1
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Crisalli AM, Chen YT, Cai A, Li D, Cho BP. Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts. Nucleic Acids Res 2023; 51:12043-12053. [PMID: 37953358 PMCID: PMC10711442 DOI: 10.1093/nar/gkad1038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/27/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5'-CTTCTC#G*NCCTCATTC-3'], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3' flanking pyrimidine were better bypassed when the 5' base was 5mC, whereas sequences with a 3' purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.
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Affiliation(s)
- Alicia M Crisalli
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Yi-Tzai Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Ang Cai
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Bongsup P Cho
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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2
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Ayerdurai V, Garcia-Cruz A, Piechowska J, Cieplak M, Borowicz P, Noworyta KR, Spolnik G, Danikiewicz W, Lisowski W, Pietrzyk-Le A, D’Souza F, Kutner W, Sharma PS. Selective Impedimetric Chemosensing of Carcinogenic Heterocyclic Aromatic Amine in Pork by dsDNA-Mimicking Molecularly Imprinted Polymer Film-Coated Electrodes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14689-14698. [PMID: 34841873 PMCID: PMC8662733 DOI: 10.1021/acs.jafc.1c05084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Inspired by the easy intercalation of quinoxaline heterocyclic aromatic amines (HAAs) in double-stranded DNA (dsDNA), we synthesized a nucleobase-functionalized molecularly imprinted polymer (MIP) as the recognition unit of an impedimetric chemosensor for the selective determination of a 2-amino-3,7,8-trimethyl-3H-imidazo[4,5-f]quinoxaline (7,8-DiMeIQx) HAA. HAAs are generated in meat and fish processed at high temperatures. They are considered to be potent hazardous carcinogens. The MIP film was prepared by potentiodynamic electropolymerization of a pre-polymerization complex of two adenine- and one thymine-substituted bis(2,2'-bithien-5-yl)methane functional monomer molecules with one 7,8-DiMeIQx template molecule, in the presence of the 2,4,5,2',4',5'-hexa(thiophene-2-yl)-3,3'-bithiophene cross-linking monomer, in solution. The as-formed MIP chemosensor allowed for the selective impedimetric determination of 7,8-DiMeIQx in the 47 to 400 μM linear dynamic concentration range with a limit of detection of 15.5 μM. The chemosensor was successfully applied for 7,8-DiMeIQx determination in the pork meat extract as a proof of concept.
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Affiliation(s)
- Viknasvarri Ayerdurai
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Alvaro Garcia-Cruz
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Joanna Piechowska
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Maciej Cieplak
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Paweł Borowicz
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof R. Noworyta
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Grzegorz Spolnik
- Institute
of Organic Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Witold Danikiewicz
- Institute
of Organic Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Wojciech Lisowski
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Agnieszka Pietrzyk-Le
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Francis D’Souza
- Department
of Chemistry, University of North Texas, 1155 Union Circle No. 305070, Denton, Texas 76203-5017, United States
| | - Wlodzinierz Kutner
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty
of Mathematics and Natural Sciences, School of Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3, 01-938 Warsaw, Poland
| | - Piyush Sindhu Sharma
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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4
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Bellamri M, Walmsley SJ, Turesky RJ. Metabolism and biomarkers of heterocyclic aromatic amines in humans. Genes Environ 2021; 43:29. [PMID: 34271992 PMCID: PMC8284014 DOI: 10.1186/s41021-021-00200-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/27/2021] [Indexed: 12/15/2022] Open
Abstract
Heterocyclic aromatic amines (HAAs) form during the high-temperature cooking of meats, poultry, and fish. Some HAAs also arise during the combustion of tobacco. HAAs are multisite carcinogens in rodents, inducing cancer of the liver, gastrointestinal tract, pancreas, mammary, and prostate glands. HAAs undergo metabolic activation by N-hydroxylation of the exocyclic amine groups to produce the proposed reactive intermediate, the heteroaryl nitrenium ion, which is the critical metabolite implicated in DNA damage and genotoxicity. Humans efficiently convert HAAs to these reactive intermediates, resulting in HAA protein and DNA adduct formation. Some epidemiologic studies have reported an association between frequent consumption of well-done cooked meats and elevated cancer risk of the colorectum, pancreas, and prostate. However, other studies have reported no associations between cooked meat and these cancer sites. A significant limitation in epidemiology studies assessing the role of HAAs and cooked meat in cancer risk is their reliance on food frequency questionnaires (FFQ) to gauge HAA exposure. FFQs are problematic because of limitations in self-reported dietary history accuracy, and estimating HAA intake formed in cooked meats at the parts-per-billion level is challenging. There is a critical need to establish long-lived biomarkers of HAAs for implementation in molecular epidemiology studies designed to assess the role of HAAs in health risk. This review article highlights the mechanisms of HAA formation, mutagenesis and carcinogenesis, the metabolism of several prominent HAAs, and the impact of critical xenobiotic-metabolizing enzymes on biological effects. The analytical approaches that have successfully biomonitored HAAs and their biomarkers for molecular epidemiology studies are presented.
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Affiliation(s)
- Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, MN, 55455, USA.,Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Scott J Walmsley
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, MN, 55455, USA.,Institute of Health Informatics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA.
