB1 exposures. Liver cytochrome P450 oxidizes AFB1 to the epoxide, which in turn reacts with N7-guanine in DNA, producing the cationic trans-8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 adduct (AFB1-N7-Gua). The opening of the imidazole ring of AFB1-N7-Gua under physiological conditions causes the formation of the cis- and trans-diastereomers of 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua). These adducts primarily lead to G → T mutations, with AFB1-FapyGua being significantly more mutagenic than AFB1-N7-Gua. The unequivocal identification and accurate quantification of these AFB1-Gua adducts as biomarkers are essential for a fundamental understanding and prevention of AFB1-induced hepatocellular carcinogenesis. Among a variety of analytical techniques used for this purpose, liquid chromatography-tandem mass spectrometry, with the use of the stable isotope-labeled analogues of AFB1-FapyGua and AFB1-N7-Gua as internal standards, provides the greatest accuracy and sensitivity. cis-AFB1-FapyGua-15N5, trans-AFB1-FapyGua-15N5, and AFB1-N7-Gua-15N5 have been synthesized and used successfully as internal standards. However, the availability of these standards from either academic institutions or commercial sources ceased to exist. Thus, quantitative genomic data regarding AFB1-induced DNA damage in animal models and humans remain challenging to obtain. Previously, AFB1-N7-Gua-15N5 was prepared by reacting AFB1-exo-8,9-epoxide with the uniformly 15N5-labeled DNA isolated from algae grown in a pure 15N-environment, followed by alkali treatment, resulting in the conversion of AFB1-N7-Gua-15N5 to AFB1-FapyGua-15N5. In the present work, we used a different and simpler approach to synthesize cis-AFB1-FapyGua-15N5, trans-AFB1-FapyGua-15N5, and AFB1-N7-Gua-15N5 from a partial double-stranded 11-mer Gua-15N5-labeled oligodeoxynucleotide, followed by isolation and purification. We also show the validation of these 15N5-labeled standards for the measurement of cis-AFB1-FapyGua, trans-AFB1-FapyGua, and AFB1-N7-Gua in DNA of livers of AFB1-treated mice.
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Affiliation(s)
- Pawel Jaruga
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Rachana Tomar
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Melis Kant
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Vladimir Vartanian
- Oregon
Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Benjamin Sexton
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Carmelo J. Rizzo
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Robert J. Turesky
- Masonic
Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael P. Stone
- Department
of Chemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - R. Stephen Lloyd
- Oregon
Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Miral Dizdaroglu
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
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Christov PP, Richie-Jannetta R, Kingsley PJ, Vemulapalli A, Kim K, Sulikowski GA, Rizzo CJ, Ketkar A, Eoff RL, Rouzer CA, Marnett LJ. Site-Specific Synthesis of Oligonucleotides Containing 6-Oxo-M 1dG, the Genomic Metabolite of M 1dG, and Liquid Chromatography-Tandem Mass Spectrometry Analysis of Its In Vitro Bypass by Human Polymerase ι. Chem Res Toxicol 2021; 34:2567-2578. [PMID: 34860508 PMCID: PMC10518890 DOI: 10.1021/acs.chemrestox.1c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The lipid peroxidation product malondialdehyde and the DNA peroxidation product base-propenal react with dG to generate the exocyclic adduct, M1dG. This mutagenic lesion has been found in human genomic and mitochondrial DNA. M1dG in genomic DNA is enzymatically oxidized to 6-oxo-M1dG, a lesion of currently unknown mutagenic potential. Here, we report the synthesis of an oligonucleotide containing 6-oxo-M1dG and the results of extension experiments aimed at determining the effect of the 6-oxo-M1dG lesion on the activity of human polymerase iota (hPol ι). For this purpose, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed to obtain reliable quantitative data on the utilization of poorly incorporated nucleotides. Results demonstrate that hPol ι primarily incorporates deoxycytidine triphosphate (dCTP) and thymidine triphosphate (dTTP) across from 6-oxo-M1dG with approximately equal efficiency, whereas deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP) are poor substrates. Following the incorporation of a single nucleotide opposite the lesion, 6-oxo-M1dG blocks further replication by the enzyme.
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Affiliation(s)
- Plamen P. Christov
- Department of Chemistry, Vanderbilt University; Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Robyn Richie-Jannetta
- A. B. Hancock, Jr., Memorial Laboratory for Cancer Research, Departments of Biochemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Philip J. Kingsley
- A. B. Hancock, Jr., Memorial Laboratory for Cancer Research, Departments of Biochemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Anoop Vemulapalli
- A. B. Hancock, Jr., Memorial Laboratory for Cancer Research, Departments of Biochemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Kwangho Kim
- Department of Chemistry, Vanderbilt University; Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Gary A. Sulikowski
- Department of Chemistry, Vanderbilt University; Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Carmelo J. Rizzo
- Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Amit Ketkar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Robert L. Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Carol A. Rouzer
- A. B. Hancock, Jr., Memorial Laboratory for Cancer Research, Departments of Biochemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Lawrence J. Marnett
- Department of Chemistry, Vanderbilt University; Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- A. B. Hancock, Jr., Memorial Laboratory for Cancer Research, Departments of Biochemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
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5
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Ghodke PP, Mali JR, Patra A, Rizzo CJ, Guengerich FP, Egli M. Enzymatic bypass and the structural basis of miscoding opposite the DNA adduct 1,N 2-ethenodeoxyguanosine by human DNA translesion polymerase η. J Biol Chem 2021; 296:100642. [PMID: 33839151 PMCID: PMC8121704 DOI: 10.1016/j.jbc.2021.100642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022] Open
Abstract
Etheno (ε)-adducts, e.g., 1,N2-ε−guanine (1,N2-ε-G) and 1,N6-ε−adenine (1,N6-ε-A), are formed through the reaction of DNA with metabolites of vinyl compounds or with lipid peroxidation products. These lesions are known to be mutagenic, but it is unknown how they lead to errors in DNA replication that are bypassed by DNA polymerases. Here we report the structural basis of misincorporation frequencies across from 1,N2-ε-G by human DNA polymerase (hpol) η. In single-nucleotide insertions opposite the adduct 1,N2-ε-G, hpol η preferentially inserted dGTP, followed by dATP, dTTP, and dCTP. This preference for purines was also seen in the first extension step. Analysis of full-length extension products by LC-MS/MS revealed that G accounted for 85% of nucleotides inserted opposite 1,N2-ε-G in single base insertion, and 63% of bases inserted in the first extension step. Extension from the correct nucleotide pair (C) was not observed, but the primer with A paired opposite 1,N2-ε-G was readily extended. Crystal structures of ternary hpol η insertion-stage complexes with nonhydrolyzable nucleotides dAMPnPP or dCMPnPP showed a syn orientation of the adduct, with the incoming A staggered between adducted base and the 5’-adjacent T, while the incoming C and adducted base were roughly coplanar. The formation of a bifurcated H-bond between incoming dAMPnPP and 1,N2-ε-G and T, compared with the single H-bond formed between incoming dCMPnPP and 1,N2-ε-G, may account for the observed facilitated insertion of dGTP and dATP. Thus, preferential insertion of purines by hpol η across from etheno adducts contributes to distinct outcomes in error-prone DNA replication.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Jyotirling R Mali
- Department of Chemistry, College of Arts and Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Amritraj Patra
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Carmelo J Rizzo
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Department of Chemistry, College of Arts and Science, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA.
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Chen H, Cui Z, Hejazi L, Yao L, Walmsley SJ, Rizzo CJ, Turesky RJ. Kinetics of DNA Adducts and Abasic Site Formation in Tissues of Mice Treated with a Nitrogen Mustard. Chem Res Toxicol 2020; 33:988-998. [PMID: 32174110 DOI: 10.1021/acs.chemrestox.0c00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nitrogen mustards (NM) are an important class of chemotherapeutic drugs used in the treatment of malignant tumors. The accepted mechanism of action of NM is through the alkylation of DNA bases. NM-adducts block DNA replication in cancer cells by forming cytotoxic DNA interstrand cross-links. We previously characterized several adducts formed by reaction of bis(2-chloroethyl)ethylamine (NM) with calf thymus (CT) DNA and the MDA-MB-231 mammary tumor cell line. The monoalkylated N7-guanine (NM-G) adduct and its cross-link (G-NM-G) were major lesions. The cationic NM-G undergoes a secondary reaction through depurination to form an apurinic (AP) site or reacts with hydroxide to yield the stable ring-opened N5-substituted formamidopyrimidine (NM-Fapy-G) adduct. Both of these lesions are mutagenic and may contribute to secondary tumor development, a major clinical limitation of NM chemotherapy. We established a kinetic model with NM-treated female mice and measured the rates of formation and removal of NM-DNA adducts and AP sites. We employed liquid chromatography-mass spectrometry (LC-MS) to measure NM-G, G-NM-G, and NM-Fapy-G adducts in liver, lung, and spleen over 168 h. NM-G reached a maximum level within 6 h in all organs and then rapidly declined. The G-NM-G cross-link and NM-FapyG were more persistent with half-lives over three-times longer than NM-G. We quantified AP site lesions in the liver and showed that NM treatment increased AP site levels by 3.7-fold over the basal levels at 6 h. The kinetics of AP site repair closely followed the rate of removal of NM-G; however, AP sites remained 1.3-fold above basal levels 168 h post-treatment with NM. Our data provide new insights into NM-induced DNA damage and biological processing in vivo. The quantitative measurement of the spectrum of NM adducts and AP sites can serve as biomarkers in the design and assessment of the efficacy of novel chemotherapeutic regimens.
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Affiliation(s)
| | | | | | | | | | - Carmelo J Rizzo
- Departments of Chemistry and Biochemistry, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37067, United States
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Chen H, Yao L, Brown C, Rizzo CJ, Turesky RJ. Quantitation of Apurinic/Apyrimidinic Sites in Isolated DNA and in Mammalian Tissue with a Reduced Level of Artifacts. Anal Chem 2019; 91:7403-7410. [PMID: 31055913 DOI: 10.1021/acs.analchem.9b01351] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The apurinic/apyrimidinic (AP) site is a common lesion of DNA damage. The levels of AP sites reported in the literature cover a wide range, which is primarily due to the artifactual generation or loss of AP sites during processing of the DNA. Herein, we have developed a method for quantitating AP sites with a largely reduced level of artifacts by derivatizing AP sites before DNA isolation. A rapid digestion of nuclear protein was performed to minimize enzymatic DNA repair, followed by direct derivatization of AP sites in the nuclear lysate with O-(pyridin-3-yl-methyl)hydroxylamine, yielding an oxime derivative that is stable through the subsequent DNA processing steps. Quantitation was done using highly selective and sensitive liquid chromatography-tandem mass spectrometry, with a limit of quantitation at 2.2 lesions per 108 nucleotides (nts, 0.9 fmol on column). The method was applied in vivo to measure AP sites in rats undergoing oxidative stress [liver, 3.31 ± 0.47/107 nts (dosed) vs 0.91 ± 0.06/107 nts (control); kidney, 1.60 ± 0.07/107 nts (dosed) vs 1.13 ± 0.12/107 nts (control)]. The basal AP level was significantly lower than literature values. The method was also used to measure AP sites induced by the chemotherapeutic nitrogen mustard in vitro.
