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Han M, Zhang Z, Liu S, Sheng Y, Waigi MG, Hu X, Qin C, Ling W. Genotoxicity of organic contaminants in the soil: A review based on bibliometric analysis and methodological progress. CHEMOSPHERE 2023; 313:137318. [PMID: 36410525 DOI: 10.1016/j.chemosphere.2022.137318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/26/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Organic contaminants (OCs) are ubiquitous in the environment, posing severe threats to human health and ecological balance. In particular, OCs and their metabolites could interact with genetic materials to induce genotoxicity, which has attracted considerable attention. In this review, bibliometric analysis was executed to analyze the publications on the genotoxicity of OCs in soil from 1992 to 2021. The result indicated that significant contributions were made by China and the United States in this field and the research hotspots were biological risks, damage mechanisms, and testing methods. Based on this, in this review, we summarized the manifestations and influencing factors of genotoxicity of OCs to soil organisms, the main damage mechanisms, and the most commonly utilized testing methods. OCs can induce genotoxicity and the hierarchical response of soil organisms, which could be influenced by the physicochemical properties of OCs and the properties of soil. Specific mechanisms of genotoxicity can be classified into DNA damage, epigenetic toxicity, and chromosomal aberrations. OCs with different molecular weights lead to genetic material damage by inducing the generation of ROS or forming adducts with DNA, respectively. The micronucleus test and the comet test are the most commonly used testing methods. Moreover, this review also pointed out that future studies should focus on the relationships between bioaccessibilities and genotoxicities, transcriptional regulatory factors, and potential metabolites of OCs to elaborate on the biological risks and mechanisms of genotoxicity from an overall perspective.
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Affiliation(s)
- Miao Han
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zaifeng Zhang
- Jiangsu Province Nantong Environmental Monitoring Center, Nantong 226006, PR China
| | - Si Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Youying Sheng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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Wu J, Zhang M, Song L, Tan Y, Taniguchi Y, Hipolito CJ, Zhang Y, Yin Y. Implications of N7-hydrogen and C8-keto on the base pairing, mutagenic potential and repair of 8-oxo-2'-deoxy-adenosine: Investigation by nucleotide analogues. Bioorg Chem 2022; 127:106029. [PMID: 35858520 DOI: 10.1016/j.bioorg.2022.106029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/20/2022] [Accepted: 07/12/2022] [Indexed: 11/02/2022]
Abstract
Oxidative lesions, such as 8-oxo-dG and 8-oxo-dA, are continuously generated from exposure to reactive oxygen species. While 8-oxo-dG has been extensively studied, 8-oxo-dA has not received as much attention until recently. Herein, we report the synthesis of duplex DNAs incorporating dA, 8-oxo-dA, 7-deaza-dA, 8-Br-dA, and 8-Br-7-deaza-dA, which have different substitutions at 7- and 8-position, for the investigation into the implications of N7-hydrogen and C8-keto on the base pairing preference, mutagenic potential and repair of 8-oxo-dA. Base pairing study suggested that the polar N7-hydrogen and C8-keto of 8-oxo-dA, rather than the syn-preference, might be essential for 8-oxo-dA to form a stable base pair with dG. Insertion and extension studies using KF-exo- and human DNA polymerase β indicated that the efficient dGTP insertion opposite 8-oxo-dA and extension past 8-oxo-dA:dG are contingent upon not only the stable base pair with dG, but also the flexibility of the active site in polymerase. The N7-hydrogen in 8-oxo-dA or C7-hydrogen in 7-deaza-dA and 8-Br-7-deaza-dA was suggested to be important for the recognition by hOGG1, although the excision efficiencies of 7-deaza-dA and 8-Br-7-deaza-dA were much lower than 8-oxo-dA. This study provides an insight into the structure-function relationship of 8-oxo-dA by nucleotide analogues.
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Affiliation(s)
- Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Mengmeng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yahong Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
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Li K, Li Z, Wu J, Gong Y, Guo L, Xie J. In Vitro Evaluation of DNA Damage Effect Markers toward Five Nitrogen Mustards Based on Liquid Chromatography-Tandem Mass Spectrometry. Chem Res Toxicol 2021; 35:99-110. [PMID: 34969250 DOI: 10.1021/acs.chemrestox.1c00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Endogenous DNA lesions frequently occur due to internal effects such as oxidative stress, inflammation, endogenous alkylation, and epigenetic modifications. However, exposure to chemical toxicants from the environment, diet, or drugs can also induce significant endogenous DNA damage. The quantification of endogenous DNA damage effect markers might reflect the actual DNA damage level of chemical toxicants. Herein, we report a liquid chromatography-triple quadrupole tandem mass spectrometry (LC-QqQ MS/MS) method for simultaneous determination of eight representative endogenous DNA damage biomarkers, including five endogenous DNA damage effect markers (oxidative damage, 8-oxo-dG; lipid peroxidation, εdA and N2-Et-dG; inflammation, 5-Cl-dC; and endogenous alkylation, O6-Me-dG), and three epigenetic modifications (5-m-dC, 5-hm-dC, and N6-Me-dA). The method validation was performed, and the linear range was 0.05 pg to 2 ng (on-column), the limit of detection was 0.02 pg (on-column), and the precision, accuracy, matrix effect, and recovery were all between 85 and 115%. We then applied this method to evaluate endogenous DNA damage to human embryonic lung fibroblast cells exposed to five nitrogen mustards [NMs, i.e., HN1, HN2, HN3, chlorambucil (CB), and cyclophosphamide (CTX)], where curcumin exposure was used as a control due to its inability to induce the formation of endogenous DNA adducts. The amounts of eight DNA adducts in the low-, middle-, and high-concentration exposure groups of five NMs were almost all significantly different from those in the blank group (P < 0.05). We obtained a positive correlation between the contents of eight DNA damage biomarkers and the inhibition dose of five NMs, except for N2-Et-dG and 5-Cl-dC. Via further principal component analysis and partial least squares discriminant analysis, we clustered all NMs into three units with different cytotoxicity levels, that is, HN2 and HN1 (highly toxic), HN3 and CB (moderately toxic), and CTX (less toxic). Moreover, for the same concentration of HN1/2/3 exposure groups, as the cytotoxicity increased according to the order of HN3 < HN1 < HN2, the contents of 8-oxo-dG, 5-m-dC, 5-hm-dC, and N6-Me-dA increased, whereas the content of O6-Me-dG decreased. Therefore, the contents of these DNA damage effect markers were somewhat related to the cytotoxicity and concentration of NMs. We hope that this method will provide an alternative evaluation approach for the toxicological effects of NMs and the safety of the medication.