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5
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Tavakoli A, Paul D, Mu H, Kuchlyan J, Baral S, Ansari A, Broyde S, Min JH. Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein. RSC Chem Biol 2021; 2:523-536. [PMID: 34041491 PMCID: PMC8142930 DOI: 10.1039/d0cb00192a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
Biomolecular structural changes upon binding/unbinding are key to their functions. However, characterization of such dynamical processes is difficult as it requires ways to rapidly and specifically trigger the assembly/disassembly as well as ways to monitor the resulting changes over time. Recently, various chemical strategies have been developed to use light to trigger changes in oligonucleotide structures, and thereby their activities. Here we report that photocleavable DNA can be used to modulate the DNA binding of the Rad4/XPC DNA repair complex using light. Rad4/XPC specifically recognizes diverse helix-destabilizing/distorting lesions including bulky organic adduct lesions and functions as a key initiator for the eukaryotic nucleotide excision repair (NER) pathway. We show that the 6-nitropiperonyloxymethyl (NPOM)-modified DNA is recognized by the Rad4 protein as a specific substrate and that the specific binding can be abolished by light-induced cleavage of the NPOM group from DNA in a dose-dependent manner. Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations despite its bulky NPOM adduct, but Rad4-binding causes it to be heterogeneously distorted. Subsequent extensive conformational searches and molecular dynamics simulations demonstrate that NPOM in DNA can be housed in the major groove of the DNA, with stacking interactions among the nucleotide pairs remaining largely unperturbed and thus retaining overall B-DNA conformation. Our work suggests that photoactivable DNA may be used as a DNA lesion surrogate to study DNA repair mechanisms such as nucleotide excision repair.
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Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
| | - Debamita Paul
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
| | - Hong Mu
- Department of Biology, New York UniversityNew YorkNY 10003USA
| | - Jagannath Kuchlyan
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
| | - Saroj Baral
- Department of Physics, University of Illinois at ChicagoChicagoIL 60607USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at ChicagoChicagoIL 60607USA
| | - Suse Broyde
- Department of Biology, New York UniversityNew YorkNY 10003USA
| | - Jung-Hyun Min
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
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6
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Berger FD, Sturla SJ, Kung RW, Montina T, Wetmore SD, Manderville RA. Conformational Preference and Fluorescence Response of a C-Linked C8-Biphenyl-Guanine Lesion in the NarI Mutational Hotspot: Evidence for Enhanced Syn Adduct Formation. Chem Res Toxicol 2017; 31:37-47. [DOI: 10.1021/acs.chemrestox.7b00266] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Florence D. Berger
- Department
of Health Sciences and Technology, Institute of Food, Nutrition, and
Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Shana J. Sturla
- Department
of Health Sciences and Technology, Institute of Food, Nutrition, and
Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Ryan W. Kung
- Department
of Chemistry and Biochemistry, and the Canadian Centre for Research
in Advanced Fluorine Technologies, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Tony Montina
- Department
of Chemistry and Biochemistry, and the Canadian Centre for Research
in Advanced Fluorine Technologies, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department
of Chemistry and Biochemistry, and the Canadian Centre for Research
in Advanced Fluorine Technologies, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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7
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Abstract
The eukaryotic global genomic nucleotide excision repair (GG-NER) pathway is the major mechanism that removes most bulky and some nonbulky lesions from cellular DNA. There is growing evidence that certain DNA lesions are repaired slowly or are entirely resistant to repair in cells, tissues, and in cell extract model assay systems. It is well established that the eukaryotic DNA lesion-sensing proteins do not detect the damaged nucleotide, but recognize the distortions/destabilizations in the native DNA structure caused by the damaged nucleotides. In this article, the nature of the structural features of certain bulky DNA lesions that render them resistant to NER, or cause them to be repaired slowly, is compared to that of those that are good-to-excellent NER substrates. Understanding the structural features that distinguish NER-resistant DNA lesions from good NER substrates may be useful for interpreting the biological significance of biomarkers of exposure of human populations to genotoxic environmental chemicals. NER-resistant lesions can survive to replication and cause mutations that can initiate cancer and other diseases. Furthermore, NER diminishes the efficacy of certain chemotherapeutic drugs, and the design of more potent pharmaceuticals that resist repair can be advanced through a better understanding of the structural properties of DNA lesions that engender repair-resistance.