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Affiliation(s)
- Haoqing Chen
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Lihua Yao
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Christina Brown
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Carmelo J Rizzo
- Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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Bamberger SN, Malik CK, Voehler MW, Brown SK, Pan H, Johnson-Salyard TL, Rizzo CJ, Stone MP. Configurational and Conformational Equilibria of N 6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA. Chem Res Toxicol 2018; 31:924-935. [PMID: 30169026 DOI: 10.1021/acs.chemrestox.8b00135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The most common lesion in DNA occurring due to clinical treatment with Temozolomide or cellular exposures to other methylating agents is 7-methylguanine (N7-Me-dG). It can undergo a secondary reaction to form N6-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG). MeFapy-dG undergoes epimerization in DNA to produce either α or β deoxyribose anomers. Additionally, conformational rotation around the formyl bond, C5- N5 bond, and glycosidic bond may occur. To characterize and quantitate the mixture of these isomers in DNA, a 13C-MeFapy-dG lesion, in which the CH3 group of the MeFapy-dG was isotopically labeled, was incorporated into the trimer 5'-TXT-3' and the dodecamer 5'-CATXATGACGCT-3' (X = 13C-MeFapy-dG). NMR spectroscopy of both the trimer and dodecamer revealed that the MeFapy-dG lesion exists in single strand DNA as ten configurationally and conformationally discrete species, eight of which may be unequivocally assigned. In the duplex dodecamer, the MeFapy-dG lesion exists as six configurationally and conformationally discrete species. Analyses of NMR data in the single strand trimer confirm that for each deoxyribose anomer, atropisomerism occurs around the C5- N5 bond to produce R a and S a atropisomers. Each atropisomer exhibits geometrical isomerism about the formyl bond yielding E and Z conformations. 1H NMR experiments allow the relative abundances of the species to be determined. For the single strand trimer, the α and β anomers exist in a 3:7 ratio, favoring the β anomer. For the β anomer, with respect to the C5- N5 bond, the R a and S a atropisomers are equally populated. However, the Z geometrical isomer of the formyl moiety is preferred. For the α anomer, the E- S a isomer is present at 12%, whereas all other isomers are present at 5-7%. DNA processing enzymes may differentially recognize different isomers of the MeFapy-dG lesion. Moreover, DNA sequence-specific differences in the populations of configurational and conformational species may modulate biological responses to the MeFapy-dG lesion.
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Affiliation(s)
- Stephanie N Bamberger
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Chanchal K Malik
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Markus W Voehler
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Summer K Brown
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Hope Pan
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Tracy L Johnson-Salyard
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Carmelo J Rizzo
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Michael P Stone
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
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9
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Minko IG, Rizzo CJ, Lloyd RS. Mutagenic potential of nitrogen mustard-induced formamidopyrimidine DNA adduct: Contribution of the non-canonical α-anomer. J Biol Chem 2017; 292:18790-18799. [PMID: 28972137 DOI: 10.1074/jbc.m117.802520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/15/2017] [Indexed: 12/14/2022] Open
Abstract
Nitrogen mustards (NMs) are DNA-alkylating compounds that represent the earliest anticancer drugs. However, clinical use of NMs is limited because of their own mutagenic properties. The mechanisms of NM-induced mutagenesis remain unclear. The major product of DNA alkylation by NMs is a cationic NM-N7-dG adduct that can yield the imidazole ring-fragmented lesion, N5-NM-substituted formamidopyrimidine (NM-Fapy-dG). Characterization of this adduct is complicated because it adopts different conformations, including both a canonical β- and an unnatural α-anomeric configuration. Although formation of NM-Fapy-dG in cellular DNA has been demonstrated, its potential role in NM-induced mutagenesis is unknown. Here, we created site-specifically modified single-stranded vectors for replication in primate (COS7) or Escherichia coli cells. In COS7 cells, NM-Fapy-dG caused targeted mutations, predominantly G → T transversions, with overall frequencies of ∼11-12%. These frequencies were ∼2-fold higher than that induced by 8-oxo-dG adduct. Replication in E. coli was essentially error-free. To elucidate the mechanisms of bypass of NM-Fapy-dG, we performed replication assays in vitro with a high-fidelity DNA polymerase, Saccharomyces cerevisiae polymerase (pol) δ. It was found that pol δ could catalyze high-fidelity synthesis past NM-Fapy-dG, but only on a template subpopulation, presumably containing the β-anomeric adduct. Consistent with the low mutagenic potential of the β-anomer in vitro, the mutation frequency was significantly reduced when conditions for vector preparation were modified to favor this configuration. Collectively, these data implicate the α-anomer as a major contributor to NM-Fapy-dG-induced mutagenesis in primate cells.
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Affiliation(s)
- Irina G Minko
- From the Oregon Institute of Occupational Health Sciences and
| | - Carmelo J Rizzo
- the Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - R Stephen Lloyd
- From the Oregon Institute of Occupational Health Sciences and .,the Departments of Molecular and Medical Genetics and Physiology and Pharmacology, Oregon Health & Science University, Portland, Oregon 97239 and
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10
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Sha Y, Minko IG, Malik CK, Rizzo CJ, Lloyd RS. Error-prone replication bypass of the imidazole ring-opened formamidopyrimidine deoxyguanosine adduct. Environ Mol Mutagen 2017; 58:182-189. [PMID: 28436537 PMCID: PMC5476229 DOI: 10.1002/em.22089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
Addition of hydroxyl radicals to the C8 position of 2'-deoxyguanosine generates an 8-hydroxyguanyl radical that can be converted into either 8-oxo-7,8-dihydro-2'-deoxyguanosine or N-(2-deoxy-d-pentofuranosyl)-N-(2,6-diamino-4-hydroxy-5-formamidopyrimidine) (Fapy-dG). The Fapy-dG adduct can adopt different conformations and in particular, can exist in an unnatural α anomeric configuration in addition to canonical β configuration. Previous studies reported that in 5'-TGN-3' sequences, Fapy-dG predominantly induced G → T transversions in both mammalian cells and Escherichia coli, suggesting that mutations could be formed either via insertion of a dA opposite the 5' dT due to primer/template misalignment or as result of direct miscoding. To address this question, single-stranded vectors containing a site-specific Fapy-dG adduct were generated to vary the identity of the 5' nucleotide. Following vector replication in primate cells (COS7), complex mutation spectra were observed that included ∼3-5% G → T transversions and ∼14-21% G → A transitions. There was no correlation apparent between the identity of the 5' nucleotide and spectra of mutations. When conditions for vector preparation were modified to favor the β anomer, frequencies of both G → T and G → A substitutions were significantly reduced. Mutation frequencies in wild-type E. coli and a mutant deficient in damage-inducible DNA polymerases were significantly lower than detected in COS7 and spectra were dominated by deletions. Thus, mutagenic bypass of Fapy-dG can proceed via mechanisms that are different from the previously proposed primer/template misalignment or direct misinsertions of dA or dT opposite to the β anomer of Fapy-dG. Environ. Mol. Mutagen. 58:182-189, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yan Sha
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Irina G. Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Chanchal K. Malik
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Carmelo J. Rizzo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - R. Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, USA
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11
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Gruppi F, Hejazi L, Christov PP, Krishnamachari S, Turesky RJ, Rizzo CJ. Characterization of nitrogen mustard formamidopyrimidine adduct formation of bis(2-chloroethyl)ethylamine with calf thymus DNA and a human mammary cancer cell line. Chem Res Toxicol 2015; 28:1850-60. [PMID: 26285869 DOI: 10.1021/acs.chemrestox.5b00297] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A robust, quantitative ultraperformance liquid chromatography ion trap multistage scanning mass spectrometric (UPLC/MS(3)) method was established to characterize and measure five guanine adducts formed by reaction of the chemotherapeutic nitrogen mustard (NM) bis(2-chloroethyl)ethylamine with calf thymus (CT) DNA. In addition to the known N7-guanine (NM-G) adduct and its cross-link (G-NM-G), the ring-opened formamidopyrimidine (FapyG) monoadduct (NM-FapyG) and cross-links in which one (FapyG-NM-G) or both (FapyG-NM-FapyG) guanines underwent ring-opening to FapyG units were identified. Authentic standards of all adducts were synthesized and characterized by NMR and mass spectrometry. These adducts were quantified in CT DNA treated with NM (1 μM) as their deglycosylated bases. A two-stage neutral thermal hydrolysis was developed to mitigate the artifactual formation of ring-opened FapyG adducts involving hydrolysis of the cationic adduct at 37 °C, followed by hydrolysis of the FapyG adducts at 95 °C. The limit of quantification values ranged between 0.3 and 1.6 adducts per 10(7) DNA bases when the equivalent of 5 μg of DNA hydrolysate was assayed on column. The principal adduct formed was the G-NM-G cross-link, followed by the NM-G monoadduct; the FapyG-NM-G cross-link adduct; and the FapyG-NM-FapyG was below the limit of detection. The NM-FapyG adducts were formed in CT DNA at a level ∼20% that of the NM-G adduct. NM-FapyG has not been previously quanitified, and the FapyG-NM-G and FapyG-NM-FapyG adducts have not been previously characterized. Our validated analytical method was then applied to measure DNA adduct formation in the MDA-MB-231 mammary tumor cell line exposed to NM (100 μM) for 24 h. The major adduct formed was NM-G (970 adducts per 10(7) bases), followed by G-NM-G (240 adducts per 10(7) bases), NM-FapyG (180 adducts per 10(7) bases), and, last, the FapyG-NM-G cross-link adduct (6.0 adducts per 10(7) bases). These lesions are expected to contribute to NM-mediated toxicity and genotoxicity in vivo.
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Affiliation(s)
- Francesca Gruppi
- Departments of Chemistry and Biochemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Leila Hejazi
- Masonic Cancer Center and Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota , 2231 Sixth Street South East, Minneapolis, Minnesota 55455, United States
| | - Plamen P Christov
- Departments of Chemistry and Biochemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Sesha Krishnamachari
- Masonic Cancer Center and Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota , 2231 Sixth Street South East, Minneapolis, Minnesota 55455, United States
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota , 2231 Sixth Street South East, Minneapolis, Minnesota 55455, United States
| | - Carmelo J Rizzo
- Departments of Chemistry and Biochemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville, Tennessee 37235, United States
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12
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Bose A, Pande P, Jasti VP, Millsap AD, Hawkins EK, Rizzo CJ, Basu AK. DNA polymerases κ and ζ cooperatively perform mutagenic translesion synthesis of the C8-2'-deoxyguanosine adduct of the dietary mutagen IQ in human cells. Nucleic Acids Res 2015. [PMID: 26220181 PMCID: PMC4787813 DOI: 10.1093/nar/gkv750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The roles of translesion synthesis (TLS) DNA polymerases in bypassing the C8-2'-deoxyguanosine adduct (dG-C8-IQ) formed by 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a highly mutagenic and carcinogenic heterocyclic amine found in cooked meats, were investigated. Three plasmid vectors containing the dG-C8-IQ adduct at the G1-, G2- or G3-positions of the NarI site (5'-G1G2CG3CC-3') were replicated in HEK293T cells. Fifty percent of the progeny from the G3 construct were mutants, largely G→T, compared to 18% and 24% from the G1 and G2 constructs, respectively. Mutation frequency (MF) of dG-C8-IQ was reduced by 38-67% upon siRNA knockdown of pol κ, whereas it was increased by 10-24% in pol η knockdown cells. When pol κ and pol ζ were simultaneously knocked down, MF of the G1 and G3 constructs was reduced from 18% and 50%, respectively, to <3%, whereas it was reduced from 24% to <1% in the G2 construct. In vitro TLS using yeast pol ζ showed that it can extend G3*:A pair more efficiently than G3*:C pair, but it is inefficient at nucleotide incorporation opposite dG-C8-IQ. We conclude that pol κ and pol ζ cooperatively carry out the majority of the error-prone TLS of dG-C8-IQ, whereas pol η is involved primarily in its error-free bypass.
