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Andrés CMC, de la Lastra JMP, Juan CA, Plou FJ, Pérez-Lebeña E. Chemical Insights into Oxidative and Nitrative Modifications of DNA. Int J Mol Sci 2023; 24:15240. [PMID: 37894920 PMCID: PMC10607741 DOI: 10.3390/ijms242015240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2'-deoxyribose oxidation products in DNA.
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Affiliation(s)
| | - José Manuel Pérez de la Lastra
- Institute of Natural Products and Agrobiology, CSIC-Spanish Research Council, Avda. AstrofísicoFco. Sánchez, 3, 38206 La Laguna, Spain
| | - Celia Andrés Juan
- Cinquima Institute and Department of Organic Chemistry, Faculty of Sciences, Valladolid University, Paseo de Belén, 7, 47011 Valladolid, Spain;
| | - Francisco J. Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, 28049 Madrid, Spain;
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2
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Kant M, Jaruga P, Coskun E, Ward S, Stark AD, Baumann T, Becker D, Adhikary A, Sevilla MD, Dizdaroglu M. Ne-22 Ion-Beam Radiation Damage to DNA: From Initial Free Radical Formation to Resulting DNA-Base Damage. ACS OMEGA 2021; 6:16600-16611. [PMID: 34235332 PMCID: PMC8246699 DOI: 10.1021/acsomega.1c01954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
We report on the physicochemical processes and the products of DNA damage involved in Ne-22 ion-beam radiation of hydrated (12 ± 3 H2O/nucleotide) salmon testes DNA at 77 K. Free radicals trapped at 77 K were identified using electron spin resonance (ESR) spectroscopy. The measurement of DNA damage using two different techniques of mass spectrometry revealed the formation of numerous DNA products. Results obtained by ESR spectroscopy showed that as the linear energy transfer (LET) of the ion-beam radiation increases along the beam track, the production of DNA radicals correspondingly increases until just before the Bragg peak is reached. Yields of DNA products along the ion-beam track were in excellent agreement with the radical production. This work is the first to use the combination of ESR spectroscopy and mass spectrometric techniques enabling a better understanding of mechanisms of radiation damage to DNA by heavy ion beams detailing the formation of DNA free radicals and their subsequent products.
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Affiliation(s)
- Melis Kant
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Pawel Jaruga
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Erdem Coskun
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience & Biotechnology Research, University of Maryland, 9600 Gudelsky Way, Rockville, Maryland 20850, United
States
| | - Samuel Ward
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Alexander D. Stark
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Thomas Baumann
- National
Superconducting Cyclotron Laboratory, Michigan
State University, 640
South Shaw Lane, East Lansing, Michigan 48824, United
States
| | - David Becker
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Michael D. Sevilla
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Miral Dizdaroglu
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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3
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A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice: Impact of Sex and Age. Int J Mol Sci 2020; 21:ijms21186600. [PMID: 32917005 PMCID: PMC7555950 DOI: 10.3390/ijms21186600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023] Open
Abstract
Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2’-deoxyguanosine (8-oxodG), 5-hydroxy-2’-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
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Shinmura K, Kato H, Kawanishi Y, Goto M, Tao H, Yoshimura K, Nakamura S, Misawa K, Sugimura H. Defective repair capacity of variant proteins of the DNA glycosylase NTHL1 for 5-hydroxyuracil, an oxidation product of cytosine. Free Radic Biol Med 2019; 131:264-273. [PMID: 30552997 DOI: 10.1016/j.freeradbiomed.2018.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/20/2022]
Abstract
The NTHL1 gene encodes DNA glycosylase, which is involved in base excision repair, and biallelic mutations of this gene result in NTHL1-associated polyposis (NAP), a hereditary disease characterized by colorectal polyposis and multiple types of carcinomas. However, no proper functional characterization of variant NTHL1 proteins has been done so far. Herein, we report functional evaluation of variant NTHL1 proteins to aid in the accurate diagnosis of NAP. First, we investigated whether it would be appropriate to use 5-hydroxyuracil (5OHU), an oxidation product of cytosine, for the evaluation. In the supF forward mutation assay, 5OHU caused an increase of the mutation frequency in human cells, and the C→T mutation was predominant among the 5OHU-induced mutations. In addition, in DNA cleavage activity assay, 5OHU was excised by NTHL1 as well as four other DNA glycosylases (SMUG1, NEIL1, TDG, and UNG2). When human cells overexpressing the five DNA glycosylases were established, it was found that each of the five DNA glycosylases, including NTHL1, had the ability to suppress 5OHU-induced mutations. Based on the above results, we performed functional evaluation of eight NTHL1 variants using 5OHU-containing DNA substrate or shuttle plasmid. The DNA cleavage activity assay showed that the variants of NTHL1, Q90X, Y130X, R153X, and Q287X, but not R19Q, V179I, V217F, or G286S, showed defective repair activity for 5OHU and two other oxidatively damaged bases. Moreover, the supF forward mutation assay showed that the four truncated-type NTHL1 variants showed a reduced ability to suppress 5OHU-induced mutations in human cells. These results suggest that the NTHL1 variants Q90X, Y130X, R153X, and Q287X, but not R19Q, V179I, V217F, or G286S, were defective in 5OHU repair and the alleles encoding them were considered to be pathogenic for NAP.