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Affiliation(s)
- Nicholas E. Geacintov
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| | - Suse Broyde
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
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8
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Bose A, Millsap AD, DeLeon A, Rizzo C, Basu AK. Translesion Synthesis of the N(2)-2'-Deoxyguanosine Adduct of the Dietary Mutagen IQ in Human Cells: Error-Free Replication by DNA Polymerase κ and Mutagenic Bypass by DNA Polymerases η, ζ, and Rev1. Chem Res Toxicol 2016; 29:1549-59. [PMID: 27490094 PMCID: PMC5031085 DOI: 10.1021/acs.chemrestox.6b00221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 12/18/2022]
Abstract
Translesion synthesis (TLS) of the N(2)-2'-deoxyguanosine (dG-N(2)-IQ) adduct of the carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) was investigated in human embryonic kidney 293T cells by replicating plasmid constructs in which the adduct was individually placed at each guanine (G1, G2, or G3) of the NarI sequence (5'-CG1G2CG3CC-3'). TLS efficiency was 38%, 29%, and 25% for the dG-N(2)-IQ located at G1, G2, and G3, respectively, which suggests that dG-N(2)-IQ is bypassed more efficiently by one or more DNA polymerases at G1 than at either G2 or G3. TLS efficiency was decreased 8-35% in cells with knockdown of pol η, pol κ, pol ι, pol ζ, or Rev1. Up to 75% reduction in TLS occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down, suggesting that these three polymerases play important roles in dG-N(2)-IQ bypass. Mutation frequencies (MFs) of dG-N(2)-IQ at G1, G2, and G3 were 23%, 17%, and 11%, respectively, exhibiting a completely reverse trend of the previously reported MF of the C8-dG adduct of IQ (dG-C8-IQ), which is most mutagenic at G3 ( ( 2015 ) Nucleic Acids Res. 43 , 8340 - 8351 ). The major type of mutation induced by dG-N(2)-IQ was targeted G → T, as was reported for dG-C8-IQ. In each site, knockdown of pol κ resulted in an increase in MF, whereas MF was reduced when pol η, pol ι, pol ζ, or Rev1 was knocked down. The reduction in MF was most pronounced when pol η, pol ζ, and Rev1 were simultaneously knocked down and especially when the adduct was located at G3, where MF was reduced by 90%. We conclude that pol κ predominantly performs error-free TLS of the dG-N(2)-IQ adduct, whereas pols η, pol ζ, and Rev1 cooperatively carry out the error-prone TLS. However, in vitro experiments using yeast pol ζ and κ showed that the former was inefficient in full-length primer extension on dG-N(2)-IQ templates, whereas the latter was efficient in both error-free and error-prone extensions. We believe that the observed differences between the in vitro experiments using purified DNA polymerases, and the cellular results may arise from several factors including the crucial roles played by the accessory proteins in TLS.
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Affiliation(s)
- Arindam Bose
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Amy D. Millsap
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Arnie DeLeon
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Carmelo
J. Rizzo
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Ashis K. Basu
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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9
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Borosky GL. Mutagenicity of heteroaromatic amines: Computational study on the influence of methyl substituents. J Mol Graph Model 2016; 69:92-102. [PMID: 27592197 DOI: 10.1016/j.jmgm.2016.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/18/2016] [Accepted: 08/27/2016] [Indexed: 10/21/2022]
Abstract
Quantum mechanical calculations were performed to elucidate the factors determining the variations in mutagenic activity within groups of isomeric heteroaromatic amines that differ in the position of methyl substituents. Formation energies for noncovalent complexes and covalent DNA adducts were evaluated by means of high level quantum chemical methods. According to the computational results in this work, covalent adduct stability is proposed to influence the relative mutagenicities of structurally related heterocyclic amines. The stability of covalent C8-dG DNA adducts was found to be mainly determined by π-stacking interactions between the fused ring system of the heteroaromatic amines and the flanking nucleobases. Relative mutagenicity of amines of very related structure is proposed to be regulated by both nitrenium ion and covalent adduct stabilities.
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Affiliation(s)
- Gabriela L Borosky
- INFIQC, CONICET and Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina.
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10
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Kathuria P, Sharma P, Wetmore SD. Effect of base sequence context on the conformational heterogeneity of aristolactam-I adducted DNA: structural and energetic insights into sequence-dependent repair and mutagenicity. Toxicol Res (Camb) 2016; 5:197-209. [PMID: 30090337 PMCID: PMC6061885 DOI: 10.1039/c5tx00302d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/19/2015] [Indexed: 11/21/2022] Open
Abstract
Aristolochic acids (AAs) are nephrotoxic and potentially carcinogenic plant mutagens that form bulky DNA adducts at the exocyclic amino groups of the purines. The present work utilizes classical molecular dynamics simulations and free energy calculations to investigate the role of lesion site sequence context in dictating the conformational outcomes of DNA containing ALI-N6-dA, the most persistent and mutagenic adduct arising from the AAs. Our calculations reveal that the anti base-displaced intercalated conformer is the lowest energy conformer of damaged DNA in all sequence contexts considered (CXC, CXG, GXC and GXG). However, the experimentally-observed greater mutagenicity of the adduct in the CXG sequence context does not correlate with the relative thermodynamic stability of the adduct in different sequences. Instead, AL-N6-dA adducted DNA is least distorted in the CXG sequence context, which points toward a possible differential repair propensity of the lesion in different sequences. Nevertheless, the structural deviations between adducted DNA with different lesion site sequences are small, and therefore other factors (such as interactions between the adducted DNA and lesion-bypass polymerases during replication) are likely more important for dictating the observed sequence-dependent mutagenicity of ALI-N6-dA.