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Affiliation(s)
- Arindam Bose
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Paritosh Pande
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Vijay P Jasti
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Amy D Millsap
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Edward K Hawkins
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Carmelo J Rizzo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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13
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Chang SC, Fedeles BI, Wu J, Delaney JC, Li D, Zhao L, Christov PP, Yau E, Singh V, Jost M, Drennan CL, Marnett LJ, Rizzo CJ, Levine SS, Guengerich FP, Essigmann JM. Next-generation sequencing reveals the biological significance of the N(2),3-ethenoguanine lesion in vivo. Nucleic Acids Res 2015; 43:5489-500. [PMID: 25837992 PMCID: PMC4477646 DOI: 10.1093/nar/gkv243] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/20/2022] Open
Abstract
Etheno DNA adducts are a prevalent type of DNA damage caused by vinyl chloride (VC) exposure and oxidative stress. Etheno adducts are mutagenic and may contribute to the initiation of several pathologies; thus, elucidating the pathways by which they induce cellular transformation is critical. Although N(2),3-ethenoguanine (N(2),3-εG) is the most abundant etheno adduct, its biological consequences have not been well characterized in cells due to its labile glycosidic bond. Here, a stabilized 2'-fluoro-2'-deoxyribose analog of N(2),3-εG was used to quantify directly its genotoxicity and mutagenicity. A multiplex method involving next-generation sequencing enabled a large-scale in vivo analysis, in which both N(2),3-εG and its isomer 1,N(2)-ethenoguanine (1,N(2)-εG) were evaluated in various repair and replication backgrounds. We found that N(2),3-εG potently induces G to A transitions, the same mutation previously observed in VC-associated tumors. By contrast, 1,N(2)-εG induces various substitutions and frameshifts. We also found that N(2),3-εG is the only etheno lesion that cannot be repaired by AlkB, which partially explains its persistence. Both εG lesions are strong replication blocks and DinB, a translesion polymerase, facilitates the mutagenic bypass of both lesions. Collectively, our results indicate that N(2),3-εG is a biologically important lesion and may have a functional role in VC-induced or inflammation-driven carcinogenesis.
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Affiliation(s)
- Shiou-chi Chang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Bogdan I Fedeles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jie Wu
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - James C Delaney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Deyu Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Linlin Zhao
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, United States Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, United States
| | - Plamen P Christov
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, United States Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, United States Department of Chemistry, Vanderbilt University, Nashville, TN 37232, United States
| | - Emily Yau
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Vipender Singh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Lawrence J Marnett
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, United States Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, United States Department of Chemistry, Vanderbilt University, Nashville, TN 37232, United States Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, United States
| | - Carmelo J Rizzo
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, United States Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, United States Department of Chemistry, Vanderbilt University, Nashville, TN 37232, United States Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, United States
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, United States Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, United States Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, United States
| | - John M Essigmann
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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14
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Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site. Chem Res Toxicol 2015; 28:1455-68. [PMID: 26083477 PMCID: PMC4511292 DOI: 10.1021/acs.chemrestox.5b00140] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
The
conformation of an N2-dG adduct
arising from the heterocyclic amine 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a potent food mutagen, was determined
in 5′-d(C1T2C3X4G5C6G7C8C9A10T11C12)-3′:5′-d(G13A14T15G16G17C18G19C20C21G22A23G24)-3′; X = N2-dG-IQ, in which the modified nucleotide X4 corresponds to G1 in the 5′-d(G1G2CG3CC)-3′ NarI restriction endonuclease site. Circular dichroism (CD) revealed
blue shifts relative to the unmodified duplex, consistent with adduct-induced
twisting, and a hypochromic effect for the IQ absorbance in the near
UV region. NMR revealed that the N2-dG-IQ
adduct adopted a base-displaced intercalated conformation in which
the modified guanine remained in the anti conformation
about the glycosidic bond, the IQ moiety intercalated into the duplex,
and the complementary base C21 was displaced into the major
groove. The processing of the N2-dG-IQ
lesion by hpol η is sequence-dependent; when placed at the reiterated
G3 position, but not at the G1 position, this
lesion exhibits a propensity for frameshift replication [Choi, J.
Y., et al. (2006) J. Biol. Chem., 281, 25297–25306]. The structure of the N2-dG-IQ adduct at the nonreiterated G1 position
was compared to that of the same adduct placed at the G3 position [Stavros, K. M., et al. (2014) Nucleic Acids Res., 42, 3450–3463]. CD indicted minimal spectral
differences between the G1 vs G3N2-dG-IQ adducts. NMR indicated that the N2-dG-IQ adduct exhibited similar base-displaced intercalated
conformations at both the G1 and G3 positions.
This result differed as compared to the corresponding C8-dG-IQ adducts
placed at the same positions. The C8-dG-IQ adduct adopted a minor
groove conformation when placed at position G1 but a base-displaced
intercalated conformation when placed at position G3 in
the NarI sequence. The present studies suggest that
differences in lesion bypass by hpol η may be mediated by differences
in the 3′-flanking sequences, perhaps modulating the ability
to accommodate transient strand slippage intermediates.
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Affiliation(s)
- Kallie M Stavros
- †Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235-1822, United States
| | | | - Carmelo J Rizzo
- †Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235-1822, United States
| | - Michael P Stone
- †Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235-1822, United States
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15
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Zdżalik D, Domańska A, Prorok P, Kosicki K, van den Born E, Falnes PØ, Rizzo CJ, Guengerich FP, Tudek B. Differential repair of etheno-DNA adducts by bacterial and human AlkB proteins. DNA Repair (Amst) 2015; 30:1-10. [PMID: 25797601 PMCID: PMC4451939 DOI: 10.1016/j.dnarep.2015.02.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 02/17/2015] [Accepted: 02/25/2015] [Indexed: 11/16/2022]
Abstract
AlkB proteins are evolutionary conserved Fe(II)/2-oxoglutarate-dependent dioxygenases, which remove alkyl and highly promutagenic etheno(ɛ)-DNA adducts, but their substrate specificity has not been fully determined. We developed a novel assay for the repair of ɛ-adducts by AlkB enzymes using oligodeoxynucleotides with a single lesion and specific DNA glycosylases and AP-endonuclease for identification of the repair products. We compared the repair of three ɛ-adducts, 1,N(6)-ethenoadenine (ɛA), 3,N(4)-ethenocytosine (ɛC) and 1,N(2)-ethenoguanine (1,N(2)-ɛG) by nine bacterial and two human AlkBs, representing four different structural groups defined on the basis of conserved amino acids in the nucleotide recognition lid, engaged in the enzyme binding to the substrate. Two bacterial AlkB proteins, MT-2B (from Mycobacterium tuberculosis) and SC-2B (Streptomyces coelicolor) did not repair these lesions in either double-stranded (ds) or single-stranded (ss) DNA. Three proteins, RE-2A (Rhizobium etli), SA-2B (Streptomyces avermitilis), and XC-2B (Xanthomonas campestris) efficiently removed all three lesions from the DNA substrates. Interestingly, XC-2B and RE-2A are the first AlkB proteins shown to be specialized for ɛ-adducts, since they do not repair methylated bases. Three other proteins, EcAlkB (Escherichia coli), SA-1A, and XC-1B removed ɛA and ɛC from ds and ssDNA but were inactive toward 1,N(2)-ɛG. SC-1A repaired only ɛA with the preference for dsDNA. The human enzyme ALKBH2 repaired all three ɛ-adducts in dsDNA, while only ɛA and ɛC in ssDNA and repair was less efficient in ssDNA. ALKBH3 repaired only ɛC in ssDNA. Altogether, we have shown for the first time that some AlkB proteins, namely ALKBH2, RE-2A, SA-2B and XC-2B can repair 1,N(2)-ɛG and that ALKBH3 removes only ɛC from ssDNA. Our results also suggest that the nucleotide recognition lid is not the sole determinant of the substrate specificity of AlkB proteins.
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Affiliation(s)
- Daria Zdżalik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Domańska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Paulina Prorok
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Konrad Kosicki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Pål Ø Falnes
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carmelo J Rizzo
- Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - F Peter Guengerich
- Department of Biochemistry, Center in Molecular Toxicology, and Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Barbara Tudek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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16
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Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M. Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase η and Sulfolobus solfataricus P2 Polymerase IV. J Am Chem Soc 2015; 137:7011-4. [PMID: 25988947 DOI: 10.1021/jacs.5b02701] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
N(6)-(2-Deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dG) arises from N7-methylation of deoxyguanosine followed by imidazole ring opening. The lesion has been reported to persist in animal tissues. Previous in vitro replication bypass investigations of the MeFapy-dG adduct revealed predominant insertion of C opposite the lesion, dependent on the identity of the DNA polymerase (Pol) and the local sequence context. Here we report crystal structures of ternary Pol·DNA·dNTP complexes between MeFapy-dG-adducted DNA template:primer duplexes and the Y-family polymerases human Pol η and P2 Pol IV (Dpo4) from Sulfolobus solfataricus. The structures of the hPol η and Dpo4 complexes at the insertion and extension stages, respectively, are representative of error-free replication, with MeFapy-dG in the anti conformation and forming Watson-Crick pairs with dCTP or dC.
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Affiliation(s)
- Amritraj Patra
- †Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Surajit Banerjee
- ‡Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,§Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Building 436E, Argonne, Illinois 60439, United States
| | - Tracy L Johnson Salyard
- ‡Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Chanchal K Malik
- ‡Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Plamen P Christov
- ‡Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Carmelo J Rizzo
- ‡Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael P Stone
- ‡Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Martin Egli
- †Department of Biochemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
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17
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Christov PP, Son KJ, Rizzo CJ. Synthesis and characterization of oligonucleotides containing a nitrogen mustard formamidopyrimidine monoadduct of deoxyguanosine. Chem Res Toxicol 2014; 27:1610-8. [PMID: 25136769 PMCID: PMC4164228 DOI: 10.1021/tx5002354] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
N5-Substituted formamidopyrimidine
adducts have been observed from the reaction of dGuo or DNA with aziridine
containing electrophiles, including nitrogen mustards. However, the
role of substituted Fapy-dGuo adducts in the biological response to
nitrogen mustards and related species has not been extensively explored.
We have developed chemistry for the site-specific synthesis of oligonucleotides
containing an N5-nitrogen mustard Fapy-dGuo
using the phosphoramidite approach. The lesion was found to be a good
substrate for Escherichia coli endonuclease
IV and formamidopyrimidine glycosylase.
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Affiliation(s)
- Plamen P Christov
- 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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18
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Singh V, Fedeles BI, Li D, Delaney JC, Kozekov ID, Kozekova A, Marnett LJ, Rizzo CJ, Essigmann JM. Mechanism of repair of acrolein- and malondialdehyde-derived exocyclic guanine adducts by the α-ketoglutarate/Fe(II) dioxygenase AlkB. Chem Res Toxicol 2014; 27:1619-31. [PMID: 25157679 PMCID: PMC4164229 DOI: 10.1021/tx5002817] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
The
structurally related exocyclic guanine adducts α-hydroxypropano-dG
(α-OH-PdG), γ-hydroxypropano-dG (γ-OH-PdG), and
M1dG are formed when DNA is exposed to the reactive aldehydes
acrolein and malondialdehyde (MDA). These lesions are believed to
form the basis for the observed cytotoxicity and mutagenicity of acrolein
and MDA. In an effort to understand the enzymatic pathways and chemical
mechanisms that are involved in the repair of acrolein- and MDA-induced
DNA damage, we investigated the ability of the DNA repair enzyme AlkB,
an α-ketoglutarate/Fe(II) dependent dioxygenase, to process
α-OH-PdG, γ-OH-PdG, and M1dG in both single-
and double-stranded DNA contexts. By monitoring the repair reactions
using quadrupole time-of-flight (Q-TOF) mass spectrometry, it was
established that AlkB can oxidatively dealkylate γ-OH-PdG most
efficiently, followed by M1dG and α-OH-PdG. The AlkB
repair mechanism involved multiple intermediates and complex, overlapping
repair pathways. For example, the three exocyclic guanine adducts
were shown to be in equilibrium with open-ring aldehydic forms, which
were trapped using (pentafluorobenzyl)hydroxylamine (PFBHA) or NaBH4. AlkB repaired the trapped open-ring form of γ-OH-PdG
but not the trapped open-ring of α-OH-PdG. Taken together, this
study provides a detailed mechanism by which three-carbon bridge exocyclic
guanine adducts can be processed by AlkB and suggests an important
role for the AlkB family of dioxygenases in protecting against the
deleterious biological consequences of acrolein and MDA.