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Affiliation(s)
- Kazuya Shinmura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Japan.
| | - Hisami Kato
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Japan
| | - Yuichi Kawanishi
- Advanced Research Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masanori Goto
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Hong Tao
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Japan
| | - Katsuhiro Yoshimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Japan
| | - Satoki Nakamura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Japan
| | - Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Japan
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Jaruga P, Coskun E, Kimbrough K, Jacob A, Johnson WE, Dizdaroglu M. Biomarkers of oxidatively induced DNA damage in dreissenid mussels: A genotoxicity assessment tool for the Laurentian Great Lakes. ENVIRONMENTAL TOXICOLOGY 2017; 32:2144-2153. [PMID: 28568507 PMCID: PMC5669367 DOI: 10.1002/tox.22427] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 05/03/2023]
Abstract
Activities of fast growing human population are altering freshwater ecosystems, endangering their inhabitants and public health. Organic and trace compounds have a high potential for adverse impacts on aquatic organisms in some Great Lakes tributaries. Toxic compounds in tissues of organisms living in contaminated environments change their metabolism and alter cellular components. We measured oxidatively induced DNA damage in the soft tissues of dreissenid mussels to check on the possible contaminant-induced impact on their DNA. The animals were obtained from archived samples of the National Oceanic and Atmospheric Administration (NOAA) Mussel Watch Program. Mussels were collected from the harbor of Ashtabula River in Ohio, and a reference area located at the Lake Erie shore. Using gas chromatography-tandem mass spectrometry with isotope dilution, we identified and quantified numerous oxidatively modified DNA bases and 8,5'-cyclopurine-2'-deoxynucleosides. We found significant differences in the concentrations of these potentially mutagenic and/or lethal lesions in the DNA of mussels from the harbor as compared to the animals collected at the reference site. These results align NOAA's data showing that elevated concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and heavy metals were found in mussels within the harbor as compared to mussels collected in the reference site. The measured DNA lesions can be used as biomarkers for identifying DNA damage in mussels from polluted and reference sites. Such biomarkers are needed to identify the bioeffects of contaminants in affected organisms, as well as whether remedial actions have proven successful in reducing observed toxic effects.
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Affiliation(s)
- Pawel Jaruga
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Correspondence to: P. Jaruga, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8315, Gaithersburg, MD 20899, USA, Phone: 301-975-4617; Fax: 301-975-2125;
| | - Erdem Coskun
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Kimani Kimbrough
- NOAA’s National Centers for Coastal Ocean Science, National Oceanic and Atmospheric Administration, Silver Spring, MD 20910, United States
| | - Annie Jacob
- Consolidated Safety Services, 10301 Democracy Lane, Suite 300 Fairfax, Virginia 22030, United States
| | - W. Edward Johnson
- NOAA’s National Centers for Coastal Ocean Science, National Oceanic and Atmospheric Administration, Silver Spring, MD 20910, United States
| | - Miral Dizdaroglu
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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6
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Lee AJ, Wallace SS. Hide and seek: How do DNA glycosylases locate oxidatively damaged DNA bases amidst a sea of undamaged bases? Free Radic Biol Med 2017; 107:170-178. [PMID: 27865982 PMCID: PMC5433924 DOI: 10.1016/j.freeradbiomed.2016.11.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/11/2016] [Accepted: 11/13/2016] [Indexed: 01/10/2023]
Abstract
The first step of the base excision repair (BER) pathway responsible for removing oxidative DNA damage utilizes DNA glycosylases to find and remove the damaged DNA base. How glycosylases find the damaged base amidst a sea of undamaged bases has long been a question in the BER field. Single molecule total internal reflection fluorescence microscopy (SM TIRFM) experiments have allowed for an exciting look into this search mechanism and have found that DNA glycosylases scan along the DNA backbone in a bidirectional and random fashion. By comparing the search behavior of bacterial glycosylases from different structural families and with varying substrate specificities, it was found that glycosylases search for damage by periodically inserting a wedge residue into the DNA stack as they redundantly search tracks of DNA that are 450-600bp in length. These studies open up a wealth of possibilities for further study in real time of the interactions of DNA glycosylases and other BER enzymes with various DNA substrates.
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Affiliation(s)
- Andrea J Lee
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA.
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7
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Thomas EM, Testa SM. The colorimetric determination of selectively cleaved adenosines and guanosines in DNA oligomers using bicinchoninic acid and copper. J Biol Inorg Chem 2016; 22:31-46. [PMID: 27807667 DOI: 10.1007/s00775-016-1405-4] [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: 07/19/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
Colorimetric methods combined with color-changing chemical probes are widely used as simple yet effective tools for identifying and quantifying a wide variety of molecules in solution. For nucleic acids (DNA and RNA), perhaps the most commonly used colorimetric probe is potassium permanganate, which can be used to identify single-stranded pyrimidines (thymine and cytosine) in polymers. Unfortunately, permanganate is not an effective probe for identifying purines (adenine and guanine), especially in the presence of the more reactive pyrimidines. Therefore, robust methods for discriminating between the purines remain elusive, thereby creating a barrier toward developing more complex colorimetric applications. In this proof-of-principle study, we demonstrate that bicinchoninic acid (BCA) and copper, when combined with purine-specific chemical cleavage reactions, can be a colorimetric probe for the identification and quantification of adenosines and/or guanosines in single-stranded DNA oligomers, even in the presence of pyrimidines. Furthermore, the reactions are stoichiometric, which allows for the quantification of the number of adenosines and/or guanosines in these oligomers. Because the BCA/copper reagent detects the reducing sugar, 2-deoxyribose, that results from the chemical cleavage of a given nucleotide's N-glycosidic bond, these colorimetric assays are effectively detecting apurinic sites in DNA oligomers, which are known to occur via DNA damage in biological systems. We demonstrate that simple digital analysis of the color-changing chromophore (BCA/copper) is all that is necessary to obtain quantifiable and reproducible data, which indicates that these assays should be broadly accessible.