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Affiliation(s)
- Preetleen Kathuria
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
| | - Purshotam Sharma
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
- Centre for Computational Sciences , Central University of Punjab , Bathinda , Punjab , India 151001
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West , Lethbridge , Alberta , Canada T1K 3M4 . ; ; Tel: +1 403-329-2323
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11
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Toxicology of DNA Adducts Formed Upon Human Exposure to Carcinogens. ADVANCES IN MOLECULAR TOXICOLOGY 2016. [DOI: 10.1016/b978-0-12-804700-2.00007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Politica DA, Malik CK, Basu AK, Stone MP. Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct. Chem Res Toxicol 2015; 28:2253-66. [PMID: 26641105 DOI: 10.1021/acs.chemrestox.5b00277] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
3-Nitrobenzanthrone (3-NBA), an environmental mutagen found in diesel exhaust and a suspected carcinogen, undergoes metabolic reduction followed by reaction with DNA to form aminobenzanthrone (ABA) adducts, with the major alkylation product being N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone (C8-dG-ABA). Site-specific synthesis of the C8-dG-ABA adduct in the oligodeoxynucleotide 5'-d(GTGCXTGTTTGT)-3':5'-d(ACAAACACGCAC)-3'; X = C8-dG-ABA adduct, including codons 272-275 of the p53 gene, has allowed for investigation into the structural and thermodynamic properties of this adduct. The conformation of the C8-dG-ABA adduct was determined using NMR spectroscopy and was refined using molecular dynamics (MD) calculations restrained by experimentally determined interproton distance restraints obtained from NOE experiments. The refined structure revealed that the C8-dG-ABA adduct formed a base-displaced intercalated conformation. The adducted guanine was shifted into the syn conformation about the glycosidic bond. The 5'- and 3'-neighboring base pairs remained intact. While this facilitated π-stacking interactions between the ABA moiety and neighboring bases, the thermal melting temperature (Tm) of the adduct-containing duplex showed a decrease of 11 °C as compared to the corresponding unmodified oligodeoxynucleotide duplex. Overall, in this sequence, the base-displaced intercalated conformation of the C8-dG-ABA lesion bears similarity to structures of other arylamine C8-dG adducts. However, in this sequence, the base-displaced intercalated conformation for the C8-dG-ABA adduct differs from the conformation of the N(2)-dG-ABA adduct reported by de los Santos and co-workers, in which it is oriented in the minor groove toward the 5' end of the duplex, with the modified guanine remaining in the anti conformation about the glyosidic torsion angle, and the complementary base remaining within the duplex. The results are discussed in relationship to differences between the C8-dG-ABA and N(2)-dG-ABA adducts with respect to susceptibility to nucleotide excision repair (NER).
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Affiliation(s)
- Dustin A Politica
- Departments of Chemistry and Biochemistry, Center in Molecular Toxicology, Vanderbilt Institute of Chemical Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Chanchal K Malik
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Michael P Stone
- Departments of Chemistry and Biochemistry, Center in Molecular Toxicology, Vanderbilt Institute of Chemical Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville, Tennessee 37235, United States
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13
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Sproviero M, Verwey AMR, Witham AA, Manderville RA, Sharma P, Wetmore SD. Enhancing Bulge Stabilization through Linear Extension of C8-Aryl-Guanine Adducts to Promote Polymerase Blockage or Strand Realignment to Produce a C:C Mismatch. Chem Res Toxicol 2015. [PMID: 26225720 DOI: 10.1021/acs.chemrestox.5b00233] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Aryl radicals can react at the C8-site of 2'-deoxyguanosine (dG) to produce DNA adducts with a C8-C linkage (denoted C-linked). Such adducts are structurally distinct from those possessing a flexible amine (N-linked) or ether (O-linked) linkage, which separates the C8-aryl moiety from the guanine nucleobase. In the current study, two model C-linked C8-dG adducts, namely, C8-benzo[b]thienyl-dG ([BTh]G) and C8-(pyren-1-yl)-dG ([Py]G), were incorporated into the NarI (12mer, NarI(12) and 22mer, NarI(22)) hotspot sequence for frameshift mutations in bacteria. For the first time, C-linked C8-dG adducts are shown to stabilize the -2 deletion duplex within the NarI sequence. Primer-elongation assays employing Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) demonstrates the influence of C8-aryl ring size and shape in promoting Dpo4 blockage or strand realignment to produce a C:C mismatch downstream of the adduct site. Molecular dynamics simulations of the -2 deletion duplex suggest that both anti and syn adduct structures are energetically accessible. These findings provide a rationale for describing the biochemical outcome induced by C-linked C8-dG adducts when processed by Dpo4.
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Affiliation(s)
- Michael Sproviero
- †Department of Chemistry and Toxicology, University of Guelph, Guelph, ON Canada N1G 2W1
| | - Anne M R Verwey
- †Department of Chemistry and Toxicology, University of Guelph, Guelph, ON Canada N1G 2W1
| | - Aaron A Witham
- †Department of Chemistry and Toxicology, University of Guelph, Guelph, ON Canada N1G 2W1
| | - Richard A Manderville
- †Department of Chemistry and Toxicology, University of Guelph, Guelph, ON Canada N1G 2W1
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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] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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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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Witham AA, Verwey AMR, Sproviero M, Manderville RA, Sharma P, Wetmore SD. Chlorine functionalization of a model phenolic C8-guanine adduct increases conformational rigidity and blocks extension by a Y-family DNA polymerase. Chem Res Toxicol 2015; 28:1346-56. [PMID: 26004422 DOI: 10.1021/acs.chemrestox.5b00143] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Certain phenoxyl radicals can attach covalently to the C8-site of 2'-deoxyguanosine (dG) to afford oxygen-linked C8-dG adducts. Such O-linked adducts can be chemically synthesized through a nucleophilic displacement reaction between a phenolate and a suitably protected 8-Br-dG derivative. This permits the generation of model O-linked C8-dG adducts on scales suitable for insertion into oligonucleotide substrates using solid-phase DNA synthesis. Variation of the C8-aryl moiety provides an opportunity to derive structure-activity relationships on adduct conformation in duplex DNA and replication bypass by DNA polymerases. In the current study, the influence of chlorine C8-dG functionalization on in vitro DNA replication by Klenow fragment exo(-) (Kf(-)) and the Y-family polymerase (Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4)) has been determined. Model O-linked C8-dG adducts derived from the pentachlorophenoxyl radical ([PCP]G) and 2,4,6-trichlorophenoxyl radical ([TCP]G) were inserted into the reiterated G3-position of the NarI sequence (12-mer, NarI(12); and 22-mer, NarI(22)), which is a known hotspot for frameshift mutations mediated by N-linked polycyclic C8-dG adducts in bacterial mutagenesis. Within the NarI(12) duplex, the unsubstituted C8-phenoxy-dG ([PhO]G) adduct adopts a minimally perturbed B-form helix. Chlorination of [PhO]G to afford [PCP]G does not significantly change the adduct conformation within the NarI(12) duplex, as predicted by molecular dynamics simulations. However, when using NarI(22) for DNA synthesis in vitro, the chlorinated [PCP]G and [TCP]G lesions significantly block DNA replication by Kf(-) and Dpo4, whereas [PhO]G is readily bypassed. These findings highlight the impact that chlorine substituents impart to bulky C8-dG lesions.