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Affiliation(s)
- Kexin Li
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, 100850 Beijing, China
| | - Zehua Li
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, 100850 Beijing, China
| | - Jianfeng Wu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, 100850 Beijing, China
| | - Ying Gong
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, 100850 Beijing, China
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, 100850 Beijing, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, 100850 Beijing, China
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4
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Song X, Wang Y, Gao L. Mechanism of antioxidant properties of quercetin and quercetin-DNA complex. J Mol Model 2020; 26:133. [PMID: 32399900 DOI: 10.1007/s00894-020-04356-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/18/2020] [Indexed: 12/20/2022]
Abstract
Quercetin is the most abundant flavonoid with potent antioxidant activities. In the current research, the antioxidant properties of quercetin and quercetin-DNA complex were investigated theoretically and experimentally. Free radical scavenging experiments with thiobarbituric acid-reactive substances (TBARS) and 1,1-diphenyl-2-trinitrophenylhydrazine (DPPH) indicate that quercetin can protect DNA from free radical damage, and the antioxidant activity of the quercetin-DNA complex is stronger than quercetin. Deoxyriboseadenine-quercetin-dimethylphosphinic acid (DA-Q-P) model was extracted from molecular docking. The contributions of hydroxyl groups in quercetin and DA-Q-P model molecules to the antioxidant activity were investigated by computation of bond dissociation enthalpy (BDE) parameter and Fukui function, at B3LYP/6-311++G(2d,2p) level of theory. The results outlined that the hydroxyl groups from the B ring (3'-OH and 4'-OH) have a lower BDE compared with the ones from the A and C rings (3-OH, 5-OH, and 7-OH) and hence define antioxidant activity. The computational result based on Fukui function shows that the B ring is an electrophilic region. The interaction of antioxidant with DNA discovered at the molecular level could provide the structural basis of the antioxidant property of active ingredients in the flavonoids. It is of great significance to study the interaction mechanism between the small drug molecules with DNA at the molecular level.
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Affiliation(s)
- Xiaoli Song
- College of Chemistry and Chemical Engineering, Yulin University, Yulin, 719000, Shaanxi, China.
| | - Yali Wang
- College of Chemistry and Chemical Engineering, Yulin University, Yulin, 719000, Shaanxi, China.
| | - Liguo Gao
- College of Chemistry and Chemical Engineering, Yulin University, Yulin, 719000, Shaanxi, China.
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Wilson KA, Wetmore SD. Conformational Flexibility of the Benzyl-Guanine Adduct in a Bypass Polymerase Active Site Permits Replication: Insights from Molecular Dynamics Simulations. Chem Res Toxicol 2017; 30:2013-2022. [PMID: 28810119 DOI: 10.1021/acs.chemrestox.7b00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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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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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Gentile F, Arcaro A, Pizzimenti S, Daga M, Cetrangolo GP, Dianzani C, Lepore A, Graf M, Ames PRJ, Barrera G. DNA damage by lipid peroxidation products: implications in cancer, inflammation and autoimmunity. AIMS GENETICS 2017; 4:103-137. [PMID: 31435505 PMCID: PMC6690246 DOI: 10.3934/genet.2017.2.103] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/12/2017] [Indexed: 12/19/2022]
Abstract
Oxidative stress and lipid peroxidation (LPO) induced by inflammation, excess metal storage and excess caloric intake cause generalized DNA damage, producing genotoxic and mutagenic effects. The consequent deregulation of cell homeostasis is implicated in the pathogenesis of a number of malignancies and degenerative diseases. Reactive aldehydes produced by LPO, such as malondialdehyde, acrolein, crotonaldehyde and 4-hydroxy-2-nonenal, react with DNA bases, generating promutagenic exocyclic DNA adducts, which likely contribute to the mutagenic and carcinogenic effects associated with oxidative stress-induced LPO. However, reactive aldehydes, when added to tumor cells, can exert an anticancerous effect. They act, analogously to other chemotherapeutic drugs, by forming DNA adducts and, in this way, they drive the tumor cells toward apoptosis. The aldehyde-DNA adducts, which can be observed during inflammation, play an important role by inducing epigenetic changes which, in turn, can modulate the inflammatory process. The pathogenic role of the adducts formed by the products of LPO with biological macromolecules in the breaking of immunological tolerance to self antigens and in the development of autoimmunity has been supported by a wealth of evidence. The instrumental role of the adducts of reactive LPO products with self protein antigens in the sensitization of autoreactive cells to the respective unmodified proteins and in the intermolecular spreading of the autoimmune responses to aldehyde-modified and native DNA is well documented. In contrast, further investigation is required in order to establish whether the formation of adducts of LPO products with DNA might incite substantial immune responsivity and might be instrumental for the spreading of the immunological responses from aldehyde-modified DNA to native DNA and similarly modified, unmodified and/or structurally analogous self protein antigens, thus leading to autoimmunity.