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Affiliation(s)
- Vipender Singh
- Departments of Biological Engineering, ‡Chemistry, and §Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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19
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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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20
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Abstract
The synthesis of G-N2-(CH2)3-N2-G trimethylene DNA interstrand cross-links (ICLs) in a 5'-CG-3' and 5'-GC-3' sequence from oligodeoxynucleotides containing N2-(3-aminopropyl)-2'-deoxyguanosine and 2-fluoro-O6-(trimethylsilylethyl)inosine is presented. Automated solid-phase DNA synthesis was used for unmodified bases and modified nucleotides were incorporated via their corresponding phosphoramidite reagent by a manual coupling protocol. The preparation of the phosphoramidite reagents for incorporation of N2-(3-aminopropyl)-2'-deoxyguanosine is reported. The high-purity trimethylene DNA interstrand cross-link product is obtained through a nucleophilic aromatic substitution reaction between the N2-(3-aminopropyl)-2'-deoxyguanosine and 2-fluoro-O6-(trimethylsilylethyl)inosine containing oligodeoxynucleotides.
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Affiliation(s)
- Francesca Gruppi
- Departments of Chemistry and Biochemistry, Center for Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Tracy L. Johnson Salyard
- Departments of Chemistry and Biochemistry, Center for Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Carmelo J. Rizzo
- Departments of Chemistry and Biochemistry, Center for Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
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21
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Stavros KM, Hawkins EK, Rizzo CJ, Stone MP. Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence. Nucleic Acids Res 2014; 42:3450-63. [PMID: 24366876 PMCID: PMC3950664 DOI: 10.1093/nar/gkt1109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/18/2013] [Accepted: 10/21/2013] [Indexed: 12/14/2022] Open
Abstract
2-Amino-3-methylimidazo[4,5-f]quinolone (IQ), a heterocyclic amine found in cooked meats, undergoes bioactivation to a nitrenium ion, which alkylates guanines at both the C8-dG and N2-dG positions. The conformation of a site-specific N2-dG-IQ adduct in an oligodeoxynucleotide duplex containing the iterated CG repeat restriction site of the NarI endonuclease has been determined. The IQ moiety intercalates, with the IQ H4a and CH3 protons facing the minor groove, and the IQ H7a, H8a and H9a protons facing the major groove. The adducted dG maintains the anti-conformation about the glycosyl bond. The complementary dC is extruded into the major groove. The duplex maintains its thermal stability, which is attributed to stacking between the IQ moiety and the 5'- and 3'-neighboring base pairs. This conformation is compared to that of the C8-dG-IQ adduct in the same sequence, which also formed a 'base-displaced intercalated' conformation. However, the C8-dG-IQ adopted the syn conformation placing the Watson-Crick edge of the modified dG into the major groove. In addition, the C8-dG-IQ adduct was oriented with the IQ CH3 group and H4a and H5a facing the major groove. These differences may lead to differential processing during DNA repair and replication.
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Affiliation(s)
| | | | | | - Michael P. Stone
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235-1822, USA
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22
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Maddukuri L, Shuck SC, Eoff RL, Zhao L, Rizzo CJ, Guengerich FP, Marnett LJ. Replication, repair, and translesion polymerase bypass of N⁶-oxopropenyl-2'-deoxyadenosine. Biochemistry 2013; 52:8766-76. [PMID: 24171480 DOI: 10.1021/bi401103k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The oxidative stress products malondialdehyde and base propenal react with DNA bases forming the adduction products 3-(2'-deoxy-β-D-erythro-pentofuranosyl)pyrimido[1,2-a]purin-10(3H)-one (M1dG) and N(6)-(oxypropenyl)-2'-deoxyadenosine (OPdA). M1dG is mutagenic in vivo and miscodes in vitro, but little work has been done on OPdA. To improve our understanding of the effect of OPdA on polymerase activity and mutagenicity, we evaluated the ability of the translesion DNA polymerases hPols η, κ, and ι to bypass OPdA in vitro. hPols η and κ inserted dNTPs opposite the lesion and extended the OPdA-modified primer to the terminus. hPol ι inserted dNTPs opposite OPdA but failed to fully extend the primer. Steady-state kinetic analysis indicated that these polymerases preferentially insert dTTP opposite OPdA, although less efficiently than opposite dA. Minimal incorrect base insertion was observed for all polymerases, and dCTP was the primary mis-insertion event. Examining replicative and repair polymerases revealed little effect of OPdA on the Sulfolobus solfataricus polymerase Dpo1 or the Klenow fragment of Escherichia coli DNA polymerase I. Bacteriophage T7 DNA polymerase displayed a reduced level of OPdA bypass compared to unmodified DNA, and OPdA nearly completely blocked the activity of base excision repair polymerase hPol β. This work demonstrates that bypass of OPdA is generally error-free, modestly decreases the catalytic activity of most polymerases, and blocks hPol β polymerase activity. Although mis-insertion opposite OPdA is relatively weak, the efficiency of bypass may introduce A → G transitions observed in vivo.
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Affiliation(s)
- Leena Maddukuri
- A. B. Hancock Jr. Memorial Laboratory for Cancer Research, †Department of Biochemistry, ‡Department of Chemistry, and §Department of Pharmacology, Center in Molecular Toxicology, Vanderbilt Institute of Chemical Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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23
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Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP. Ring-opening of the γ-OH-PdG adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4. Chem Res Toxicol 2013; 26:1348-60. [PMID: 23947567 PMCID: PMC3775444 DOI: 10.1021/tx400200b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Acrolein, a mutagenic aldehyde, reacts with deoxyguanosine (dG) to form 3-(2'-deoxy-β-d-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a] purin-10(3H)-one (γ-OH-PdG). When placed opposite deoxycytosine (dC) in DNA, γ-OH-PdG undergoes ring-opening to the N(2)-(3-oxopropyl)-dG. Ring-opening of the adduct has been hypothesized to facilitate nonmutagenic bypass, particularly by DNA polymerases of the Y family. This study examined the bypass of γ-OH-PdG by Sulfolobus solfataricus Dpo4, the prototypic Y-family DNA polymerase, using templates that contained the adduct in either the 5'-CXG-3' or the 5'-TXG-3' sequence context. Although γ-OH-PdG partially blocked Dpo4-catalyzed DNA synthesis, full primer extension was observed, and the majority of bypass products were error-free. Conversion of the adduct into an irreversibly ring-opened derivative prior to reaction facilitated bypass and further improved the fidelity. Structures of ternary Dpo4·DNA·dNTP complexes were determined with primers that either were positioned immediately upstream of the lesion (preinsertion complexes) or had a 3'-terminal dC opposite the lesion (postinsertion complexes); the incoming nucleotides, either dGTP or dATP, were complementary to the template 5'-neighbor nucleotide. In both postinsertion complexes, the adduct existed as ring-opened species, and the resulting base-pair featured Watson-Crick hydrogen bonding. The incoming nucleotide paired with the 5'-neighbor template, while the primer 3'-hydroxyl was positioned to facilitate extension. In contrast, γ-OH-PdG was in the ring-closed form in both preinsertion complexes, and the overall structure did not favor catalysis. These data provide insights into γ-OH-PdG chemistry during replication bypass by the Dpo4 DNA polymerase and may explain why γ-OH-PdG-induced mutations due to primer-template misalignment are uncommon.
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Affiliation(s)
- Ganesh Shanmugam
- Department
of Chemistry, Center
in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - Irina G. Minko
- Center for
Research on Occupational
and Environmental Toxicology, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Surajit Banerjee
- Department
of Chemistry, Center
in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - Plamen P. Christov
- Department
of Chemistry, Center
in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - Ivan D. Kozekov
- Department
of Chemistry, Center
in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - Carmelo J. Rizzo
- Department
of Chemistry, Center
in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States,Department
of Biochemistry,
Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - R. Stephen Lloyd
- Center for
Research on Occupational
and Environmental Toxicology, Oregon Health & Science
University, Portland, Oregon 97239, United States,Department of Molecular and
Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Martin Egli
- Department
of Biochemistry,
Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - Michael P. Stone
- Department
of Chemistry, Center
in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States,Department
of Biochemistry,
Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt
Institute of Chemical Biology, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235,
United States,Tel: 615-322-2589. Fax: 615-322-7591. E-mail:
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24
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Christov PP, Hawkins EK, Kett NR, Rizzo CJ. Simplified synthesis of individual stereoisomers of the 4-hydroxynonenal adducts of deoxyguanosine. Tetrahedron Lett 2013; 54:4289-4291. [PMID: 23935223 DOI: 10.1016/j.tetlet.2013.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We previously reported the synthesis of the 1,N2-deoxyguanosine adducts of 4-hydroxynonenal, an important product of lipid peroxidation, which involved the nucleophilic aromatic substitution reaction of an O6-protected-2-fluoroinosine with 4-amino-1,2,5-trihydroxydecanal followed by periodate oxidation of the vicinal diol.3 An improved synthesis of the amino triols has been developed. The syn and anti diasteromers of a key intermediate, 4-nitro-5-hydroxy-1-decene, were synthesized by a Henry reaction and separated; each diastereomer was further separated into individual enantiomers by chiral supercritical fluid chromatography. Of note, dihydroxylation of the terminal olefin under conventional conditions with catalytic OsO4 and a tertiary amine oxide as the stoichiometric oxidant led to scrambling of stereochemistry at C4. The scrambling was not observed when t-butylhydroperoxide was used as the oxidant.
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Affiliation(s)
- Plamen P Christov
- Vanderbilt Institute of Chemical Biology Synthesis Core, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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25
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Earley LF, Minko IG, Christov PP, Rizzo CJ, Lloyd RS. Mutagenic spectra arising from replication bypass of the 2,6-diamino-4-hydroxy-N(5)-methyl formamidopyrimidine adduct in primate cells. Chem Res Toxicol 2013; 26:1108-14. [PMID: 23763662 DOI: 10.1021/tx4001495] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA exposures to electrophilic methylating agents that are commonly used during chemotherapeutic treatments cause diverse chemical modifications of nucleobases, with reaction at N7-dG being the most abundant. Although this base modification frequently results in destabilization of the glycosyl bond and spontaneous depurination, the adduct can react with hydroxide ion to yield a stable, ring-opened MeFapy-dG, and this lesion has been reported to persist in animal tissues. Results from prior in vitro replication bypass investigations of the MeFapy-dG adduct had revealed complex spectra of replication errors that differed depending on the identity of DNA polymerase and the local sequence context. In this study, a series of nine site-specifically modified MeFapy-dG-containing oligodeoxynucleotides were engineered into a shuttle vector and subjected to replication in primate cells. In all nine sequence contexts examined, MeFapy-dG was shown to be associated with a strong mutator phenotype, predominantly causing base substitutions, with G to T transversions being most common. Single and dinucleotide deletions were also found in a subset of the sequence contexts. Interestingly, single-nucleotide deletions occurred at not only the adducted site, but also one nucleotide downstream of the adduct. Standard models for primer-template misalignment could account for some but not all mutations observed. These data demonstrate that in addition to mutagenesis predicted from replication of DNAs containing O(6)-Me-dG and O(4)-Me-dT, the MeFapy-dG adduct likely contributes to mutagenic events following chemotherapeutic treatments.