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Affiliation(s)
- Elizabeth M Thomas
- Department of Chemistry, University of Kentucky, 550 Rose Street, Lexington, KY, 40506, USA
| | - Stephen M Testa
- Department of Chemistry, University of Kentucky, 550 Rose Street, Lexington, KY, 40506, USA.
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8
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Valente WJ, Ericson NG, Long AS, White PA, Marchetti F, Bielas JH. Mitochondrial DNA exhibits resistance to induced point and deletion mutations. Nucleic Acids Res 2016; 44:8513-8524. [PMID: 27550180 PMCID: PMC5062989 DOI: 10.1093/nar/gkw716] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/04/2016] [Indexed: 12/17/2022] Open
Abstract
The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient sensitivity and accuracy, a link between mtDNA damage and mutation has not been established. To test the hypothesis that mtDNA-damaging agents induce mtDNA mutations, we exposed MutaTMMouse mice to benzo[a]pyrene (B[a]P) or N-ethyl-N-nitrosourea (ENU), daily for 28 consecutive days, and quantified mtDNA point and deletion mutations in bone marrow and liver using our newly developed Digital Random Mutation Capture (dRMC) and Digital Deletion Detection (3D) assays. Surprisingly, our results demonstrate mutagen treatment did not increase mitochondrial point or deletion mutation frequencies, despite evidence both compounds increase nuclear DNA mutations and demonstrated B[a]P adduct formation in mtDNA. These findings contradict models of mtDNA mutagenesis that assert the elevated rate of mtDNA mutation stems from damage sensitivity and abridged repair capacity. Rather, our results demonstrate induced mtDNA damage does not readily convert into mutation. These findings suggest robust mitochondrial damage responses repress induced mutations after mutagen exposure.
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Affiliation(s)
- William J Valente
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98195, USA Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra S Long
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA Department of Pathology, University of Washington, Seattle, WA 98195, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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9
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Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
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10
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Legay R, Massou S, Azéma J, Martino R, Malet-Martino M. Hydrolytic pathway of 5-fluorouracil in aqueous solutions for clinical use. J Pharm Biomed Anal 2014; 98:446-62. [DOI: 10.1016/j.jpba.2014.06.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/06/2014] [Accepted: 06/11/2014] [Indexed: 01/14/2023]
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Wallace SS. DNA glycosylases search for and remove oxidized DNA bases. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:691-704. [PMID: 24123395 PMCID: PMC3997179 DOI: 10.1002/em.21820] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 05/19/2023]
Abstract
This review article presents, an overview of the DNA glycosylases that recognize oxidized DNA bases using the Fpg/Nei family of DNA glycosylases as models for how structure can inform function. For example, even though human NEIL1 and the plant and fungal orthologs lack the zinc finger shown to be required for binding, DNA crystal structures revealed a "zincless finger" with the same properties. Moreover, the "lesion recognition loop" is not involved in lesion recognition, rather, it stabilizes 8-oxoG in the active site pocket. Unlike the other Fpg/Nei family members, Neil3 lacks two of the three void-filling residues that stabilize the DNA duplex and interact with the opposite strand to the damage which may account for its preference for lesions in single-stranded DNA. Also single-molecule approaches show that DNA glycosylases search for their substrates in a sea of undamaged DNA by using a wedge residue that is inserted into the DNA helix to probe for the presence of damage.
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Affiliation(s)
- Susan S. Wallace
- Department of Microbiology and Molecular Genetics The Markey Center for Molecular Genetics The University of Vermont Stafford Hall, 95 Carrigan Drive Burlington, VT 05405-0068, USA Tel: (802) 656-2164; Fax: (802) 656-8749
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12
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Abstract
Endogenous and exogenous sources cause free radical-induced DNA damage in living organisms by a variety of mechanisms. The highly reactive hydroxyl radical reacts with the heterocyclic DNA bases and the sugar moiety near or at diffusion-controlled rates. Hydrated electron and H atom also add to the heterocyclic bases. These reactions lead to adduct radicals, further reactions of which yield numerous products. These include DNA base and sugar products, single- and double-strand breaks, 8,5'-cyclopurine-2'-deoxynucleosides, tandem lesions, clustered sites and DNA-protein cross-links. Reaction conditions and the presence or absence of oxygen profoundly affect the types and yields of the products. There is mounting evidence for an important role of free radical-induced DNA damage in the etiology of numerous diseases including cancer. Further understanding of mechanisms of free radical-induced DNA damage, and cellular repair and biological consequences of DNA damage products will be of outmost importance for disease prevention and treatment.