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Affiliation(s)
- Fabrizio Gentile
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso, Italy
| | - Alessia Arcaro
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso, Italy
| | - Stefania Pizzimenti
- Department of Clinical and Biological Sciences, University of Torino, Torino, Italy
| | - Martina Daga
- Department of Clinical and Biological Sciences, University of Torino, Torino, Italy
| | | | - Chiara Dianzani
- Department of Drug Science and Technology, University of Torino, Torino, Italy
| | - Alessio Lepore
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Maria Graf
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Paul R. J. Ames
- CEDOC, NOVA Medical School, Universidade NOVA de Lisboa, Lisboa, Portugal, and Department of Haematology, Dumfries Royal Infirmary, Dumfries, Scotland, UK
| | - Giuseppina Barrera
- Department of Clinical and Biological Sciences, University of Torino, Torino, Italy
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8
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O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ. Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η. Chem Sci 2016; 7:4896-4904. [PMID: 27574558 PMCID: PMC5001687 DOI: 10.1039/c6sc00666c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Conformation of the α-carbon of O4-alkylthymidine was shown to exert an influence on human DNA polymerase η (hPol η) bypass. Crystal structures of hPol η·DNA·dNTP ternary complexes reveal a unique conformation adopted by O4-methylthymidine, where the nucleobase resides nestled at the active site ceiling where hydrogen-bonding with the incoming nucleotide is prevented.
DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O4-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4–O4 bond on processing by human DNA polymerase η (hPol η) was studied for oligonucleotides containing O4-methylthymidine (O4MedT), O4-ethylthymidine (O4EtdT), and analogs restricting the O4-methylene group in an anti-orientation. Primer extension assays revealed that the O4-alkyl orientation influences hPol η bypass. Crystal structures of hPol η·DNA·dNTP ternary complexes with O4MedT or O4EtdT in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn-O4-methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O4-methylthymidine with hPol η, inaccessible for the other analogs due to steric/conformational restriction, is consistent with differences observed for nucleotide incorporation and supports the concept that lesion conformation influences extension across DNA damage. Together, these results provide mechanistic insights on the mutagenicity of O4MedT and O4EtdT when acted upon by hPol η.
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Affiliation(s)
- D K O'Flaherty
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B1R6, Canada
| | - A Patra
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Y Su
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - F P Guengerich
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - M Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - C J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B1R6, Canada
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Beker W, Stachowicz-Kuśnierz A, Zaklika J, Ziobro A, Ordon P, Komorowski L. Atomic polarization justified Fukui indices and the affinity indicators in aromatic heterocycles and nucleobases. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Palermo GD, Neri QV, Cozzubbo T, Rosenwaks Z. Perspectives on the assessment of human sperm chromatin integrity. Fertil Steril 2014; 102:1508-17. [DOI: 10.1016/j.fertnstert.2014.10.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/02/2014] [Accepted: 10/06/2014] [Indexed: 12/13/2022]
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Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
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13
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Buraka E, Chen CYC, Gavare M, Grube M, Makarenkova G, Nikolajeva V, Bisenieks I, Brūvere I, Bisenieks E, Duburs G, Sjakste N. DNA-binding studies of AV-153, an antimutagenic and DNA repair-stimulating derivative of 1,4-dihydropiridine. Chem Biol Interact 2014; 220:200-7. [PMID: 25016077 DOI: 10.1016/j.cbi.2014.06.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 06/20/2014] [Accepted: 06/30/2014] [Indexed: 01/24/2023]
Abstract
UNLABELLED The ability to intercalate between DNA strands determines the cytotoxic activity of numerous anticancer drugs. Strikingly, intercalating activity was also reported for some compounds considered to be antimutagenic. The aim of this study was to determine the mode of interaction of DNA with the antimutagenic and DNA repair-stimulating dihydropyridine (DHP) AV-153. DNA and AV-153 interactions were studied by means of UV/VIS spectroscopy, fluorimetry and infrared spectroscopy. Compound AV-153 is a 1,4 dihydropyridine with ethoxycarbonyl groups in positions 3 and 5. Computer modeling of AV-153 and DNA interactions suggested an ability of the compound to dock between DNA strands at a single strand break site in the vicinity of two pyrimidines, which was confirmed in the present study. AV-153 evidently interacted with DNA, as addition of DNA to AV-153 solutions resulted in pronounced hyperchromic and bathochromic effects on the spectra. Base modification in a plasmid by peroxynitrite only minimally changed binding affinity of the compound; however, induction of single-strand breaks using Fenton's reaction greatly increased binding affinity. The affinity did not change when the ionic strength of the solution was changed from 5 to 150 mM NaCl, although it increased somewhat at 300 mM. Neither was it influenced by temperature changes from 25 to 40°C, however, it decreased when the pH of the solution was changed from 7.4 to 4.7. AV-153 competed with EBr for intercalation sites in DNA: 116 mM of the compound caused a two-fold decrease in fluorescence intensity. FT-IR spectral data analyses indicated formation of complexes between DNA and AV-153. The second derivative spectra analyses indicated interaction of AV-153 with guanine, cytosine and thymine bases, but no interaction with adenine was detected. CONCLUSIONS The antimutagenic substance AV-153 appears to intercalate between the DNA strands at the site of a DNA nick in the vicinity of two pyrimidines.
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Affiliation(s)
- E Buraka
- Department of Medical Biochemistry, Faculty of Medicine, University of Latvia, No. 4 Kronvalda Boulevard, Riga LV-1010, Latvia; Latvian Institute of Organic Synthesis, No. 21 Aizkraukles Street, Riga LV-1006, Latvia
| | - C Yu-Chian Chen
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan; Department of Bioinformatics, Asia University, Taichung 41354, Taiwan
| | - M Gavare
- Institute of Microbiology and Biotechnology, University of Latvia, No. 4 Kronvalda Boulevard, Riga LV-1010, Latvia
| | - M Grube
- Institute of Microbiology and Biotechnology, University of Latvia, No. 4 Kronvalda Boulevard, Riga LV-1010, Latvia
| | - G Makarenkova
- Faculty of Biology, University of Latvia, No. 4 Kronvalda Boulevard, Riga LV-1010, Latvia
| | - V Nikolajeva
- Faculty of Biology, University of Latvia, No. 4 Kronvalda Boulevard, Riga LV-1010, Latvia
| | - I Bisenieks
- Latvian Institute of Organic Synthesis, No. 21 Aizkraukles Street, Riga LV-1006, Latvia
| | - I Brūvere
- Latvian Institute of Organic Synthesis, No. 21 Aizkraukles Street, Riga LV-1006, Latvia
| | - E Bisenieks
- Latvian Institute of Organic Synthesis, No. 21 Aizkraukles Street, Riga LV-1006, Latvia
| | - G Duburs
- Latvian Institute of Organic Synthesis, No. 21 Aizkraukles Street, Riga LV-1006, Latvia
| | - N Sjakste
- Department of Medical Biochemistry, Faculty of Medicine, University of Latvia, No. 4 Kronvalda Boulevard, Riga LV-1010, Latvia; Latvian Institute of Organic Synthesis, No. 21 Aizkraukles Street, Riga LV-1006, Latvia.