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Affiliation(s)
- Aaron A Witham
- †Departments of Chemistry and Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Anne M R Verwey
- †Departments of Chemistry and Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Michael Sproviero
- †Departments of Chemistry and Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Richard A Manderville
- †Departments of Chemistry and Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Purshotam Sharma
- ‡Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- ‡Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
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16
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Sharma P, Manderville RA, Wetmore SD. Structural and energetic characterization of the major DNA adduct formed from the food mutagen ochratoxin A in the NarI hotspot sequence: influence of adduct ionization on the conformational preferences and implications for the NER propensity. Nucleic Acids Res 2014; 42:11831-45. [PMID: 25217592 PMCID: PMC4191402 DOI: 10.1093/nar/gku821] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The nephrotoxic food mutagen ochratoxin A (OTA) produces DNA adducts in rat kidneys, the major lesion being the C8-linked-2′-deoxyguanosine adduct (OTB-dG). Although research on other adducts stresses the importance of understanding the structure of the associated adducted DNA, site-specific incorporation of OTB-dG into DNA has yet to be attempted. The present work uses a robust computational approach to determine the conformational preferences of OTB-dG in three ionization states at three guanine positions in the NarI recognition sequence opposite cytosine. Representative adducted DNA helices were derived from over 2160 ns of simulation and ranked via free energies. For the first time, a close energetic separation between three distinct conformations is highlighted, which indicates OTA-adducted DNA likely adopts a mixture of conformations regardless of the sequence context. Nevertheless, the preferred conformation depends on the flanking bases and ionization state due to deviations in discrete local interactions at the lesion site. The structural characteristics of the lesion thus discerned have profound implications regarding its repair propensity and mutagenic outcomes, and support recent experiments suggesting the induction of double-strand breaks and deletion mutations upon OTA exposure. This combined structural and energetic characterization of the OTB-dG lesion in DNA will encourage future biochemical experiments on this potentially genotoxic lesion.
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Affiliation(s)
- Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Richard A Manderville
- Department of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
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17
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Wilson KA, Wetmore SD. Complex Conformational Heterogeneity of the Highly Flexible O6-Benzyl-guanine DNA Adduct. Chem Res Toxicol 2014; 27:1310-25. [PMID: 24941023 DOI: 10.1021/tx500178x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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18
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Jain V, Vaidyanathan VG, Patnaik S, Gopal S, Cho BP. Conformational insights into the lesion and sequence effects for arylamine-induced translesion DNA synthesis: 19F NMR, surface plasmon resonance, and primer kinetic studies. Biochemistry 2014; 53:4059-71. [PMID: 24915610 PMCID: PMC4075988 DOI: 10.1021/bi5003212] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Adduct-induced DNA damage can affect
transcription efficiency and
DNA replication and repair. We previously investigated the effects
of the 3′-next flanking base (G*CT vs G*CA; G*, FABP, N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl;
FAF, N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene)
on the conformation of arylamine-DNA lesions in relation to E. coli nucleotide excision repair (JainV., HiltonB., LinB., PatnaikS., LiangF., DarianE., ZouY., MackerellA. D.Jr., and ChoB. P. (2013) Nucleic Acids Res., 41, 869−88023180767). Here,
we report the differential effects of the same pair of sequences on
DNA replication in vitro by the polymerases exofree
Klenow fragment (Kf-exo–) and Dpo4. We obtained
dynamic 19F NMR spectra for two 19-mer modified templates
during primer elongation: G*CA [d(5′-CTTACCATCG*CAACCATTC-3′)]
and G*CT [d(5′-CTTACCATCG*CTACCATTC-3′)].
We found that lesion stacking is favored in the G*CT sequence compared to the G*CA counterpart. Surface
plasmon resonance binding results showed consistently weaker affinities
for the modified DNA with the binding strength in the order of FABP
> FAF and G*CA > G*CT. Primer extension was stalled at
(n) and near (n – 1 and n + 1) the lesion site, and the extent of blockage and the extension
rates across the lesion were influenced by not only the DNA sequences
but also the nature of the adduct’s chemical structure (FAF
vs FABP) and the polymerase employed (Kf-exo– vs
Dpo4). Steady-state kinetics analysis with Kf-exo– revealed the most dramatic sequence and lesion effects at the lesion
(n) and postinsertion (n + 1) sites,
respectively. Taken together, these results provide insights into
the important role of lesion-induced conformational heterogeneity
in modulating translesion DNA synthesis.