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Affiliation(s)
- Miral Dizdaroglu
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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13
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Tainaka K, Okamoto A. ICON probes: synthesis and DNA methylation typing. ACTA ACUST UNITED AC 2012; Chapter 8:Unit 8.7.1-17. [PMID: 22147422 DOI: 10.1002/0471142700.nc0807s47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression, respectively. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis and may be a useful and effective index for cancer diagnosis. We have developed an artificial DNA probe that induces a methylation detection reaction of a target cytosine in a long DNA sequence (ICON probe). This artificial DNA allows the rapid detection of a methyl group attached at the C5 position of the target cytosine. In addition, there is no nonspecific cleavage of genomic DNA in this reaction. The ICON probe also facilitates the quantification of methylation at the target cytosine using a small amount of genomic DNA sample. This unit provides a procedure for synthesizing bipyridine-modified adenosine phosphoramidite and preparation of ICON probes. Additionally, the protocol for the methylation quantification experiments by quantitative PCR utilizing ICON probes is also presented.
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Affiliation(s)
- Kazuki Tainaka
- Advanced Science Institute, RIKEN, The Institute of Physical and Chemical Research, Wako, Saitama, Japan
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14
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Berquist BR, Wilson DM. Pathways for repairing and tolerating the spectrum of oxidative DNA lesions. Cancer Lett 2012; 327:61-72. [PMID: 22353689 DOI: 10.1016/j.canlet.2012.02.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/26/2012] [Accepted: 02/01/2012] [Indexed: 01/03/2023]
Abstract
Reactive oxygen species (ROS) arise from both endogenous and exogenous sources. These reactive molecules possess the ability to damage both the DNA nucleobases and the sugar phosphate backbone, leading to a wide spectrum of lesions, including non-bulky (8-oxoguanine and formamidopyrimidine) and bulky (cyclopurine and etheno adducts) base modifications, abasic sites, non-conventional single-strand breaks, protein-DNA adducts, and intra/interstrand DNA crosslinks. Unrepaired oxidative DNA damage can result in bypass mutagenesis during genome copying or gene expression, or blockage of the essential cellular processes of DNA replication or transcription. Such outcomes underlie numerous pathologies, including, but not limited to, carcinogenesis and neurodegeneration, as well as the aging process. Cells have adapted and evolved defense systems against the deleterious effects of ROS, and specifically devote a number of cellular DNA repair and tolerance pathways to combat oxidative DNA damage. Defects in these protective pathways trigger hereditary human diseases that exhibit increased cancer incidence, developmental defects, neurological abnormalities, and/or premature aging. We review herein classic and atypical oxidative DNA lesions, outcomes of encountering these damages during DNA replication and transcription, and the consequences of losing the ability to repair the different forms of oxidative DNA damage. We particularly focus on the hereditary human diseases Xeroderma Pigmentosum, Cockayne Syndrome and Fanconi Anemia, which may involve defects in the efficient repair of oxidative modifications to chromosomal DNA.
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Affiliation(s)
- Brian R Berquist
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, 77843, United States
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15
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Dizdaroglu M. Oxidatively induced DNA damage: mechanisms, repair and disease. Cancer Lett 2012; 327:26-47. [PMID: 22293091 DOI: 10.1016/j.canlet.2012.01.016] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 12/23/2011] [Accepted: 01/11/2012] [Indexed: 12/12/2022]
Abstract
Endogenous and exogenous sources cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. The resulting DNA lesions are mutagenic and, unless repaired, lead to a variety of mutations and consequently to genetic instability, which is a hallmark of cancer. Oxidatively induced DNA damage is repaired in living cells by different pathways that involve a large number of proteins. Unrepaired and accumulated DNA lesions may lead to disease processes including carcinogenesis. Mutations also occur in DNA repair genes, destabilizing the DNA repair system. A majority of cancer cell lines have somatic mutations in their DNA repair genes. In addition, polymorphisms in these genes constitute a risk factor for cancer. In general, defects in DNA repair are associated with cancer. Numerous DNA repair enzymes exist that possess different, but sometimes overlapping substrate specificities for removal of oxidatively induced DNA lesions. In addition to the role of DNA repair in carcinogenesis, recent evidence suggests that some types of tumors possess increased DNA repair capacity that may lead to therapy resistance. DNA repair pathways are drug targets to develop DNA repair inhibitors to increase the efficacy of cancer therapy. Oxidatively induced DNA lesions and DNA repair proteins may serve as potential biomarkers for early detection, cancer risk assessment, prognosis and for monitoring therapy. Taken together, a large body of accumulated evidence suggests that oxidatively induced DNA damage and its repair are important factors in the development of human cancers. Thus this field deserves more research to contribute to the development of cancer biomarkers, DNA repair inhibitors and treatment approaches to better understand and fight cancer.