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14
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Krokan HE, Sætrom P, Aas PA, Pettersen HS, Kavli B, Slupphaug G. Error-free versus mutagenic processing of genomic uracil—Relevance to cancer. DNA Repair (Amst) 2014; 19:38-47. [DOI: 10.1016/j.dnarep.2014.03.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Tommasi S, Zheng A, Yoon JI, Besaratinia A. Epigenetic targeting of the Nanog pathway and signaling networks during chemical carcinogenesis. Carcinogenesis 2014; 35:1726-36. [DOI: 10.1093/carcin/bgu026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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16
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Oxidative damage and mutagenesis in Saccharomyces cerevisiae: genetic studies of pathways affecting replication fidelity of 8-oxoguanine. Genetics 2013; 195:359-67. [PMID: 23893481 PMCID: PMC3781965 DOI: 10.1534/genetics.113.153874] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Oxidative damage to DNA constitutes a major threat to the faithful replication of DNA in all organisms and it is therefore important to understand the various mechanisms that are responsible for repair of such damage and the consequences of unrepaired damage. In these experiments, we make use of a reporter system in Saccharomyces cerevisiae that can measure the specific increase of each type of base pair mutation by measuring reversion to a Trp+ phenotype. We demonstrate that increased oxidative damage due to the absence of the superoxide dismutase gene, SOD1, increases all types of base pair mutations and that mismatch repair (MMR) reduces some, but not all, types of mutations. By analyzing various strains that can revert only via a specific CG → AT transversion in backgrounds deficient in Ogg1 (encoding an 8-oxoG glycosylase), we can study mutagenesis due to a known 8-oxoG base. We show as expected that MMR helps prevent mutagenesis due to this damaged base and that Pol η is important for its accurate replication. In addition we find that its accurate replication is facilitated by template switching, as loss of either RAD5 or MMS2 leads to a significant decrease in accurate replication. We observe that these ogg1 strains accumulate revertants during prolonged incubation on plates, in a process most likely due to retromutagenesis.
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17
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Lewis SEM, John Aitken R, Conner SJ, Iuliis GD, Evenson DP, Henkel R, Giwercman A, Gharagozloo P. The impact of sperm DNA damage in assisted conception and beyond: recent advances in diagnosis and treatment. Reprod Biomed Online 2013; 27:325-37. [PMID: 23948450 DOI: 10.1016/j.rbmo.2013.06.014] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 04/09/2013] [Accepted: 06/26/2013] [Indexed: 12/17/2022]
Abstract
Sperm DNA damage is a useful biomarker for male infertility diagnosis and prediction of assisted reproduction outcomes. It is associated with reduced fertilization rates, embryo quality and pregnancy rates, and higher rates of spontaneous miscarriage and childhood diseases. This review provides a synopsis of the most recent studies from each of the authors, all of whom have major track records in the field of sperm DNA damage in the clinical setting. It explores current laboratory tests and the accumulating body of knowledge concerning the relationship between sperm DNA damage and clinical outcomes. The paper proceeds to discuss the strengths, weaknesses and clinical applicability of current sperm DNA tests. Next, the biological significance of DNA damage in the male germ line is considered. Finally, as sperm DNA damage is often the result of oxidative stress in the male reproductive tract, the potential contribution of antioxidant therapy in the clinical management of this condition is discussed. DNA damage in human spermatozoa is an important attribute of semen quality. It should be part of the clinical work up and properly controlled trials addressing the effectiveness of antioxidant therapy should be undertaken as a matter of urgency. Sperm DNA damage is a useful biomarker for male infertility diagnosis and prediction of assisted reproduction outcomes. It is associated with reduced fertilization rates, embryo quality and pregnancy rates, and higher rates of spontaneous miscarriage and childhood diseases. With all of these fertility check points, it shows more promise than conventional semen parameters from a diagnostic perspective. Despite this, few infertility clinics use it routinely. This review provides a synopsis of the most recent studies from each of the authors, all of whom have major track records in the field of sperm DNA damage in the clinical setting. It explores current laboratory tests and the accumulating body of knowledge concerning the relationship between sperm DNA damage and clinical outcomes. The paper proceeds to discuss the strengths and weaknesses and clinical applicability of current sperm DNA fragmentation tests. Next, the biological significance of DNA damage in the male germ line is considered. Finally, as sperm DNA damage is often the result of increased oxidative stress in the male reproductive tract, the potential contribution of antioxidant therapy in the clinical management of this condition is discussed. As those working in this field of clinical research, we conclude that DNA damage in human spermatozoa is an important attribute of semen quality which should be carefully assessed in the clinical work up of infertile couples and that properly controlled trials addressing the effectiveness of antioxidant therapy should be undertaken as a matter of urgency.
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Affiliation(s)
- Sheena E M Lewis
- Centre for Public Health, Institute of Clinical Sciences, Queen's University Belfast, Grosvenor Road, Belfast BT12 6BJ, Northern Ireland, UK.