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Affiliation(s)
- Vipin Jain
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
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19
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Nauwelaërs G, Bellamri M, Fessard V, Turesky RJ, Langouët S. DNA adducts of the tobacco carcinogens 2-amino-9H-pyrido[2,3-b]indole and 4-aminobiphenyl are formed at environmental exposure levels and persist in human hepatocytes. Chem Res Toxicol 2013; 26:1367-77. [PMID: 23898916 PMCID: PMC3904354 DOI: 10.1021/tx4002226] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aromatic amines and structurally related heterocyclic aromatic amines (HAAs) are produced during the combustion of tobacco or during the high-temperature cooking of meat. Exposure to some of these chemicals may contribute to the etiology of several common types of human cancers. 2-Amino-9H-pyrido[2,3-b]indole (AαC) is the most abundant HAA formed in mainstream tobacco smoke: it arises in amounts that are 25-100 times greater than the levels of the arylamine, 4-aminobiphenyl (4-ABP), a human carcinogen. 2-Amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) is a prevalent HAA formed in cooked meats. AαC and MeIQx are rodent carcinogens; however, their carcinogenic potency in humans is unknown. A preliminary assessment of the carcinogenic potential of these HAAs in humans was conducted by examining the capacity of primary human hepatocytes to form DNA adducts of AαC and MeIQx, in comparison to 4-ABP, followed by the kinetics of DNA adduct removal by cellular enzyme repair systems. The principal DNA adducts formed were N-(deoxyguanosin-8-yl) (dG-C8) adducts. Comparable levels of DNA adducts were formed with AαC and 4-ABP, whereas adduct formation was ∼5-fold lower for MeIQx. dG-C8-AαC and dG-C8-4-ABP were formed at comparable levels in a concentration-dependent manner in human hepatocytes treated with procarcinogens over a 10,000-fold concentration range (1 nM-10 μM). Pretreatment of hepatocytes with furafylline, a selective inhibitor of cytochrome P450 1A2, resulted in a strong diminution of DNA adducts signifying that P450 1A2 is a major P450 isoform involved in bioactivation of these procarcinogens. The kinetics of adduct removal varied for each hepatocyte donor. Approximately half of the DNA adducts were removed within 24 h of treatment; however, the remaining lesions persisted over 5 days. The high levels of AαC present in tobacco smoke and its propensity to form persistent DNA adducts in human hepatocytes suggest that AαC can contribute to DNA damage and the risk of hepatocellular cancer in smokers.
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20
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Kuska MS, Witham AA, Sproviero M, Manderville RA, Majdi Yazdi M, Sharma P, Wetmore SD. Structural Influence of C8-Phenoxy-Guanine in the NarI Recognition DNA Sequence. Chem Res Toxicol 2013; 26:1397-408. [DOI: 10.1021/tx400252g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Michael S. Kuska
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Aaron A. Witham
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Michael Sproviero
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Mohadeseh Majdi Yazdi
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Purshotam Sharma
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
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21
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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22
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C8-linked bulky guanosine DNA adducts: experimental and computational insights into adduct conformational preferences and resulting mutagenicity. Future Med Chem 2012; 4:1981-2007. [PMID: 23088278 DOI: 10.4155/fmc.12.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bulky DNA adducts are formed through the covalent attachment of aryl groups to the DNA nucleobases. Many of these adducts are known to possess conformational heterogeneity, which is responsible for the variety of mutagenic outcomes associated with these lesions. The present contribution reviews several conformational and mutagenic themes that are prevalent among the DNA adducts formed at the C8-site of the guanine nucleobase. The most important conclusions obtained (to date) from experiments are summarized including the anti/syn conformational preference of the adducts, their potential to inflict DNA mutations and mismatch stabilization, and their interactions with DNA polymerases and repair enzymes. Additionally, the unique role that computer calculations can play in understanding the structural properties of these adducts are highlighted.
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23
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Rao H, Zeng X, Wang Y, He H, Zhu F, Li Z, Chen Y. Identification of DNA adduct formation of small molecules by molecular descriptors and machine learning methods. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.616891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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24
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Vaidyanathan VG, Cho BP. Sequence Effects on Translesion Synthesis of an Aminofluorene–DNA Adduct: Conformational, Thermodynamic, and Primer Extension Kinetic Studies. Biochemistry 2012; 51:1983-95. [DOI: 10.1021/bi2017443] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- V. G. Vaidyanathan
- Department of Biomedical and Pharmaceutical
Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Bongsup P. Cho
- Department of Biomedical and Pharmaceutical
Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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25
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Jain V, Hilton B, Patnaik S, Zou Y, Chiarelli MP, Cho BP. Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence. Nucleic Acids Res 2012; 40:3939-51. [PMID: 22241773 PMCID: PMC3351159 DOI: 10.1093/nar/gkr1307] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Nucleotide excision repair (NER) is a major repair pathway that recognizes and corrects various lesions in cellular DNA. We hypothesize that damage recognition is an initial step in NER that senses conformational anomalies in the DNA caused by lesions. We prepared three DNA duplexes containing the carcinogen adduct N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene (FAAF) at G(1), G(2) or G(3) of NarI sequence (5'-CCG(1)G(2)CG(3)CC-3'). Our (19)F-NMR/ICD results showed that FAAF at G(1) and G(3) prefer syn S- and W-conformers, whereas anti B-conformer was predominant for G(2). We found that the repair of FAAF occurs in a conformation-specific manner, i.e. the highly S/W-conformeric G(3) and -G(1) duplexes incised more efficiently than the B-type G(2) duplex (G(3)∼G(1)> G(2)). The melting and thermodynamic data indicate that the S- and W-conformers produce greater DNA distortion and thermodynamic destabilization. The N-deacetylated N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (FAF) adducts in the same NarI sequence are repaired 2- to 3-fold less than FAAF: however, the incision efficiency was in order of G(2)∼G(1)> G(3), a reverse trend of the FAAF case. We have envisioned the so-called N-acetyl factor as it could raise conformational barriers of FAAF versus FAF. The present results provide valuable conformational insight into the sequence-dependent UvrABC incisions of the bulky aminofluorene DNA adducts.