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Affiliation(s)
- Lauriel F Earley
- Center for Research on Occupational and Environmental Toxicology and §Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239, United States
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26
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Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY, Rizzo CJ, Egli M, Guengerich FP. Basis of miscoding of the DNA adduct N2,3-ethenoguanine by human Y-family DNA polymerases. J Biol Chem 2012; 287:35516-35526. [PMID: 22910910 DOI: 10.1074/jbc.m112.403253] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
N(2),3-Ethenoguanine (N(2),3-εG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g. lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies exploring the miscoding potential of this lesion are quite indirect because of the lability of the glycosidic bond. We utilized a 2'-fluoro isostere approach to stabilize this lesion and synthesized oligonucleotides containing 2'-fluoro-N(2),3-ε-2'-deoxyarabinoguanosine to investigate the miscoding potential of N(2),3-εG by Y-family human DNA polymerases (pols). In primer extension assays, pol η and pol κ replicated through N(2),3-εG, whereas pol ι and REV1 yielded only 1-base incorporation. Steady-state kinetics revealed that dCTP incorporation is preferred opposite N(2),3-εG with relative efficiencies in the order of pol κ > REV1 > pol η ≈ pol ι, and dTTP misincorporation is the major miscoding event by all four Y-family human DNA pols. Pol ι had the highest dTTP misincorporation frequency (0.71) followed by pol η (0.63). REV1 misincorporated dTTP and dGTP with much lower frequencies. Crystal structures of pol ι with N(2),3-εG paired to dCTP and dTTP revealed Hoogsteen-like base pairing mechanisms. Two hydrogen bonds were observed in the N(2),3-εG:dCTP base pair, whereas only one appears to be present in the case of the N(2),3-εG:dTTP pair. Base pairing mechanisms derived from the crystal structures explain the slightly favored dCTP insertion for pol ι in steady-state kinetic analysis. Taken together, these results provide a basis for the mutagenic potential of N(2),3-εG.
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Affiliation(s)
- Linlin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Matthew G Pence
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Plamen P Christov
- Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Zdzislaw Wawrzak
- Northwestern University Synchrotron Research Center, Life Sciences Collaborative Access Team, Argonne, Illinois 60439
| | - Jeong-Yun Choi
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Gyeonggi-do 440-746, Republic of Korea
| | - Carmelo J Rizzo
- Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146; Department of Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
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27
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Christov PP, Yamanaka K, Choi JY, Takata KI, Wood RD, Guengerich FP, Lloyd RS, Rizzo CJ. Replication of the 2,6-diamino-4-hydroxy-N(5)-(methyl)-formamidopyrimidine (MeFapy-dGuo) adduct by eukaryotic DNA polymerases. Chem Res Toxicol 2012; 25:1652-61. [PMID: 22721435 DOI: 10.1021/tx300113e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
N(6)-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dGuo) has been identified as a stable DNA adduct that arises from the reaction of DNA with a variety of methylating agents. Since this lesion persists in DNA and may contribute to the overall mutagenesis from electrophilic methylating agents, the MeFapy-dGuo lesion was incorporated into oligonucleotides, and its replication bypass was examined in vitro with a panel of eukaryotic high fidelity (hPols α, β, and δ/PCNA) and translesion (hPols η, κ, ι, Rev1, ν, and yPol ζ) polymerases to address its miscoding potential. The MeFapy-dGuo was found to be a strong block to the high fidelity polymerases at either the insertion or the extension step. Efficient translesion synthesis was observed for hPols η and κ, and the combined activities of hRev1 and yPol ζ. The nucleotide sequences of the extension products were determined by mass spectrometry. The error-free extension product was the most abundant product observed for each polymerase. Misreplication products, which included misinsertion of Thy, Gua, and Ade opposite the MeFapy-dGuo lesion, as well as an interesting one-nucleotide deletion product, were observed when hPols η and κ were employed; these events accounted for 8-29% of the total extension products observed. The distribution and abundance of the misreplication products were dependent on the polymerases and local sequence context of the lesion. Collectively, these data suggest that although MeFapy-dGuo adducts represent a relatively minor proportion of the total alkylated lesions, their miscoding potentials could significantly contribute to genomic instability.
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Affiliation(s)
- Plamen P Christov
- Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37235, USA
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28
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Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS, Rizzo CJ, Egli M, Guengerich FP. Replication of N2,3-Ethenoguanine by DNA Polymerases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201109004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS, Rizzo CJ, Egli M, Guengerich FP. Replication of N2,3-ethenoguanine by DNA polymerases. Angew Chem Int Ed Engl 2012; 51:5466-9. [PMID: 22488769 DOI: 10.1002/anie.201109004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/27/2012] [Indexed: 12/15/2022]
Affiliation(s)
- Linlin Zhao
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
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30
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Banerjee S, Christov P, Kozekova A, Rizzo CJ, Egli M, Stone MP. Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV. Chem Res Toxicol 2012; 25:422-35. [PMID: 22313351 PMCID: PMC3285121 DOI: 10.1021/tx200460j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
trans-4-Hydroxynonenal (HNE) is the major peroxidation product of ω-6 polyunsaturated fatty acids in vivo. Michael addition of the N(2)-amino group of dGuo to HNE followed by ring closure of N1 onto the aldehyde results in four diastereomeric 1,N(2)-dGuo (1,N(2)-HNE-dGuo) adducts. The (6S,8R,11S)-HNE-1,N(2)-dGuo adduct was incorporated into the 18-mer templates 5'-d(TCATXGAATCCTTCCCCC)-3' and d(TCACXGAATCCTTCCCCC)-3', where X = (6S,8R,11S)-HNE-1,N(2)-dGuo adduct. These differed in the identity of the template 5'-neighbor base, which was either Thy or Cyt, respectively. Each of these templates was annealed with either a 13-mer primer 5'-d(GGGGGAAGGATTC)-3' or a 14-mer primer 5'-d(GGGGGAAGGATTCC)-3'. The addition of dNTPs to the 13-mer primer allowed analysis of dNTP insertion opposite to the (6S,8R,11S)-HNE-1,N(2)-dGuo adduct, whereas the 14-mer primer allowed analysis of dNTP extension past a primed (6S,8R,11S)-HNE-1,N(2)-dGuo:dCyd pair. The Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) belongs to the Y-family of error-prone polymerases. Replication bypass studies in vitro reveal that this polymerase inserted dNTPs opposite the (6S,8R,11S)-HNE-1,N(2)-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base was dCyt, the polymerase inserted primarily dGTP, whereas if the template 5'-neighbor base was dThy, the polymerase inserted primarily dATP. The latter event would predict low levels of Gua → Thy mutations during replication bypass when the template 5'-neighbor base is dThy. When presented with a primed (6S,8R,11S)-HNE-1,N(2)-dGuo:dCyd pair, the polymerase conducted full-length primer extension. Structures for ternary (Dpo4-DNA-dNTP) complexes with all four template-primers were obtained. For the 18-mer:13-mer template-primers in which the polymerase was confronted with the (6S,8R,11S)-HNE-1,N(2)-dGuo adduct, the (6S,8R,11S)-1,N(2)-dGuo lesion remained in the ring-closed conformation at the active site. The incoming dNTP, either dGTP or dATP, was positioned with Watson-Crick pairing opposite the template 5'-neighbor base, dCyt or dThy, respectively. In contrast, for the 18-mer:14-mer template-primers with a primed (6S,8R,11S)-HNE-1,N(2)-dGuo:dCyd pair, ring opening of the adduct to the corresponding N(2)-dGuo aldehyde species occurred. This allowed Watson-Crick base pairing at the (6S,8R,11S)-HNE-1,N(2)-dGuo:dCyd pair.
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Harris CM, Stec DF, Christov PP, Kozekov ID, Rizzo CJ, Harris TM. Deoxyguanosine forms a bis-adduct with E,E-muconaldehyde, an oxidative metabolite of benzene: implications for the carcinogenicity of benzene. Chem Res Toxicol 2011; 24:1944-56. [PMID: 21972945 PMCID: PMC3408037 DOI: 10.1021/tx2002838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Benzene is employed in large quantities in the chemical industry and is an ubiquitous contaminant in the environment. There is strong epidemiological evidence that benzene exposure induces hematopoietic malignancies, especially acute myeloid leukemia, in humans, but the chemical mechanisms remain obscure. E,E-Muconaldehyde is one of the products of metabolic oxidation of benzene. This paper explores the proposition that E,E-muconaldehyde is capable of forming Gua-Gua cross-links. If formed in DNA, the replication and repair of such cross-links might introduce structural defects that could be the origin of the carcinogenicity. We have investigated the reaction of E,E-muconaldehyde with dGuo and found that the reaction yields two pairs of interconverting diastereomers of a novel heptacyclic bis-adduct having a spiro ring system linking the two Gua residues. The structures of the four diastereomers have been established by NMR spectroscopy and their absolute configurations by comparison of CD spectra with those of model compounds having known configurations. The final two steps in the formation of the bis-nucleoside (5-ring → 6-ring → 7-ring) have significant reversibility, which is the basis for the observed epimerization. The 6-ring precursor was trapped from the equilibrating mixture by reduction with NaBH(4). The anti relationship of the two Gua residues in the heptacyclic bis-adduct precludes it from being formed in B DNA, but the 6-ring precursor could readily be accommodated as an interchain or intrachain cross-link. It should be possible to form similar cross-links of dCyt, dAdo, the ε-amino group of lysine, the imidazole NH of histidine, and N termini of peptides with the dGuo-muconaldehyde monoadduct.
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Affiliation(s)
| | - Donald F. Stec
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | | | - Ivan D. Kozekov
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Carmelo J. Rizzo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Thomas M. Harris
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
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Huang H, Wang H, Kozekova A, Rizzo CJ, Stone MP. Formation of a N2-dG:N2-dG carbinolamine DNA cross-link by the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N2-dG adduct. J Am Chem Soc 2011; 133:16101-10. [PMID: 21916419 PMCID: PMC3187658 DOI: 10.1021/ja205145q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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Michael addition of trans-4-hydroxynonenal (HNE) to deoxyguanosine yields diastereomeric 1,N2-dG adducts in DNA. When placed opposite dC in the 5′-CpG-3′ sequence, the (6S,8R,11S) diastereomer forms a N2-dG:N2-dG interstrand cross-link [Wang, H.; Kozekov, I. D.; Harris, T. M.; Rizzo, C. J. J. Am. Chem. Soc.2003, 125, 5687–5700]. We refined its structure in 5′-d(G1C2T3A4G5C6X7A8G9T10C11C12)-3′·5′-d(G13G14A15C16T17C18Y19C20T21A22G23C24)-3′ [X7 is the dG adjacent to the C6 carbon of the cross-link or the α-carbon of the (6S,8R,11S) 1,N2-dG adduct, and Y19 is the dG adjacent to the C8 carbon of the cross-link or the γ-carbon of the HNE-derived (6S,8R,11S) 1,N2-dG adduct; the cross-link is in the 5′-CpG-3′ sequence]. Introduction of 13C at the C8 carbon of the cross-link revealed one 13C8→H8 correlation, indicating that the cross-link existed predominantly as a carbinolamine linkage. The H8 proton exhibited NOEs to Y19 H1′, C20 H1′, and C20 H4′, orienting it toward the complementary strand, consistent with the (6S,8R,11S) configuration. An NOE was also observed between the HNE H11 proton and Y19 H1′, orienting the former toward the complementary strand. Imine and pyrimidopurinone linkages were excluded by observation of the Y19N2H and X7 N1H protons, respectively. A strong H8→H11 NOE and no 3J(13C→H) coupling for the 13C8–O–C11–H11 eliminated the tetrahydrofuran species derived from the (6S,8R,11S) 1,N2-dG adduct. The (6S,8R,11S) carbinolamine linkage and the HNE side chain were located in the minor groove. The X7N2 and Y19N2 atoms were in the gauche conformation with respect to the linkage, maintaining Watson–Crick hydrogen bonds at the cross-linked base pairs. A solvated molecular dynamics simulation indicated that the anti conformation of the hydroxyl group with respect to C6 of the tether minimized steric interaction and predicted hydrogen bonds involving O8H with C20O2 of the 5′-neighbor base pair G5·C20 and O11H with C18O2 of X7·C18. These may, in part, explain the stability of this cross-link and the stereochemical preference for the (6S,8R,11S) configuration.