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18
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Cai Y, Zheng H, Ding S, Kropachev K, Schwaid AG, Tang Y, Mu H, Wang S, Geacintov NE, Zhang Y, Broyde S. Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility. Chem Res Toxicol 2013; 26:1115-25. [PMID: 23758590 DOI: 10.1021/tx400156a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The crystal structure of Rad4/Rad23, the yeast homolog of the human nucleotide excision repair (NER) lesion recognition factor XPC-RAD23B ( Min , J. H. and Pavletich , N. P. ( 2007 ) Nature 449 , 570 - 575 ) reveals that the lesion-partner base is flipped out of the helix and binds to amino acids of the protein. This suggests the hypothesis that the flipping of this partner base must overcome a free energy barrier, which constitutes one element contributing to changes in the thermodynamic properties induced by the DNA damage and sensed by the recognition protein. We explored this hypothesis by computing complete flipping free energy profiles for two lesions derived from the procarcinogenic polycyclic aromatic hydrocarbons (PAHs), dibenzo[a,l]pyrene (DB[a,l]P) and benzo[a]pyrene (B[a]P), R-trans-anti-DB[a,l]P-N(6)-dA (R-DB[a,l]P-dA) and R-trans-anti-B[a]P-N(6)-dA (R-B[a]P-dA), and the corresponding unmodified duplex. The DB[a,l]P and B[a]P adducts differ in number and organization of their aromatic rings. We integrate these results with prior profiles for the R-trans-anti-DB[a,l]P-dG adduct ( Zheng , H. et al. ( 2010 ) Chem. Res. Toxicol. 23 , 1868 - 1870 ). All adopt conformational themes involving intercalation of the PAH aromatic ring system into the DNA duplex; however, R-DB[a,l]P-dA and R-B[a]P-dA intercalate from the major groove, while R-DB[a,l]P-dG intercalates from the minor groove. These structural differences produce different computed van der Waals stacking interaction energies between the flipping partner base with the lesion aromatic ring system and adjacent bases; we find that the better the stacking, the higher the relative flipping free energy barrier and hence lower flipping probability. The better relative NER susceptibilities correlate with greater ease of flipping in these three differently intercalated lesions. In addition to partner base flipping, the Rad4/Rad23 crystal structure shows that a protein-β-hairpin, BHD3, intrudes from the major groove side between the DNA strands at the lesion site. We present a molecular modeling study for the R-DB[a,l]P-dG lesion in Rad4/Rad23 showing BHD3 β-hairpin intrusion with lesion eviction, and we hypothesize that lesion steric effects play a role in the recognition of intercalated adducts.
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Affiliation(s)
- Yuqin Cai
- Department of Biology, New York University , New York, New York 10003, United States
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19
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Vaidyanathan VG, Liang F, Beard WA, Shock DD, Wilson SH, Cho BP. Insights into the conformation of aminofluorene-deoxyguanine adduct in a DNA polymerase active site. J Biol Chem 2013; 288:23573-85. [PMID: 23798703 DOI: 10.1074/jbc.m113.476150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The active site conformation of the mutagenic fluoroaminofluorene-deoxyguanine adduct (dG-FAF, N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) has been investigated in the presence of Klenow fragment of Escherichia coli DNA polymerase I (Kfexo(-)) and DNA polymerase β (pol β) using (19)F NMR, insertion assay, and surface plasmon resonance. In a single nucleotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked conformation, and this heterogeneity is retained upon binding pol β. The addition of a non-hydrolysable 2'-deoxycytosine-5'-[(α,β)-methyleno]triphosphate (dCMPcPP) nucleotide analog to the binary complex results in an increase of the major groove conformation of the adduct at the expense of the stacked conformation. Similar results were obtained with the addition of an incorrect dAMPcPP analog but with formation of the minor groove binding conformer. In contrast, dG-FAF adduct at the replication fork for the Kfexo(-) complex adopts a mix of the major and minor groove conformers with minimal effect upon the addition of non-hydrolysable nucleotides. For pol β, the insertion of dCTP was preferred opposite the dG-FAF adduct in a single nucleotide gap assay consistent with (19)F NMR data. Surface plasmon resonance binding kinetics revealed that pol β binds tightly with DNA in the presence of correct dCTP, but the adduct weakens binding with no nucleotide specificity. These results provide molecular insights into the DNA binding characteristics of FAF in the active site of DNA polymerases and the role of DNA structure and sequence on its coding potential.
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Affiliation(s)
- Vaidyanathan G Vaidyanathan
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, USA
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20
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Nishimoto A, Jitsuzaki D, Onizuka K, Taniguchi Y, Nagatsugi F, Sasaki S. 4-vinyl-substituted pyrimidine nucleosides exhibit the efficient and selective formation of interstrand cross-links with RNA and duplex DNA. Nucleic Acids Res 2013; 41:6774-81. [PMID: 23778430 PMCID: PMC3711451 DOI: 10.1093/nar/gkt197] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The formation of interstrand cross-links in nucleic acids can have a strong impact on biological function of nucleic acids; therefore, many cross-linking agents have been developed for biological applications. Despite numerous studies, there remains a need for cross-linking agents that exhibit both efficiency and selectivity. In this study, a 4-vinyl-substituted analog of thymidine (T-vinyl derivative) was designed as a new cross-linking agent, in which the vinyl group is oriented towards the Watson–Crick face to react with the amino group of an adenine base. The interstrand cross-link formed rapidly and selectively with a uridine on the RNA substrate at the site opposite to the T-vinyl derivative. A detailed analysis of cross-link formation while varying the flanking bases of the RNA substrates indicated that interstrand cross-link formation is preferential for the adenine base on the 5′-side of the opposing uridine. In the absence of a 5′-adenine, a uridine at the opposite position underwent cross-linking. The oligodeoxynucleotides probe incorporating the T-vinyl derivative efficiently formed interstrand cross-links in parallel-type triplex DNA with high selectivity for dA in the homopurine strand. The efficiency and selectivity of the T-vinyl derivative illustrate its potential use as a unique tool in biological and materials research.