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Affiliation(s)
- Vipin Jain
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
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26
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Millen AL, Kamenz BL, Leavens FMV, Manderville RA, Wetmore SD. Conformational flexibility of C8-phenoxylguanine adducts in deoxydinucleoside monophosphates. J Phys Chem B 2011; 115:12993-3002. [PMID: 21942470 DOI: 10.1021/jp2057332] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
M06-2X/6-31G(d,p) is used to calculate the structure of all natural deoxydinucleoside monophosphates with G in the 5' or 3' position, the anti or syn conformation, and each natural (A, C, G, T) base in the corresponding flanking position. When the ortho or para C8-phenoxyl-2'-deoxyguanosine (C8-phenoxyl-dG) adduct replaces G in each model, there is little change in the relative base-base orientation or backbone conformation. However, the orientation of the C8-phenoxyl group can be characterized according to the position (5' versus 3'), conformation (anti versus syn), and isomer (ortho versus para) of damage. Although the degree of coplanarity between the phenoxyl ring and G base in the ortho adduct is highly affected by the sequence since the hydroxyl group can interact with neighboring bases, the para adduct generally does not exhibit discrete interactions with flanking bases. For both adducts, steric clashes between the phenoxyl group and the backbone or flanking base destabilize the anti conformation preferred by the natural nucleotide and thereby result in a clear preference for the syn conformation regardless of the sequence or position. This contrasts the conclusions drawn from smaller (nucleoside, nucleotide) models previously used in the literature, which stresses the importance of using models that address the steric constraints present due to the surrounding environment. Since replication errors for other C8-dG bulky adducts have been linked to a preference for the syn conformation, our findings provide insight into the possible mutagenicity of phenolic adducts.
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Affiliation(s)
- Andrea L Millen
- Department of Chemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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27
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Dahlmann HA, Sturla SJ. Synthesis of oxygen-linked 8-phenoxyl-deoxyguanosine nucleoside analogues. European J Org Chem 2011; 2011. [PMID: 24273446 DOI: 10.1002/ejoc.201100013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nucleobase adducts, which form in vivo by the nucleophilic attack of nucleobases on exogenous electrophilic species, can impact conformation and biological influences of the adducted nucleoside. Contemporary studies aim to address the occurrence and relevance of O-linked 8-phenoxy-purine adducts; however, preparative techniques for synthesizing these nucleosides were not previously described. Reported herein is a relatively facile synthesis of O-linked 8-dG phenol adducts with a wide variety of electron-donating, electron-withdrawing, and sterically demanding phenols.
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Affiliation(s)
- Heidi A Dahlmann
- ETH Zürich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 9, Zürich 8006, Switzerland
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28
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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] [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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Millen AL, Churchill CDM, Manderville RA, Wetmore SD. Effect of Watson−Crick and Hoogsteen Base Pairing on the Conformational Stability of C8-Phenoxyl-2′-deoxyguanosine Adducts. J Phys Chem B 2010; 114:12995-3004. [DOI: 10.1021/jp105817p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Cassandra D. M. Churchill
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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30
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Liang F, Cho BP. Enthalpy-entropy contribution to carcinogen-induced DNA conformational heterogeneity. Biochemistry 2010; 49:259-66. [PMID: 19961237 DOI: 10.1021/bi901629p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA damage by adduct formation is a critical step for the initiation of carcinogenesis. Aromatic amines are strong inducers of environmental carcinogenesis. Their DNA adducts are known to exist in an equilibrium between the major groove (B) and base-displaced stacked (S) conformations. However, the factors governing such heterogeneity remain unclear. Here we conducted extensive calorimetry/NMR/CD studies on the model DNA lesions caused by fluorinated 2-aminfluorene (FAF) and 4-aminobiphenyl (FABP) in order to gain thermodynamic and kinetic insights into the S/B conformational equilibrium. We demonstrate that there are large differences in enthalpy-entropy compensations for FABP and FAF. The small and flexible FABP exclusively adopts the less perturbed B conformer with small enthalpy (DeltaDeltaH-2.7 kcal/mol)/entropy (DeltaDeltaS-0.7 eu) change. In contrast, FAF stacks better and exists as a mixture of B and S conformers with large enthalpy (DeltaDeltaH-13.4 kcal/mol)/entropy (DeltaDeltaS-34.2 eu) compensation. van't Hoff analysis of dynamic (19)F NMR data indicated DeltaH(B<-->S) = 4.1 kcal/mol in favor of the B conformer and DeltaS(B<-->S) = 15.6 cal mol(-1) K(-1) in favor of the intercalated S conformer. These findings demonstrate that the favorable entropy of the S conformer over B conformer determines the S/B population ratios at physiological temperatures.