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Affiliation(s)
- Miral Dizdaroglu
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Onyshchenko MI, Gaynutdinov TI, Englund EA, Appella DH, Neumann RD, Panyutin IG. Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region. Nucleic Acids Res 2011; 39:7114-23. [PMID: 21593130 PMCID: PMC3167611 DOI: 10.1093/nar/gkr259] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Guanine-rich sequences are highly abundant in the human genome, especially in regulatory regions. Because guanine-rich sequences have the unique ability to form G-quadruplexes, these structures may play a role in the regulation of gene transcription. In previous studies, we demonstrated that formation of G-quadruplexes could be induced with peptide nucleic acids (PNAs). PNAs designed to bind the C-rich strand upstream of the human BCL2 gene promoted quadruplex formation in the complementary G-rich strand. However, the question whether G-quadruplex formation was essential for PNA invasion remained unanswered. In this study, we compared PNA invasion in the native and mutant, i.e. not forming G-quadruplex, BCL2 sequences and showed that G-quadruplex is required for effective PNA invasion into duplex DNA. This finding provides strong evidence for not only sequence-specific, but also quadruplex specific, gene targeting with PNA probes. In addition, we examined DNA-duplex invasion potential of PNAs of various charges. Using the gel shift assay, chemical probing and dimethyl sulfate (DMS) protection studies, we determined that uncharged zwitterionic PNA has the highest binding specificity while preserving efficient duplex invasion.
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Affiliation(s)
- Mykola I Onyshchenko
- Imaging Sciences Training Program, Clinical Center and National Institute of Biomedical Imaging and Bioengineering, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Schalow BJ, Courcelle CT, Courcelle J. Escherichia coli Fpg glycosylase is nonrendundant and required for the rapid global repair of oxidized purine and pyrimidine damage in vivo. J Mol Biol 2011; 410:183-93. [PMID: 21601577 DOI: 10.1016/j.jmb.2011.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/03/2011] [Accepted: 05/03/2011] [Indexed: 01/13/2023]
Abstract
Endonuclease (Endo) III and formamidopyrimidine-N-glycosylase (Fpg) are two of the predominant DNA glycosylases in Escherichia coli that remove oxidative base damage. In cell extracts and purified form, Endo III is generally more active toward oxidized pyrimidines, while Fpg is more active towards oxidized purines. However, the substrate specificities of these enzymes partially overlap in vitro. Less is known about the relative contribution of these enzymes in restoring the genomic template following oxidative damage. In this study, we examined how efficiently Endo III and Fpg repair their oxidative substrates in vivo following treatment with hydrogen peroxide. We found that Fpg was nonredundant and required to rapidly remove its substrate lesions on the chromosome. In addition, Fpg also repaired a significant portion of the lesions recognized by Endo III, suggesting that it plays a prominent role in the global repair of both purine damage and pyrimidine damage in vivo. By comparison, Endo III did not affect the repair rate of Fpg substrates and was only responsible for repairing a subset of its own substrate lesions in vivo. The absence of Endo VIII or nucleotide excision repair did not significantly affect the global repair of either Fpg or Endo III substrates in vivo. Surprisingly, replication recovered after oxidative DNA damage in all mutants examined, even when lesions persisted in the DNA, suggesting the presence of an efficient mechanism to process or overcome oxidative damage encountered during replication.
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Affiliation(s)
- Brandy J Schalow
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97207, USA.
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18
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Okamoto A, Sugizaki K, Nakamura A, Yanagisawa H, Ikeda S. 5-Hydroxymethylcytosine-selective oxidation with peroxotungstate. Chem Commun (Camb) 2011; 47:11231-3. [DOI: 10.1039/c1cc14782j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Baumann A, Lohmann W, Jahn S, Karst U. On-Line Electrochemistry/Electrospray Ionization Mass Spectrometry (EC/ESI-MS) for the Generation and Identification of Nucleotide Oxidation Products. ELECTROANAL 2010. [DOI: 10.1002/elan.200900358] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Felício D, Almeida C, Silva A, Leitão A. Hydrogen peroxide induces a specific DNA base change profile in the presence of the iron chelator 2,2’ dipyridyl in Escherichia coli. Braz J Med Biol Res 2009. [DOI: 10.1590/s0100-879x2009007500001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - A.B. Silva
- Universidade Federal do Rio de Janeiro, Brasil
| | - A.C. Leitão
- Universidade Federal do Rio de Janeiro, Brasil
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21
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Thiviyanathan V, Somasunderam A, Volk DE, Hazra TK, Mitra S, Gorenstein DG. Base-pairing properties of the oxidized cytosine derivative, 5-hydroxy uracil. Biochem Biophys Res Commun 2007; 366:752-7. [PMID: 18078807 DOI: 10.1016/j.bbrc.2007.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 12/04/2007] [Indexed: 11/19/2022]
Abstract
The most abundant base-substitution mutation resulting from oxidative damage to DNA is the GC to AT transition mutation. 5-hydroxyuracil (5-OHU), produced by the oxidative deamination of cystosine, has been established as the major chemical precursor for this most abundant transition mutation. Results from NMR spectroscopy and UV melting experiments show that 5-OHU would form the most stable pair with G, and the least stable pair with C. The hydroxyl group in the 5th position of the 5-OHU residue may play a role in increasing the stability of the 5-OHU:G pair over the normal Watson-Crick pair, the 5-OHU:A. The 5-OHU:C base pair would be least stable, and would destabilize the base-stacking in the duplex. Our results explain why certain DNA polymerases preferentially incorporate G opposite to 5-OHU over A and why C does not get incorporated against 5-OHU during DNA replication in vivo.