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Affiliation(s)
- Atsushi Nishimoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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21
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Quinn R, Basanta-Sanchez M, Rose RE, Fabris D. Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:703-12. [PMID: 23722961 PMCID: PMC3767442 DOI: 10.1002/jms.3207] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 03/18/2013] [Accepted: 03/21/2013] [Indexed: 05/14/2023]
Abstract
The challenges posed by the analysis of mono-nucleotide mixtures by direct infusion electrospray ionization were examined in the context of recent advances of mass spectrometry (MS) technologies. In particular, we evaluated the merits of high-resolution mass analysis, multistep gas-phase dissociation, and ion mobility determinations for the characterization of species with very similar or identical elemental composition. The high resolving power afforded by a linear trap quadrupole-orbitrap allowed the complete differentiation of overlapping isotopic distributions produced by nucleotides that differed by a single mass unit. Resolving (12)C signals from nearly overlapped (13)C contributions provided the exact masses necessary to calculate matching elemental compositions for unambiguous formulae assignment. However, it was the ability to perform sequential steps of gas-phase dissociation (i.e. MS(n)-type analysis) that proved more valuable for discriminating between truly isobaric nucleotides, such as the AMP/dGMP and UMP/ΨMP couples, which were differentiated in the mixture from their unique fragmentation patterns. The identification of diagnostic fragments enabled the deconvolution of dissociation spectra containing the products of coexisting isobars that could not be individually isolated in the mass-selection step. Approaches based on ion mobility spectrometry-MS provided another dimension upon which isobaric nucleotides could be differentiated according to their distinctive mobility behaviors. Subtle structural variations, such as the different positions of an oxygen atom in AMP/dGMP or the glycosidic bond in UMP/ΨMP, produced detectable differences in the respective ion mobility profiles, which enabled the differentiation of the isobaric couples in the mixture. Parallel activation of all ions emerging from the ion mobility element provided an additional dimension for differentiating these analytes on the basis of both mobility and fragmentation properties.
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Affiliation(s)
| | | | | | - Daniele Fabris
- Corresponding author: The RNA Institute, University at Albany (SUNY), Life Sciences Research Building room 1109, 1200 Washington Ave., Albany, NY 12222, Ph. (518) 437-3364, Fax (518) 442-3462,
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22
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Šrut M, Štambuk A, Klobučar GI. What is Comet assay not telling us: AFLP reveals wider aspects of genotoxicity. Toxicol In Vitro 2013; 27:1226-32. [DOI: 10.1016/j.tiv.2013.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/07/2013] [Accepted: 02/12/2013] [Indexed: 01/03/2023]
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23
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Ruiz Y, Suárez P, Alonso A, Longo E, San Juan F. Mutagenicity test using Vibrio harveyi in the assessment of water quality from mussel farms. WATER RESEARCH 2013; 47:2742-2756. [PMID: 23510693 DOI: 10.1016/j.watres.2013.02.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 02/05/2013] [Accepted: 02/11/2013] [Indexed: 06/01/2023]
Abstract
This work analyses the mutagenicity of seawater from mussel farms using the Vibrio harveyi mutagenicity test and its relationship with the accumulated pollutants and the development of gonadal neoplasia in mussels. Histological disorders identified as germinoma were observed in the gonad of Mytilus galloprovincialis during the period of study. The prevalence of this pathology is significantly correlated with certain levels of pollutants accumulated in mussels, mainly of PAHs and PCBs, whose toxic equivalents were calculated as EROD induction equivalency. The mutagenicity and toxicity of the water surrounding mussel's farms is clearly correlated with the pollutants accumulated and with the neoplasia prevalence in mussels. Such correlations are corroborated by a multivariate analysis. Our results conclude with the utility of V. harveyi test as an optimal and rapid method in the monitoring of the quality of the water from mussel farms and as a tool to control the risks of pollution on mussel production and its safety for human food.
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Affiliation(s)
- Yolanda Ruiz
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain.
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24
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McNeill DR, Paramasivam M, Baldwin J, Huang J, Vyjayanti VN, Seidman MM, Wilson DM. NEIL1 responds and binds to psoralen-induced DNA interstrand crosslinks. J Biol Chem 2013; 288:12426-36. [PMID: 23508956 DOI: 10.1074/jbc.m113.456087] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent evidence suggests a role for base excision repair (BER) proteins in the response to DNA interstrand crosslinks, which block replication and transcription, and lead to cell death and genetic instability. Employing fluorescently tagged fusion proteins and laser microirradiation coupled with confocal microscopy, we observed that the endonuclease VIII-like DNA glycosylase, NEIL1, accumulates at sites of oxidative DNA damage, as well as trioxsalen (psoralen)-induced DNA interstrand crosslinks, but not to angelicin monoadducts. While recruitment to the oxidative DNA lesions was abrogated by the anti-oxidant N-acetylcysteine, this treatment did not alter the accumulation of NEIL1 at sites of interstrand crosslinks, suggesting distinct recognition mechanisms. Consistent with this conclusion, recruitment of the NEIL1 population variants, G83D, C136R, and E181K, to oxidative DNA damage and psoralen-induced interstrand crosslinks was differentially affected by the mutation. NEIL1 recruitment to psoralen crosslinks was independent of the nucleotide excision repair recognition factor, XPC. Knockdown of NEIL1 in LN428 glioblastoma cells resulted in enhanced recruitment of XPC, a more rapid removal of digoxigenin-tagged psoralen adducts, and decreased cellular sensitivity to trioxsalen plus UVA, implying that NEIL1 and BER may interfere with normal cellular processing of interstrand crosslinks. While exhibiting no enzymatic activity, purified NEIL1 protein bound stably to psoralen interstrand crosslink-containing synthetic oligonucleotide substrates in vitro. Our results indicate that NEIL1 recognizes specifically and distinctly interstrand crosslinks in DNA, and can obstruct the efficient removal of lethal crosslink adducts.