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Affiliation(s)
- Hai Huang
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt University, Nashville, Tennessee 37235, United States
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Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP. 1,N2-Etheno-2'-deoxyguanosine adopts the syn conformation about the glycosyl bond when mismatched with deoxyadenosine. Chem Res Toxicol 2011; 24:1071-9. [PMID: 21675798 PMCID: PMC3138413 DOI: 10.1021/tx200089v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The oligodeoxynucleotide 5′-CGCATXGAATCC-3′·5′-GGATTCAATGCG-3′ containing 1,N2-etheno-2′-deoxyguanosine (1,N2-εdG) opposite deoxyadenosine (named the 1,N2-εdG·dA duplex) models the mismatched adenine product associated with error-prone bypass of 1,N2-εdG by the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) and by Escherichia coli polymerases pol I exo– and pol II exo–. At pH 5.2, the Tm of this duplex was increased by 3 °C as compared to the duplex in which the 1,N2-εdG lesion is opposite dC, and it was increased by 2 °C compared to the duplex in which guanine is opposite dA (the dG·dA duplex). A strong NOE between the 1,N2-εdG imidazole proton and the anomeric proton of the attached deoxyribose, accompanied by strong NOEs to the minor groove A20 H2 proton and the mismatched A19 H2 proton from the complementary strand, establish that 1,N2-εdG rotated about the glycosyl bond from the anti to the syn conformation. The etheno moiety was placed into the major groove. This resulted in NOEs between the etheno protons and T5 CH3. A strong NOE between A20 H2 and A19 H2 protons established that A19, opposite to 1,N2-εdG, adopted the anti conformation and was directed toward the helix. The downfield shifts of the A19 amino protons suggested protonation of dA. Thus, the protonated 1,N2-εdG·dA base pair was stabilized by hydrogen bonds between 1,N2-εdG N1 and A19 N1H+ and between 1,N2-εdG O9 and A19N6H. The broad imino proton resonances for the 5′- and 3′-flanking bases suggested that both neighboring base pairs were perturbed. The increased stability of the 1,N2-εdG·dA base pair, compared to that of the 1,N2-εdG·dC base pair, correlated with the mismatch adenine product observed during the bypass of 1,N2-εdG by the Dpo4 polymerase, suggesting that stabilization of this mismatch may be significant with regard to the biological processing of 1,N2-εdG.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235-1822, USA
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Huang H, Wang H, Voehler MW, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP. γ-Hydroxy-1,N2-propano-2'-deoxyguanosine DNA adduct conjugates the N-terminal amine of the KWKK peptide via a carbinolamine linkage. Chem Res Toxicol 2011; 24:1123-33. [PMID: 21561113 PMCID: PMC3138414 DOI: 10.1021/tx200113n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The γ-hydroxy-1,N(2)-propano-2'-deoxyguanosine adduct (γ-OH-PdG) was introduced into 5'-d(GCTAGCXAGTCC)-3'·5'-d(GGACTCGCTAGC)-3' (X = γ-OH-PdG). In the presence of excess peptide KWKK, (13)C isotope-edited NMR revealed the formation of two spectroscopically distinct DNA-KWKK conjugates. These involved the reaction of the KWKK N-terminal amino group with the N(2)-dG propylaldehyde tautomer of the γ-OH-PdG lesion. The guanine N1 base imino resonance at the site of conjugation was observed in isotope-edited (15)N NMR experiments, suggesting that the conjugated guanine was inserted into the duplex and that the guanine imino proton was protected from exchange with water. The conjugates could be reduced in the presence of NaCNBH(3), suggesting that they existed, in part, as imine (Schiff base) linkages. However, (13)C isotope-edited NMR failed to detect the imine linkages, suggesting that these KWKK conjugates existed predominantly as diastereomeric carbinolamines, in equilibrium with trace amounts of the imines. The structures of the diastereomeric DNA-KWKK conjugates were predicted from potential energy minimization of model structures derived from the refined structure of the fully reduced cross-link [ Huang, H., Kozekov, I. D., Kozekova, A., Rizzo, C. J., McCullough, A., Lloyd, R. S., and Stone, M. P. ( 2010 ) Biochemistry , 49 , 6155 -6164 ]. Molecular dynamics calculations carried out in explicit solvent suggested that the conjugate bearing the S-carbinolamine linkage was the major species due to its potential for intramolecular hydrogen bonding. These carbinolamine DNA-KWKK conjugates thermally stabilized duplex DNA. However, the DNA-KWKK conjugates were chemically reversible and dissociated when the DNA was denatured. In this 5'-CpX-3' sequence, the DNA-KWKK conjugates slowly converted to interstrand N(2)-dG:N(2)-dG DNA cross-links and ring-opened γ-OH-PdG derivatives over a period of weeks.
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Affiliation(s)
- Hai Huang
- Department of Chemistry, Center in Molecular Toxicology, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
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Christov PP, Petrova KV, Shanmugam G, Kozekov ID, Kozekova A, Guengerich FP, Stone MP, Rizzo CJ. Comparison of the in vitro replication of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine and 1,N2-etheno-2'-deoxyguanosine lesions by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Chem Res Toxicol 2011; 23:1330-41. [PMID: 20578729 DOI: 10.1021/tx100082e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Oligonucleotides were synthesized containing the 7-(2-oxoheptyl)-etheno-dGuo adduct, which is derived from the reaction of dGuo and the lipid peroxidation product 4-oxo-2-nonenal. The in vitro replication of 7-(2-oxoheptyl)-etheno-dGuo by the model Y-family polymerase Sulfolobus solfataricus P2 DNA Polymerase IV (Dpo4) was examined in two sequences. The extension products were sequenced using an improved LC-ESI-MS/MS protocol developed in our laboratories, and the results were compared to that of the 1,N(2)-etheno-dGuo adduct in the same sequence contexts. Both etheno adducts were highly miscoding when situated in 5'-TXG-3' local sequence contexts with <4% of the extension products being derived from error-free bypass. The major extension products resulted from the misinsertion of Ade opposite the adduct and a one-base deletion. The major extension products from replication of the etheno lesions in a 5'-CXG-3' local sequence context were the result of misinsertion of Ade, a one-base deletion, and error-free bypass. Other minor extension products were also identified. The 7-(2-oxoheptyl)-etheno-dGuo lesion resulted in a larger frequency of misinsertion of Ade, whereas the 1,N(2)-etheno-dGuo gave more of the one-base deletion product. Conformational studies of duplex DNA containing the 7-(2-oxoheptyl)-etheno-dGuo in a 5'-TXG-3' sequence context by NMR indicated the presence of a pH-dependent conformational transition, likely involving the glycosyl bond at the adducted guanosine; the pK(a) for this transition was lower than that observed for the 1,N(2)-epsilon-dGuo lesion. However, the 7-(2-oxoheptyl)-etheno-dGuo lesion, the complementary Cyt, and both flanking base pairs remained disordered at all pH values, which is attributed to the presence of the hydrophobic heptyl group of the 7-(2-oxoheptyl)-etheno-dGuo lesion. The altered pK(a) value and the structural disorder at the 7-(2-oxoheptyl)-etheno-dGuo lesion site, as compared to the same sequence containing the 1,N(2)-etheno-dGuo, may contribute to higher frequency of misinsertion of Ade.
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Affiliation(s)
- Plamen P Christov
- Department of Chemistry, Department of Biochemistry, and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37235-1822, USA
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Petrova KV, Stec DF, Voehler M, Rizzo CJ. Synthesis of the four stereoisomers of 2,3-epoxy-4-hydroxynonanal and their reactivity with deoxyguanosine. Org Biomol Chem 2011; 9:1960-71. [PMID: 21258716 DOI: 10.1039/c0ob00546k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
2,3-Epoxy-4-hydroxynonanal (EHN) is a potential product of lipid peroxidation that gives rise to genotoxic etheno adducts. We have synthesized all four stereoisomers of EHN and individually reacted them with 2'-deoxyguanosine. In addition to 1,N(2)-etheno-2'-deoxyguanosine, 12 stereoisomeric products were isolated and characterized by (1)H NMR and circular dichroism spectroscopy. The stereochemical assignments were consistent with selective NOE spectra, vicinal coupling constants, and molecular mechanics calculations. Reversed-phase HPLC conditions were developed that could separate most of the adduct mixture.
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Affiliation(s)
- Katya V Petrova
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt University, VU Station B 351822, Nashville, Tennessee, 37235-1822, USA
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Kozekov ID, Turesky RJ, Alas GR, Harris CM, Harris TM, Rizzo CJ. Formation of deoxyguanosine cross-links from calf thymus DNA treated with acrolein and 4-hydroxy-2-nonenal. Chem Res Toxicol 2010; 23:1701-13. [PMID: 20964440 DOI: 10.1021/tx100179g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Acrolein (AC) and 4-hydroxy-2-nonenal (HNE) are endogenous bis-electrophiles that arise from the oxidation of polyunsaturated fatty acids. AC is also found in high concentrations in cigarette smoke and automobile exhaust. These reactive α,β-unsaturated aldehyde (enal) covalently modify nucleic acids, to form exocyclic adducts, where the three-carbon hydroxypropano unit bridges the N1 and N(2) positions of deoxyguanosine (dG). The bifunctional nature of these enals allows them to undergo reaction with a second nucleophilic group and form DNA cross-links. These cross-linked enal adducts are likely to contribute to the genotoxic effects of both AC and HNE. We have developed a sensitive mass spectrometric method to detect cross-linked adducts of these enals in calf thymus DNA (CT DNA) treated with AC or HNE. The AC and HNE cross-linked adducts were measured by the stable isotope dilution method, employing a linear quadrupole ion trap mass spectrometer and consecutive reaction monitoring at the MS(3) or MS(4) scan stage. The lower limit of quantification of the cross-linked adducts is ∼1 adduct per 10(8) DNA bases, when 50 μg of DNA is assayed. The cross-linked adducts occur at levels that are ∼1-2% of the levels of the monomeric 1,N(2)-dG adducts in CT DNA treated with either enal.
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Affiliation(s)
- Ivan D Kozekov
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235-1822, USA
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Maddukuri L, Eoff RL, Choi JY, Rizzo CJ, Guengerich FP, Marnett LJ. In vitro bypass of the major malondialdehyde- and base propenal-derived DNA adduct by human Y-family DNA polymerases κ, ι, and Rev1. Biochemistry 2010; 49:8415-24. [PMID: 20726503 PMCID: PMC2943251 DOI: 10.1021/bi1009024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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3-(2′-Deoxy-β-d-erythro-pentofuranosyl)pyrimido-[1,2-a]purin-10(3H)-one (M1dG) is the major adduct derived from the reaction of DNA with the lipid peroxidation product malondialdehyde and the DNA peroxidation product base propenal. M1dG is mutagenic in Escherichia coli and mammalian cells, inducing base-pair substitutions (M1dG → A and M1dG → T) and frameshift mutations. Y-family polymerases may contribute to the mutations induced by M1dG in vivo. Previous reports described the bypass of M1dG by DNA polymerases η and Dpo4. The present experiments were conducted to evaluate bypass of M1dG by the human Y-family DNA polymerases κ, ι, and Rev1. M1dG was incorporated into template-primers containing either dC or dT residues 5′ to the adduct, and the template-primers were subjected to in vitro replication by the individual DNA polymerases. Steady-state kinetic analysis of single nucleotide incorporation indicates that dCMP is most frequently inserted by hPol κ opposite the adduct in both sequence contexts, followed by dTMP and dGMP. dCMP and dTMP were most frequently inserted by hPol ι, and only dCMP was inserted by Rev1. hPol κ extended template-primers in the order M1dG:dC > M1dG:dG > M1dG:dT ∼ M1dG:dA, but neither hPol ι nor Rev1 extended M1dG-containing template-primers. Liquid chromatography−mass spectrometry analysis of the products of hPol κ-catalyzed extension verified this preference in the 3′-GXC-5′ template sequence but revealed the generation of a series of complex products in which dAMP is incorporated opposite M1dG in the 3′-GXT-5′ template sequence. The results indicate that DNA hPol κ or the combined action of hPol ι or Rev1 and hPol κ bypass M1dG residues in DNA and generate products that are consistent with some of the mutations induced by M1dG in mammalian cells.