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Affiliation(s)
- Fengting Liang
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA
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Jain N, Meneni S, Jain V, Cho BP. Influence of flanking sequence context on the conformational flexibility of aminofluorene-modified dG adduct in dA mismatch DNA duplexes. Nucleic Acids Res 2009; 37:1628-37. [PMID: 19151371 PMCID: PMC2655675 DOI: 10.1093/nar/gkn1063] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
When positioned opposite to a dA in a DNA duplex, the prototype arylamine-DNA adduct [N-(2'-deoxyguanosin-yl)-7-fluoro-2-aminofluorene (FAF)] adopts the so-called 'wedge' (W) conformation, in which the carcinogen resides in the minor groove of the duplex. All 16 FAF-modified 12-mer NG*N/NAN dA mismatch duplexes (G* = FAF, N = G, A, C, T) exhibited strongly positive induced circular dichroism in the 290-360 nm range (ICD(290-360 nm)), which supports the W conformation. The ICD(290-360 nm) intensities were the greatest for duplexes with a 3'-flanking T. The AG*N duplex series showed little adduct-induced destabilization. An exception was the AG*T duplex, which displayed two well-resolved signals in the (19)F NMR spectra. This was presumably due to a strong lesion-destabilizing effect of the 3'-T. The flanking T effect was substantiated further by findings with the TG*T duplex, which exhibited greater lesion flexibility and nucleotide excision repair recognition. Adduct conformational heterogeneity decreased in order of TG*T > AG*T > CG*T > AG*A > AG*G > AG*C. The dramatic flanking T effect on W-conformeric duplexes is consistent with the strong dependence of the ICD(290-360) on both temperature and salt concentration and could be extended to the arylamine food mutagens that are biologically relevant in humans.
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Affiliation(s)
- Nidhi Jain
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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Boer DR, Canals A, Coll M. DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes. Dalton Trans 2008:399-414. [PMID: 19122895 DOI: 10.1039/b809873p] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Barcelona, Spain
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Jain N, Li Y, Zhang L, Meneni SR, Cho BP. Probing the sequence effects on NarI-induced -2 frameshift mutagenesis by dynamic 19F NMR, UV, and CD spectroscopy. Biochemistry 2007; 46:13310-21. [PMID: 17960913 DOI: 10.1021/bi701386f] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The NarI recognition sequence (5'-G1G2CG3CN-3') is the most vulnerable hot spot for frameshift mutagenesis induced by the carcinogen 2-aminofluorene and its analogues in Escherichia coli. Lesioning of the guanine in the G3 position induces an especially high frequency of -2 deletion mutations; vulnerability to these mutations is modulated by the nature of the nucleotide in the N position (C approximately A > G > T). The objective of the present study was to probe the structural basis of this N-mediated influence on the propensity of the G3 lesion to form a slipped mutagenic intermediate (SMI) during translesion synthesis. We studied NarI-based fully paired [(5'-CTCG1G2CG3*CNATC-3')(5'-GATNCGGCCGAG-3'), N = dC or dT] and -2 deletion [(5'-CTCG1G2CG3*CNATC-3')(5'-GATNGCCGAG-3'), N = dC or dT] duplexes, in which G* was either AF [N-(2'-deoxyguanosin-8-yl)-2-aminofluorene] or the 19F probe FAF [N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene]. The latter sequences mimic the bulged SMI for -2 deletion mutations. Dynamic 19F NMR, circular dichroism, and UV melting results indicated that the NarI-dC/-2 deletion duplex adopts exclusively an intercalated conformer, whereas the NarI-dT/-2 deletion duplex exists as multiple conformers. The data support the presence of a putative equilibrium between a carcinogen-intercalated and a carcinogen-exposed SMI for the dT/-2 duplex. A similar dT-induced conformational heterogeneity was observed for the fully paired duplexes in which all three guanines were individually modified by AF or FAF. The frequency of the carcinogen stacked S-conformation was found to be highest (69-75%) at the G3 hot spot in NarI-dC duplexes. Taken together, our results support the hypothesis that the conformational stability of the SMI is a critical determinant for the efficacy of -2 frameshift mutagenesis in the NarI sequence. We also provide evidence for AF/FAF conformational compatibility in the NarI sequences.
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Affiliation(s)
- Nidhi Jain
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, USA
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Stover JS, Rizzo CJ. Synthesis of oligonucleotides containing the N2-deoxyguanosine adduct of the dietary carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline. Chem Res Toxicol 2007; 20:1972-9. [PMID: 17914884 PMCID: PMC3138521 DOI: 10.1021/tx7002867] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
2-amino-3-methylimidazo[4,5-f]quinoline (IQ) is a highly mutagenic heterocyclic amine formed in all cooked meats. IQ has been found to be a potent inducer of frameshift mutations in bacteria and carcinogenic in laboratory animals. Upon metabolic activation, IQ forms covalent adducts at the C8- and N2-positions of deoxyguanosine with a relative ratio of up to approximately 4:1. We have previously incorporated the major dGuo-C8-IQ adduct into oligonucleotides through the corresponding phosphoramidite reagent. We report here the sequence-specific synthesis of oligonucleotides containing the minor dGuo-N2-IQ adduct. Thermal melting analysis revealed that the dGuo-N2-IQ adduct significantly destabilizes duplex DNA.
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Affiliation(s)
| | - Carmelo J. Rizzo
- To whom correspondence should be addressed. Tel: 615-322-6100. Fax: 615-343-1234.
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