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Affiliation(s)
- Daniel R McNeill
- Laboratory of Molecular Gerontology, Biomedical Research Center, NIA, National Institutes of Health, Baltimore, Maryland 21224, USA
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25
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Puch CBMD, Barbier E, Sauvaigo S, Gasparutto D, Breton J. Tools and strategies for DNA damage interactome analysis. Mutat Res 2012; 752:72-83. [PMID: 23220222 DOI: 10.1016/j.mrrev.2012.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 11/01/2012] [Accepted: 11/22/2012] [Indexed: 11/26/2022]
Abstract
DNA is the target of multiple endogenous and exogenous agents generating chemical lesions on the double helix. Cellular DNA damage response pathways rely on a myriad of proteins interacting with DNA alterations. The cartography of this interactome currently includes well known actors of chromatin remodelling, DNA repair or proteins hijacked from their natural functions such as transcription factors. In order to go further into the characterisation of these protein networks, proteomics-based methods began to be used in the early 2000s. The strategies are diverse and include mainly (i) damaged DNA molecules used as targets on protein microarrays, (ii) damaged DNA probes used to trap within complex cellular extracts proteins that are then separated and identified by proteomics, (iii) identification of chromatin- bound proteins after a genotoxic stress, or (iv) identification of proteins associated with other proteins already known to be part of DNA damage interactome. All these approaches have already been performed to find new proteins recognizing oxidised bases, abasic sites, strand breaks or crosslinks generated by anticancer drugs such as nitrogen mustards and platinating agents. Identified interactions are generally confirmed using complementary methods such as electromobility shift assays or surface plasmon resonance. These strategies allowed, for example, demonstration of interactions between cisplatin-DNA crosslinks and PARP-1 or the protein complex PTW/PP. The next challenging step will be to understand the biological repercussions of these newly identified interactions which may help to unravel new mechanisms involved in genetic toxicology, discover new cellular responses to anticancer drugs or identify new biomarkers and therapeutic targets.
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Affiliation(s)
| | - Ewa Barbier
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Sylvie Sauvaigo
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Didier Gasparutto
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Jean Breton
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France; UFR de Pharmacie, Université Joseph Fourier-Grenoble 1, Domaine de la Merci, La Tronche, F-38706, France.
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26
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Tang Y, Liu Z, Ding S, Lin CH, Cai Y, Rodriguez FA, Sayer JM, Jerina DM, Amin S, Broyde S, Geacintov NE. Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing. Biochemistry 2012; 51:9751-62. [PMID: 23121427 DOI: 10.1021/bi3013577] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the nonplanar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14 position with the exocyclic amino group of guanine. Here, we present the first nuclear magnetic resonance solution structure of a DB[a,l]P-derived adduct, the 14R-(+)-trans-anti-DB[a,l]P-N(2)-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N(2)-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3'-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3'-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE-DNA adduct conformation differs from (1) the classical intercalation motif in which Watson-Crick base pairing is intact at the lesion site and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix. The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed.
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Affiliation(s)
- Yijin Tang
- Department of Chemistry, New York University, New York, NY 10003, USA
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27
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Lior-Hoffmann L, Wang L, Wang S, Geacintov NE, Broyde S, Zhang Y. Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion. Nucleic Acids Res 2012; 40:9193-205. [PMID: 22772988 PMCID: PMC3467051 DOI: 10.1093/nar/gks653] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 06/07/2012] [Accepted: 06/12/2012] [Indexed: 01/13/2023] Open
Abstract
Human DNA Pol κ is a polymerase enzyme, specialized for near error-free bypass of certain bulky chemical lesions to DNA that are derived from environmental carcinogens present in tobacco smoke, automobile exhaust and cooked food. By employing ab initio QM/MM-MD (Quantum Mechanics/Molecular Mechanics-Molecular Dynamics) simulations with umbrella sampling, we have determined the entire free energy profile of the nucleotidyl transfer reaction catalyzed by Pol κ and provided detailed mechanistic insights. Our results show that a variant of the Water Mediated and Substrate Assisted (WMSA) mechanism that we previously deduced for Dpo4 and T7 DNA polymerases is preferred for Pol κ as well, suggesting its broad applicability. The hydrogen on the 3'-OH primer terminus is transferred through crystal and solvent waters to the γ-phosphate of the dNTP, followed by the associative nucleotidyl transfer reaction; this is facilitated by a proton transfer from the γ-phosphate to the α,β-bridging oxygen as pyrophosphate leaves, to neutralize the evolving negative charge. MD simulations show that the near error-free incorporation of dCTP opposite the major benzo[a]pyrene-derived dG lesion is compatible with the WMSA mechanism, allowing for an essentially undisturbed pentacovalent phosphorane transition state, and explaining the bypass of this lesion with little mutation by Pol κ.