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Affiliation(s)
- Leena Maddukuri
- A. B. Hancock Jr. Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Christov PP, Chowdhury G, Garmendia CA, Wang F, Stover JS, Elmquist CE, Kozekova A, Angel KC, Turesky RJ, Stone MP, Guengerich FP, Rizzo CJ. The C8-2'-deoxyguanosine adduct of 2-amino-3-methylimidazo[1,2-d]naphthalene, a carbocyclic analogue of the potent mutagen 2-amino-3-methylimidazo[4,5-f]quinoline, is a block to replication in vitro. Chem Res Toxicol 2010; 23:1076-88. [PMID: 20377178 DOI: 10.1021/tx100053n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
2-Amino-3-methylimidazo[1,2-d]naphthalene (cIQ) is a carbocyclic analogue of the dietary carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) in which a naphthalene ring system replaces the quinoline unit of IQ. The activity of cIQ in Ames Salmonella typhimurium tester strain TA98 is known to be 4-5 orders of magnitude lower than IQ. cIQ undergoes efficient bioactivation with rat liver microsomes. The C8-dGuo adduct was formed when calf thymus DNA was treated with the N-hydroxy-cIQ metabolite and either acetic anhydride or extracts from cells that overexpress N-acetyl transferase (NAT). These studies indicate that bioactivation, the stability of the N-hydroxylamine ester, and the reactivity of the nitrenium ion with DNA of cIQ are similar to IQ and that none of these factors account for the differences in mutagenic potency of these analogues in Ames assays. Oligonucleotides were synthesized that contain the C8-dGuo adduct of cIQ in the frameshift-prone CG-dinucleotide repeat unit of the NarI recognition sequence. We have examined the in vitro translesion synthesis of this adduct and have found it to be a strong replication block to Escherichia coli DNA polymerase I, Klenow fragment exo(-) (Kf(-)), E. coli DNA polymerase II exo(-) (pol II(-)), and Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Previous studies by Fuchs and co-workers identified E. coli pol II as the polymerase responsible for two-base deletions of the C8-dGuo adduct of N-acetyl-2-aminofluorene in the NarI sequence. Our observation that pol II is strongly inhibited by the C8-dGuo adduct of cIQ suggests that one of the other SOS inducible polymerases (E. coli pol IV or pol V) is required for its bypass, and this accounts for the greatly attenuated mutagenicity in the Ames assays as compared with IQ.
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Affiliation(s)
- Plamen P Christov
- Department of Chemistry and Biochemistry, Vanderbilt University, Nashville, Tennessee 37235-1822, USA
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Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP. Minor groove orientation of the KWKK peptide tethered via the N-terminal amine to the acrolein-derived 1,N2-gamma-hydroxypropanodeoxyguanosine lesion with a trimethylene linkage. Biochemistry 2010; 49:6155-64. [PMID: 20604523 PMCID: PMC2907095 DOI: 10.1021/bi100364f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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DNA−protein conjugates are potentially repaired via proteolytic digestion to DNA−peptide conjugates. The latter have been modeled with the amino-terminal lysine of the peptide KWKK conjugated via a trimethylene linkage to the N2-dG amine positioned in 5′-d(GCTAGCXAGTCC)-3′·5′-d(GGACTCGCTAGC)-3′ (X = N2-dG−trimethylene link−KWKK). This linkage is a surrogate for the reversible linkage formed by the γ-OH-1,N2-propanodeoxyguanosine (γ-OH-PdG) adduct. This conjugated KWKK stabilizes the DNA. Amino acids K26, W27, K28, and K29 are in the minor groove. The W27 indolyl group does not intercalate into the DNA. The G7N2 amine and the K26 N-terminal amine nitrogens are in the trans configuration with respect to the Cα or Cγ of the trimethylene tether, respectively. The structure of this DNA−KWKK conjugate is discussed in the context of its biological processing.
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Affiliation(s)
- Hai Huang
- Department of Chemistry, Center in Molecular Toxicology, Center for Structural Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
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Christov PP, Banerjee S, Stone MP, Rizzo CJ. Selective Incision of the alpha-N-Methyl-Formamidopyrimidine Anomer by Escherichia coli Endonuclease IV. J Nucleic Acids 2010; 2010. [PMID: 20798848 PMCID: PMC2925382 DOI: 10.4061/2010/850234] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 06/04/2010] [Indexed: 01/09/2023] Open
Abstract
Formamidopyrimidines (Fapy) lesions result from ring opening of the imidazole portion of purines. Fapy lesions can isomerize from the natural β-anomeric stereochemistry to the α-configuration. We have unambiguously demonstrated that the α-methyl-Fapy-dG (MeFapy-dG) lesion is a substrate for Escherichia coli Endonuclease IV (Endo IV). Treatment of a MeFapy-dG-containing 24 mer duplex with Endo IV resulted in 36–40% incision. The catalytic efficiency of the incision was comparable to that of α-dG in the same duplex sequence. The α- and β-MeFapy-dG anomers equilibrate to ~21 : 79 ratio over ~3 days. Related studies with a duplex containing the α-Fapy-dG lesion derived from aflatoxin B1 epoxide (α-AFB-Fapy-dG) showed only low levels of incision. It is hypothesized that the steric bulk of the aflatoxin moiety interferes with the binding of the substrate to Endo IV and the incision chemistry.
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Affiliation(s)
- Plamen P Christov
- Departments of Chemistry and Biochemistry, Center in Molecular Toxicology, Vanderbilt University, VU Station B 351822, Nashville, N 37235-1822, USA
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Abstract
Trans-4-Hydroxynonenal (HNE) is a peroxidation product of omega-6 polyunsaturated fatty acids. Michael addition of HNE to deoxyguanosine yields four diastereomeric 1,N(2)-dG adducts. The adduct of (6S,8R,11S) stereochemistry forms interstrand N(2)-dG:N(2)-dG cross-links in the 5'-CpG-3' sequence. It has been compared with the (6R,8S,11R) adduct, incorporated into 5'-d(GCTAGCXAGTCC)-3' . 5'-d(GGACTCGCTAGC)-3', containing the 5'-CpG-3' sequence (X = HNE-dG). Both adducts rearrange in DNA to N(2)-dG aldehydes. These aldehydes exist in equilibrium with diastereomeric cyclic hemiacetals, in which the latter predominate at equilibrium. These cyclic hemiacetals mask the aldehydes, explaining why DNA cross-linking is slow compared to related 1,N(2)-dG adducts formed by acrolein and crotonaldehyde. Both the (6S,8R,11S) and (6R,8S,11R) cyclic hemiacetals are located within the minor groove. However, the (6S,8R,11S) cyclic hemiacetal orients in the 5'-direction, while the (6R,8S,11R) cyclic hemiacetal orients in the 3'-direction. The conformations of the diastereomeric N(2)-dG aldehydes, which are the reactive species involved in DNA cross-link formation, have been calculated using molecular mechanics methods. The (6S,8R,11S) aldehyde orients in the 5'-direction, while the (6R,8S,11R) aldehyde orients in the 3'-direction. This suggests a kinetic basis to explain, in part, why the (6S,8R,11S) HNE adduct forms interchain cross-links in the 5'-CpG-3' sequence, whereas (6R,8S,11R) HNE adduct does not. The presence of these cross-links in vivo is anticipated to interfere with DNA replication and transcription, thereby contributing to the etiology of human disease.
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Affiliation(s)
- Hai Huang
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Ivan D. Kozekov
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Albena Kozekova
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Hao Wang
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - R. Stephen Lloyd
- Center for Research on Occupational and Environmental Toxicology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098
| | - Carmelo J. Rizzo
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Michael P. Stone
- Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
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43
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Yamanaka K, Minko IG, Takata KI, Kolbanovskiy A, Kozekov ID, Wood RD, Rizzo CJ, Lloyd RS. Novel enzymatic function of DNA polymerase nu in translesion DNA synthesis past major groove DNA-peptide and DNA-DNA cross-links. Chem Res Toxicol 2010; 23:689-95. [PMID: 20102227 PMCID: PMC2838406 DOI: 10.1021/tx900449u] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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DNA polymerase ν (POLN or pol ν) is a newly discovered A family polymerase that generates a high error rate when incorporating nucleotides opposite dG; its translesion DNA synthesis (TLS) capability has only been demonstrated for high fidelity replication bypass of thymine glycol lesions. In the current investigation, we describe a novel TLS substrate specificity of pol ν, demonstrating that it is able to bypass exceptionally large DNA lesions whose linkages are through the DNA major groove. Specifically, pol ν catalyzed efficient and high fidelity TLS past peptides linked to N6-dA via a reduced Schiff base linkage with a γ-hydroxypropano-dA. Additionally, pol ν could bypass DNA interstrand cross-links with linkage between N6-dAs in complementary DNA strands. However, the chemically identical DNA−peptide and DNA interstrand cross-links completely blocked pol ν when they were located in the minor groove via a N2-dG linkage. Furthermore, we showed that pol ν incorporated a nucleotide opposite the 1,N6-etheno-dA (εdA) in an error-free manner and (+)-trans-anti-benzo[a]pyrene-7,8-dihydrodiol 9,10-epoxide-dA [(+)-BPDE-dA] in an error-prone manner, albeit with a greatly reduced capability. Collectively, these data suggest that although pol ν bypass capacity cannot be generalized to all major groove DNA adducts, this polymerase could be involved in TLS when genomic replication is blocked by extremely large major groove DNA lesions. In view of the recent observation that pol ν may have a role in cellular tolerance to DNA cross-linking agents, our findings provide biochemical evidence for the potential functioning of this polymerase in the bypass of some DNA−protein and DNA−DNA cross-links.