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Affiliation(s)
- Varatharasa Thiviyanathan
- Sealy Center for Structural Biology & Molecular Biophysics, Sealy Center for Molecular Sciences, Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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22
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Tanaka K, Tainaka K, Umemoto T, Nomura A, Okamoto A. An osmium-DNA interstrand complex: application to facile DNA methylation analysis. J Am Chem Soc 2007; 129:14511-7. [PMID: 17963391 DOI: 10.1021/ja076140r] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acids often acquire new functions by forming a variety of complexes with metal ions. Osmium, in an oxidized state, also reacts with C5-methylated pyrimidines. However, control of the sequence specificity of osmium complexation with DNA is still immature, and the value of the resulting complexes is unknown. We have designed a bipyridine-attached adenine derivative for sequence-specific osmium complexation. Sequence-specific osmium complexation was achieved by hybridization of a short DNA molecule containing this functional nucleotide to a target DNA sequence and resulted in the formation of a cross-linked structure. The interstrand cross-link clearly distinguished methylated cytosines from unmethylated cytosines and was used to quantify the degree of methylation at a specific cytosine in the genome.
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Affiliation(s)
- Kazuo Tanaka
- Frontier Research System, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
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23
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Tanaka K, Tainaka K, Kamei T, Okamoto A. Direct labeling of 5-methylcytosine and its applications. J Am Chem Soc 2007; 129:5612-20. [PMID: 17408269 DOI: 10.1021/ja068660c] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytosine methylation is one of the most important epigenetic events, and much effort has been directed to develop a simple reaction for methylcytosine detection. In this paper, we describe the design of tag-attachable ligands for direct methylcytosine labeling and their application to fluorescent and electrochemical assays. The effect of the location of bipyridine substituents on the efficiency of osmium complexation at methylcytosine was initially investigated. As a result, a bipyridine derivative with a substituent at the C4 position showed efficient complexation at the methylcytosine residue of single-stranded DNA in a reaction mixture containing potassium osmate and potassium hexacyanoferrate(III). On the basis of this result, a bipyridine derivative with a tag-attachable amino linker at the C4 position was synthesized. The efficiency of metal complex formation in the presence of the osmate and the synthetic ligand was clearly changed by the presence/absence of a methyl group at the C5 position of cytosine. The succinimidyl esters of functional labeling units were then attached to the bipyridine ligand fixed on the methylcytosine. These labels attached to methylcytosine enabled us to detect the target methylcytosine in DNA both fluorometrically and electrochemically. For example, we were able to fluorometrically obtain information on the methylation status at a specific site by means of fluorescence resonance energy transfer from a hybridized fluorescent DNA probe to a fluorescent label on methylcytosine. In addition, by the combination of electrochemically labeled methylcytosine and an electrode modified by probe DNAs, a methylcytosine-selective characteristic current signal was observed. This direct labeling of methylcytosine is a conceptually new methylation detection assay with many merits different from conventional assays.
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Affiliation(s)
- Kazuo Tanaka
- Frontier Research System, RIKEN, The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan
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24
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Tanaka K, Tainaka K, Okamoto A. Methylcytosine-selective fluorescence quenching by osmium complexation. Bioorg Med Chem 2006; 15:1615-21. [PMID: 17194597 DOI: 10.1016/j.bmc.2006.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 10/23/2022]
Abstract
We report on the control of the emission from a fluorophore fixed on DNA using the methylcytosine-selective addition of an osmium-bipyridine complex. We have synthesized DNA modified by a microenvironment-sensitive fluorophore, 2-dimethylamino-6-acyl-naphthalene. The emission from the fluorophore tethered to a probe DNA was effectively quenched by a methylcytosine glycol-osmium-bipyridine triad, which was located in the immediate neighborhood of the fluorophore. The discrimination of the cytosine methylation status at a methylation hot spot in the p53 gene was also executed using a well-designed fluorescent DNA probe.
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Affiliation(s)
- Kazuo Tanaka
- Frontier Research System, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan
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25
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Daviet S, Couvé-Privat S, Gros L, Shinozuka K, Ide H, Saparbaev M, Ishchenko AA. Major oxidative products of cytosine are substrates for the nucleotide incision repair pathway. DNA Repair (Amst) 2006; 6:8-18. [PMID: 16978929 DOI: 10.1016/j.dnarep.2006.08.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 08/01/2006] [Accepted: 08/02/2006] [Indexed: 11/21/2022]
Abstract
Most common point mutations occurring spontaneously or induced by ionizing radiation are C-->T transitions implicating cytosine as the target. Oxidative cytosine derivatives are the most abundant and mutagenic DNA damage induced by oxidative stress. Base excision repair (BER) pathway initiated by DNA glycosylases is thought to be the major pathway for the removal of these lesions. However, in alternative nucleotide incision repair (NIR) pathway the apurinic/apyrimidinic (AP) endonucleases incise DNA duplex 5' to an oxidatively damaged base in a DNA glycosylase-independent manner. Here, we characterized the substrate specificity of human major AP endonuclease, Ape1, towards 5-hydroxy-2'-deoxycytidine (5ohC) and alpha-anomeric 2'-deoxycytidine (alphadC) residues. The apparent kinetic parameters of the reactions suggest that Ape1 and the DNA glycosylases/AP lyases, hNth1 and hNeil1 repair 5ohC with a low efficiency. Nevertheless, due to the extremely high cellular concentration of Ape1, NIR was the major activity towards 5ohC in cell-free extracts. To address the physiological role of NIR function, we have characterized naturally occurring Ape1 variants including amino acids substitutions (E126A, E126D and D148E) and N-terminal truncated forms (NDelta31, NDelta35 and NDelta61). As expected, all Ape1 mutants had proficient AP endonuclease activity, however, truncated forms showed reduced NIR and 3'-->5' exonuclease activities indicating that these two functions are genetically linked and governed by the same amino acid residues. Furthermore, both Ape1-catalyzed NIR and 3'-->5' exonuclease activities generate a single-strand gap at the 5' side of a damaged base but not at an AP site in duplex DNA. We hypothesized that biochemical coupling of the nucleotide incision and exonuclease degradation may serve to remove clustered DNA damage. Our data suggest that NIR is a backup system for the BER pathway to remove oxidative damage to cytosines in vivo.