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Affiliation(s)
- Lee Lior-Hoffmann
- Department of Chemistry and Department of Biology, New York University, NY 10003, USA
| | - Lihua Wang
- Department of Chemistry and Department of Biology, New York University, NY 10003, USA
| | - Shenglong Wang
- Department of Chemistry and Department of Biology, New York University, NY 10003, USA
| | - Nicholas E. Geacintov
- Department of Chemistry and Department of Biology, New York University, NY 10003, USA
| | - Suse Broyde
- Department of Chemistry and Department of Biology, New York University, NY 10003, USA
| | - Yingkai Zhang
- Department of Chemistry and Department of Biology, New York University, NY 10003, USA
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28
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Virgilio A, Petraccone L, Esposito V, Citarella G, Giancola C, Galeone A. The abasic site lesions in the human telomeric sequence d[TA(G(3)T(2)A)(3)G(3)]: a thermodynamic point of view. Biochim Biophys Acta Gen Subj 2012; 1820:2037-43. [PMID: 23000492 DOI: 10.1016/j.bbagen.2012.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 09/06/2012] [Accepted: 09/14/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND The abasic sites represent one of the most frequent lesions of DNA and most of the events able to generate such modifications involve guanine bases. G-rich sequences are able to form quadruplex structures that have been proved to be involved in several important biological processes. METHODS In this paper, we report investigations, based on calorimetric, UV, CD and electrophoretic techniques, on 12 oligodeoxynucleotides analogues of the quadruplex forming human telomere sequence d[TA(G(3)T(2)A)(3)G(3)], in which each guanine has been replaced, one at a time, by an abasic site mimic. RESULTS Although all data show that the modified sequences preserve their ability to form quadruplex structures, the thermodynamic parameters clearly indicate that the presence of an abasic site decreases their thermal stability compared to the parent unmodified sequence, particularly if the replacement concerns one of the guanosines involved in the formation of the central G-tetrad. CONCLUSIONS The collected data indicate that the effects of the presence of abasic site lesions in telomeric quadruplex structures are site-specific. The most dramatic consequences come out when this lesion involves a guanosine in the centre of a G-run. GENERAL SIGNIFICANCE Abasic sites, by facilitating the G-quadruplex disruption, could favour the formation of the telomerase primer. Furthermore they could have implications in the pharmacological approach targeting telomere.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli, Napoli, Italy
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29
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Mu H, Kropachev K, Wang L, Zhang L, Kolbanovskiy A, Kolbanovskiy M, Geacintov NE, Broyde S. Nucleotide excision repair of 2-acetylaminofluorene- and 2-aminofluorene-(C8)-guanine adducts: molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair efficiencies. Nucleic Acids Res 2012; 40:9675-90. [PMID: 22904073 PMCID: PMC3479214 DOI: 10.1093/nar/gks788] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nucleotide excision repair (NER) efficiencies of DNA lesions can vary by orders of magnitude, for reasons that remain unclear. An example is the pair of N-(2′-deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF) and N-(2′-deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) adducts that differ by a single acetyl group. The NER efficiencies in human HeLa cell extracts of these lesions are significantly different when placed at G1, G2 or G3 in the duplex sequence (5′-CTCG1G2CG3CCATC-3′) containing the NarI mutational hot spot. Furthermore, the dG-C8-AAF adduct is a better substrate of NER than dG-C8-AF in all three NarI sequence contexts. The conformations of each of these adducts were investigated by Molecular dynamics (MD) simulation methods. In the base-displaced conformational family, the greater repair susceptibility of dG-C8-AAF in all sequences stems from steric hindrance effects of the acetyl group which significantly diminish the adduct-base stabilizing van der Waals stacking interactions relative to the dG-C8-AF case. Base sequence context effects for each adduct are caused by differences in helix untwisting and minor groove opening that are derived from the differences in stacking patterns. Overall, the greater NER efficiencies are correlated with greater extents of base sequence-dependent local untwisting and minor groove opening together with weaker stacking interactions.
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Affiliation(s)
- Hong Mu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
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Carell T, Brandmayr C, Hienzsch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M. Struktur und Funktion nicht-kanonischer Nukleobasen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201193] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Carell T, Brandmayr C, Hienzsch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M. Structure and function of noncanonical nucleobases. Angew Chem Int Ed Engl 2012; 51:7110-31. [PMID: 22744788 DOI: 10.1002/anie.201201193] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/07/2012] [Indexed: 12/19/2022]
Abstract
DNA and RNA contain, next to the four canonical nucleobases, a number of modified nucleosides that extend their chemical information content. RNA is particularly rich in modifications, which is obviously an adaptation to their highly complex and variable functions. In fact, the modified nucleosides and their chemical structures establish a second layer of information which is of central importance to the function of the RNA molecules. Also the chemical diversity of DNA is greater than originally thought. Next to the four canonical bases, the DNA of higher organisms contains a total of four epigenetic bases: m(5) dC, hm(5) dC, f(5) dC und ca(5) dC. While all cells of an organism contain the same genetic material, their vastly different function and properties inside complex higher organisms require the controlled silencing and activation of cell-type specific genes. The regulation of the underlying silencing and activation process requires an additional layer of epigenetic information, which is clearly linked to increased chemical diversity. This diversity is provided by the modified non-canonical nucleosides in both DNA and RNA.
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Affiliation(s)
- Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany.
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Cai Y, Geacintov NE, Broyde S. Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions. Biochemistry 2012; 51:1486-99. [PMID: 22242833 DOI: 10.1021/bi201794x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nucleotide excision repair (NER) machinery, the primary defense against cancer-causing bulky DNA lesions, is surprisingly inefficient in recognizing certain mutagenic DNA adducts and other forms of DNA damage. However, the biochemical basis of resistance to repair remains poorly understood. To address this problem, we have investigated a series of intercalated DNA-adenine lesions derived from carcinogenic polycyclic aromatic hydrocarbon (PAH) diol epoxide metabolites that differ in their response to the mammalian NER apparatus. These stereoisomeric PAH-derived adenine lesions represent ideal model systems for elucidating the effects of structural, dynamic, and thermodynamic properties that determine the recognition of these bulky DNA lesions by NER factors. The objective of this work was to gain a systematic understanding of the relation between aromatic ring topology and adduct stereochemistry with existing experimental NER efficiencies and known thermodynamic stabilities of the damaged DNA duplexes. For this purpose, we performed 100 ns molecular dynamics studies of the lesions embedded in identical double-stranded 11-mer sequences. Our studies show that, depending on topology and stereochemistry, stabilizing PAH-DNA base van der Waals stacking interactions can compensate for destabilizing distortions caused by these lesions that can, in turn, cause resistance to NER. The results suggest that the balance between helix stabilizing and destabilizing interactions between the adduct and nearby DNA residues can account for the variability of NER efficiencies observed in this class of PAH-DNA lesions.
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Affiliation(s)
- Yuqin Cai
- Department of Biology, New York University, New York, New York 10003, United States
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