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Affiliation(s)
- Kinrin Yamanaka
- Department of Physiology and Pharmacology, Center for Research on Occupational and Environmental Toxicology, Oregon Health & Science University, L606, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
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44
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Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP. Structure of the 1,N(2)-etheno-2'-deoxyguanosine lesion in the 3'-G(epsilon dG)T-5' sequence opposite a one-base deletion. Biochemistry 2010; 49:2615-26. [PMID: 20201499 PMCID: PMC2844103 DOI: 10.1021/bi901516d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The structure of the 1,N(2)-ethenodeoxyguanosine lesion (1,N(2)-epsilondG) has been characterized in 5'-d(CGCATXGAATCC)-3'.5'-d(GGATTCATGCG)-3' (X = 1,N(2)-epsilondG), in which there is no dC opposite the lesion. This duplex (named the 1-BD duplex) models the product of translesion bypass of 1,N(2)-epsilondG by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) [Zang, H., Goodenough, A. K., Choi, J. Y., Irimia, A., Loukachevitch, L. V., Kozekov, I. D., Angel, K. C., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2005) J. Biol. Chem. 280, 29750-29764], leading to a one-base deletion. The T(m) of this duplex is 6 degrees C higher than that of the duplex in which dC is present opposite the 1,N(2)-epsilondG lesion and 8 degrees C higher than that of the unmodified 1-BD duplex. Analysis of NOEs between the 1,N(2)-epsilondG imidazole and deoxyribose H1' protons and between the 1,N(2)-epsilondG etheno H6 and H7 protons and DNA protons establishes that 1,N(2)-epsilondG adopts the anti conformation about the glycosyl bond and that the etheno moiety is accommodated within the helix. The resonances of the 1,N(2)-epsilondG H6 and H7 etheno protons shift upfield relative to the monomer 1,N(2)-epsilondG, attributed to ring current shielding, consistent with their intrahelical location. NMR data reveal that Watson-Crick base pairing is maintained at both the 5' and 3' neighbor base pairs. The structure of the 1-BD duplex has been refined using molecular dynamics calculations restrained by NMR-derived distance and dihedral angle restraints. The increased stability of the 1,N(2)-epsilondG lesion in the absence of the complementary dC correlates with the one-base deletion extension product observed during the bypass of the 1,N(2)-epsilondG lesion by the Dpo4 polymerase, suggesting that stabilization of this bulged intermediate may be significant with regard to the biological processing of the lesion.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Center in MolecularToxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
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45
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Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ. Structural and functional analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed bypass of the malondialdehyde-deoxyguanosine adduct. Biochemistry 2009; 48:7079-88. [PMID: 19492857 PMCID: PMC2717710 DOI: 10.1021/bi9003588] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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Oxidative stress can induce the formation of reactive electrophiles, such as DNA peroxidation products, e.g., base propenals, and lipid peroxidation products, e.g., malondialdehyde. Base propenals and malondialdehyde react with DNA to form adducts, including 3-(2′-deoxy-β-d-erythro-pentofuranosyl)pyrimido[1,2-α]purin-10(3H)-one (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG (N2-OPdG). Previous work has shown that M1dG is mutagenic in bacteria and mammalian cells and that its mutagenicity in Escherichia coli is dependent on induction of the SOS response, indicating a role for translesion DNA polymerases in the bypass of M1dG. To probe the mechanism by which translesion polymerases bypass M1dG, kinetic and structural studies were conducted with a model Y-family DNA polymerase, Dpo4 from Sulfolobus solfataricus. The level of steady-state incorporation of dNTPs opposite M1dG was reduced 260−2900-fold and exhibited a preference for dATP incorporation. Liquid chromatography−tandem mass spectrometry analysis of the full-length extension products revealed a spectrum of products arising principally by incorporation of dC or dA opposite M1dG followed by partial or full-length extension. A greater proportion of −1 deletions were observed when dT was positioned 5′ of M1dG. Two crystal structures were determined, including a “type II” frameshift deletion complex and another complex with Dpo4 bound to a dC·M1dG pair located in the postinsertion context. Importantly, M1dG was in the ring-closed state in both structures, and in the structure with dC opposite M1dG, the dC residue moved out of the Dpo4 active site, into the minor groove. The results are consistent with the reported mutagenicity of M1dG and illustrate how the lesion may affect replication events.
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Affiliation(s)
- Robert L Eoff
- Department of Chemistry, A. B. Hancock Jr. Memorial Laboratory for Cancer Research, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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46
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Ben-Yehoyada M, Wang LC, Kozekov ID, Rizzo CJ, Gottesman ME, Gautier J. Checkpoint signaling from a single DNA interstrand crosslink. Mol Cell 2009; 35:704-15. [PMID: 19748363 DOI: 10.1016/j.molcel.2009.08.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Revised: 03/27/2009] [Accepted: 08/25/2009] [Indexed: 11/17/2022]
Abstract
DNA interstrand crosslinks (ICLs) are the most toxic lesions induced by chemotherapeutic agents such as mitomycin C and cisplatin. By covalently linking both DNA strands, ICLs prevent DNA melting, transcription, and replication. Studies on ICL signaling and repair have been limited, because these drugs generate additional DNA lesions that trigger checkpoint signaling. Here, we monitor sensing, signaling from, and repairing of a single site-specific ICL in cell-free extract derived from Xenopus eggs and in mammalian cells. Notably, we demonstrate that ICLs trigger a checkpoint response independently of origin-initiated DNA replication and uncoupling of DNA polymerase and DNA helicase. The Fanconi anemia pathway acts upstream of RPA-ATR-Chk1 to generate the ICL signal. The system also repairs ICLs in a reaction that involves extensive, error-free DNA synthesis. Repair occurs by both origin-dependent and origin-independent mechanisms. Our data suggest that cell sensitivity to crosslinking agents results from both checkpoint and DNA repair defects.
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Affiliation(s)
- Merav Ben-Yehoyada
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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47
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Christov PP, Angel KC, Guengerich FP, Rizzo CJ. Replication past the N5-methyl-formamidopyrimidine lesion of deoxyguanosine by DNA polymerases and an improved procedure for sequence analysis of in vitro bypass products by mass spectrometry. Chem Res Toxicol 2009; 22:1086-95. [PMID: 19397282 DOI: 10.1021/tx900047c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Oligonucleotides containing a site-specific N(6)-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dGuo) lesion were synthesized, and their in vitro replication by Escherichia coli DNA polymerase I Klenow fragment (exo(-)) and Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) resulted in the misincorporation of Ade, Gua, and Thy opposite the MeFapy-dGuo lesion in addition to the correct insertion of Cyt. However, sequencing of the full-length extension products revealed that the initial insertion of Cyt opposite the lesion was extended most efficiently. Two sequences were examined, and the misincorporation was sequence-dependent. Improvements in the method for the mass spectrometric sequencing of the extension products were developed; a 5'-biotinylated primer strand was used that contained a dUrd near the template-primer junction. The extended primer was immobilized with streptavidin-coated beads, allowing it to be washed free of polymerase, the template strand, and other reagents. The extended primer was cleaved from the solid support with uridine DNA deglycosylase and piperidine treatment, and the extension products were sequenced by LC-ESI-MS-MS. The purification steps afforded by the biotinylated primer resulted in improved sensitivity for the MS analysis. Translesion synthesis of a template with a local 5'-T-(MeFapy-dGuo)-G-3' sequence resulted in only error-free bypass and extension, whereas a template with a local 5'-T-(MeFapy-dGuo)-T-3' sequence also resulted in an interesting deletion product and the misincorporation of Ade opposite the MeFapy-dGuo lesion.
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Affiliation(s)
- Plamen P Christov
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235-1822, USA
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48
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Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP. Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes. J Biol Chem 2009; 284:17687-99. [PMID: 19542237 DOI: 10.1074/jbc.m109014274] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Previous work has shown that Y-family DNA polymerases tolerate large DNA adducts, but a substantial decrease in catalytic efficiency and fidelity occurs during bypass of N2,N2-dimethyl (Me2)-substituted guanine (N2,N2-Me2G), in contrast to a single methyl substitution. Therefore, it is unclear why the addition of two methyl groups is so disruptive. The presence of N2,N2-Me2G lowered the catalytic efficiency of the model enzyme Sulfolobus solfataricus Dpo4 16,000-fold. Dpo4 inserted dNTPs almost at random during bypass of N2,N2-Me2G, and much of the enzyme was kinetically trapped by an inactive ternary complex when N2,N2-Me2G was present, as judged by a reduced burst amplitude (5% of total enzyme) and kinetic modeling. One crystal structure of Dpo4 with a primer having a 3'-terminal dideoxycytosine (Cdd) opposite template N2,N2-Me2G in a post-insertion position showed Cdd folded back into the minor groove, as a catalytically incompetent complex. A second crystal had two unique orientations for the primer terminal Cdd as follows: (i) flipped into the minor groove and (ii) a long pairing with N2,N2-Me2G in which one hydrogen bond exists between the O-2 atom of Cdd and the N-1 atom of N2,N2-Me2G, with a second water-mediated hydrogen bond between the N-3 atom of Cdd and the O-6 atom of N2,N2-Me2G. A crystal structure of Dpo4 with dTTP opposite template N2,N2-Me2G revealed a wobble orientation. Collectively, these results explain, in a detailed manner, the basis for the reduced efficiency and fidelity of Dpo4-catalyzed bypass of N2,N2-Me2G compared with mono-substituted N2-alkyl G adducts.
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Affiliation(s)
- Huidong Zhang
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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49
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Minko IG, Kozekov ID, Harris TM, Rizzo CJ, Lloyd RS, Stone MP. Chemistry and biology of DNA containing 1,N(2)-deoxyguanosine adducts of the alpha,beta-unsaturated aldehydes acrolein, crotonaldehyde, and 4-hydroxynonenal. Chem Res Toxicol 2009; 22:759-78. [PMID: 19397281 PMCID: PMC2685875 DOI: 10.1021/tx9000489] [Citation(s) in RCA: 330] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The α,β-unsaturated aldehydes (enals) acrolein, crotonaldehyde, and trans-4-hydroxynonenal (4-HNE) are products of endogenous lipid peroxidation, arising as a consequence of oxidative stress. The addition of enals to dG involves Michael addition of the N2-amine to give N2-(3-oxopropyl)-dG adducts, followed by reversible cyclization of N1 with the aldehyde, yielding 1,N2-dG exocyclic products. The 1,N2-dG exocyclic adducts from acrolein, crotonaldehyde, and 4-HNE exist in human and rodent DNA. The enal-induced 1,N2-dG lesions are repaired by the nucleotide excision repair pathway in both Escherichia coli and mammalian cells. Oligodeoxynucleotides containing structurally defined 1,N2-dG adducts of acrolein, crotonaldehyde, and 4-HNE were synthesized via a postsynthetic modification strategy. Site-specific mutagenesis of enal adducts has been carried out in E. coli and various mammalian cells. In all cases, the predominant mutations observed are G→T transversions, but these adducts are not strongly miscoding. When placed into duplex DNA opposite dC, the 1,N2-dG exocyclic lesions undergo ring opening to the corresponding N2-(3-oxopropyl)-dG derivatives. Significantly, this places a reactive aldehyde in the minor groove of DNA, and the adducted base possesses a modestly perturbed Watson−Crick face. Replication bypass studies in vitro indicate that DNA synthesis past the ring-opened lesions can be catalyzed by pol η, pol ι, and pol κ. It also can be accomplished by a combination of Rev1 and pol ζ acting sequentially. However, efficient nucleotide insertion opposite the 1,N2-dG ring-closed adducts can be carried out only by pol ι and Rev1, two DNA polymerases that do not rely on the Watson−Crick pairing to recognize the template base. The N2-(3-oxopropyl)-dG adducts can undergo further chemistry, forming interstrand DNA cross-links in the 5′-CpG-3′ sequence, intrastrand DNA cross-links, or DNA−protein conjugates. NMR and mass spectrometric analyses indicate that the DNA interstand cross-links contain a mixture of carbinolamine and Schiff base, with the carbinolamine forms of the linkages predominating in duplex DNA. The reduced derivatives of the enal-mediated N2-dG:N2-dG interstrand cross-links can be processed in mammalian cells by a mechanism not requiring homologous recombination. Mutations are rarely generated during processing of these cross-links. In contrast, the reduced acrolein-mediated N2-dG peptide conjugates can be more mutagenic than the corresponding monoadduct. DNA polymerases of the DinB family, pol IV in E. coli and pol κ in human, are implicated in error-free bypass of model acrolein-mediated N2-dG secondary adducts, the interstrand cross-links, and the peptide conjugates.
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Affiliation(s)
- Irina G Minko
- Center for Research on Occupational and Environmental Toxicology, Oregon Health & Science University, Portland, Oregon 97239, USA
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50
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Christov PP, Brown KL, Kozekov ID, Stone MP, Harris TM, Rizzo CJ. Site-specific synthesis and characterization of oligonucleotides containing an N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion, the ring-opened product from N7-methylation of deoxyguanosine. Chem Res Toxicol 2009; 21:2324-33. [PMID: 19053322 DOI: 10.1021/tx800352a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A phosphoramidite reagent of N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-1,4-dihydro-4-oxo-5-N-methylformamidopyrimidine (MeFapy-dGuo) lesions was synthesized in four steps from 2'-deoxyguanosine. Fapy nucleosides can rearrange to the pyranose form when the 5'-hydroxyl group is unprotected. The phosphoramidite was incorporated into oligonucleotides using solid-phase synthesis by adjusting the deprotection time for removal of the 5'-dimethoxytrityl group of the MeFapy-dGuo nucleotide, thereby minimizing its rearrangement to the ribopyranose. The furanose and pyranose forms were differentiated by a series of two-dimensional NMR experiments.
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Affiliation(s)
- Plamen P Christov
- Department of Chemistr, Center in Molecular Toxicology, Vanderbilt University, Nashville, Tennessee 37235-1822, USA
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