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Affiliation(s)
- Stéphane Daviet
- Groupe Réparation de l'ADN, UMR 8126 CNRS, Univ Paris-Sud, Institut Gustave Roussy, 94805 Villejuif Cedex, France
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26
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Simon P, Gasparutto D, Gambarelli S, Saint-Pierre C, Favier A, Cadet J. Formation of isodialuric acid lesion within DNA oligomers via one-electron oxidation of 5-hydroxyuracil: characterization, stability and excision repair. Nucleic Acids Res 2006; 34:3660-9. [PMID: 16885239 PMCID: PMC1540730 DOI: 10.1093/nar/gkl496] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
5-Hydroxyuracil is a major oxidized nucleobase that can be generated by the action of •OH radical and one-electron oxidants. The latter modified base that exhibits a low ionization potential is highly susceptible to further degradation upon exposure to various oxidants. Emphasis was placed in thiswork on the formation and characterization of one-electron oxidation products of 5-hydroxyuracil within DNA fragments of defined sequence. For this purpose, 5-hydroxyuracil containing single- and double-stranded oligonucleotides of various lengths were synthesized and then exposed to the oxidizing action of iridium salts. Isodialuric acid was found to be formed almost quantitatively by a one-electron oxidation mechanism for which relevant information was inferred from a freeze-quenched ESR study. Information on the stability of isodialuric acid thus formed and its conversion products in aqueous solutions was also gained from experiments performed at acidic, neutral and alkali pH’s. Moreover, biochemical features dealing with the substrate specificity of several bacterial and yeast base excision repair enzymes to remove isodialuric acid from site-specifically modified DNA fragments were determined.
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Affiliation(s)
| | - Didier Gasparutto
- To whom the correspondence should be addressed. Tel: +33 4 38 78 45 58; Fax: +33 4 38 78 50 90;
| | - Serge Gambarelli
- Laboratoire de Résonance Magnétique, Département de Recherche Fondamentale sur la Matière CondenséeService de Chimie Inorganique et Biologique, UMR E3 CEA-UJF, CEA-Grenoble, F-38054 Grenoble Cedex 9, France
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Maier J, van Steeg H, van Oostrom C, Karger S, Paschke R, Krohn K. Deoxyribonucleic acid damage and spontaneous mutagenesis in the thyroid gland of rats and mice. Endocrinology 2006; 147:3391-7. [PMID: 16627585 DOI: 10.1210/en.2005-1669] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Thyroid tumors are a frequent finding not only in iodine-deficient regions. They are predominantly characterized by somatic genetic changes (e.g. point mutations or rearrangements). Because slow thyroid proliferation is a apparent contradiction to a high frequency of tumor initiation, we characterized mutational events in thyroid. First we studied the frequency of certain base exchanges in somatic TSH receptor (TSHR) mutations and determined the spontaneous mutation rate in thyroid and liver. Then we applied different protocols of the comet assay to quantify genomic DNA damage and conducted immunohistochemistry for 8-oxoguanine as a molecular marker for oxidative stress. Among 184 somatic mutations of the human TSHR found in thyroid tumors, C-->T transitions had a unexpectedly high frequency (>32%). The mutation rate in thyroid is 8-10 times higher than in other organs. The comet assay detected increased levels of oxidized pyrimidine (2- to 3-fold) and purine (2- to 4-fold) in thyroid, compared with liver and lung, and a 1.6-fold increase of oxidized purine, compared with spleen. Immunohistochemistry revealed high levels of 8-oxoguanine in thyroid epithelial cells. We have shown a strikingly high mutation rate in the thyroid. Furthermore, results of the comet assay as well as immunohistochemistry suggest that oxidative DNA modifications are a likely cause of the higher mutation rate. It is possible that free radicals resulting from reactive oxygen species in the thyroid generate mutations more frequently. This is also supported by the spectrum of somatic mutations in the TSHR because more frequent base changes could stem from oxidized base adducts that we detected in the comet assay and with immunohistochemistry.
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Affiliation(s)
- J Maier
- III Medical Department, University of Leipzig, Inselstrasse 22, D-04103 Leipzig, Germany
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28
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Volk DE, Thiviyanathan V, Somasunderam A, Gorenstein DG. Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels. Org Biomol Chem 2006; 4:1741-5. [PMID: 16633566 DOI: 10.1039/b602263d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxidized cytosine product 5-hydroxyuracil has been shown to be the major chemical precursor for the GC to AT transition, the most frequent substitution mutation observed in aerobic organisms. We have calculated the interaction energy of base-pair formation involving uracil or 5-hydroxyuracil, which is formed in cells by oxidative deamination of cytosine, bound to any of the natural DNA bases, A, C, G, and T, and discuss the effects of the hydroxyl group in this respect. The base-pair geometries and energies were calculated using the 6-311G(dp) basis set under four conditions: using density functional theory (DFT) without out basis set super-position error (BSSE) correction, using DFT with BSSE correction of geometries and energies, using Møller-Plesset second order perturbation theory (MP2) without BSSE correction, and using MP2 with BSSE geometry and energy correction. We find that the hydroxyl group of 5-HO-U (relative to U) has little effect on the base-pairs with A, C or one conformation of T, while making a substantial energy difference in base-pairs involving G or a different conformation of T. For most of the complexes studied, the BSSE-corrected energies at the DFT and MP2 levels of theory agreed to within 0.5 kcal.
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Affiliation(s)
- David E Volk
- Sealy Center for Structural Biology and Molecular Biophysics and the Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, 77555-1157, USA
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O'Sullivan DM, McHugh TD, Gillespie SH. Analysis of rpoB and pncA mutations in the published literature: an insight into the role of oxidative stress in Mycobacterium tuberculosis evolution? J Antimicrob Chemother 2005; 55:674-9. [PMID: 15814606 DOI: 10.1093/jac/dki069] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION It is perceived wisdom that within the host macrophage, Mycobacterium tuberculosis frequently encounters oxidative stress. Exposure of bacteria to reactive oxygen intermediates can have a mutagenic effect on the DNA. Various mutations are thought to arise as a consequence, including the oxidation of guanine residues, leading to G?C-->T?A substitution, and oxidation of cytosine resulting in a G?C-->A?T substitution. METHODS We measured the relative contribution of oxidative stress by recording the percentage of single nucleotide substitutions reported in the genes rpoB and pncA that confer resistance to the antimicrobials rifampicin and pyrazinamide, respectively, and determined whether there is an excess of G?C-->T?A or G?C-->A?T substitutions. RESULTS Out of 840 clinical isolates reported with single nucleotide mutations in the rpoB gene, 67% were G?C-->A?T changes, and 3% were G?C-->T?A substitutions. These figures were compared to the pncA gene, where out of 114 isolates, 30% of the single nucleotide mutations were G?C-->A?T transitions and 9% were G?C-->T?A changes. CONCLUSIONS While there is an excess of G?C-->A?T changes in the rpoB gene, this was not the case in the pncA gene. Fifty-three percent of mutations within the rpoB gene were C-->T mutations of the type S531L. Although this mutation gives a fitness disadvantage, it is less than other common mutations, so it is more likely that that fitness is the determinant of surviving mutation rather than oxidative stress because of the small numbers of other C-->T and G-->A mutations at other sites (12%). There was no evidence of oxygen free radicals damaging the guanine bases in either gene.
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Affiliation(s)
- Denise M O'Sullivan
- Centre for Medical Microbiology, Department of Infection, Royal Free & University College Medical School, Royal Free Campus, University College London, Rowland Hill Street, London NW3 2PF, UK
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30
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Evans MD, Dizdaroglu M, Cooke MS. Oxidative DNA damage and disease: induction, repair and significance. MUTATION RESEARCH/REVIEWS IN MUTATION RESEARCH 2004; 567:1-61. [PMID: 15341901 DOI: 10.1016/j.mrrev.2003.11.001] [Citation(s) in RCA: 877] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Revised: 11/12/2003] [Accepted: 11/12/2003] [Indexed: 04/08/2023]
Abstract
The generation of reactive oxygen species may be both beneficial to cells, performing a function in inter- and intracellular signalling, and detrimental, modifying cellular biomolecules, accumulation of which has been associated with numerous diseases. Of the molecules subject to oxidative modification, DNA has received the greatest attention, with biomarkers of exposure and effect closest to validation. Despite nearly a quarter of a century of study, and a large number of base- and sugar-derived DNA lesions having been identified, the majority of studies have focussed upon the guanine modification, 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OH-dG). For the most part, the biological significance of other lesions has not, as yet, been investigated. In contrast, the description and characterisation of enzyme systems responsible for repairing oxidative DNA base damage is growing rapidly, being the subject of intense study. However, there remain notable gaps in our knowledge of which repair proteins remove which lesions, plus, as more lesions identified, new processes/substrates need to be determined. There are many reports describing elevated levels of oxidatively modified DNA lesions, in various biological matrices, in a plethora of diseases; however, for the majority of these the association could merely be coincidental, and more detailed studies are required. Nevertheless, even based simply upon reports of studies investigating the potential role of 8-OH-dG in disease, the weight of evidence strongly suggests a link between such damage and the pathogenesis of disease. However, exact roles remain to be elucidated.
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Affiliation(s)
- Mark D Evans
- Oxidative Stress Group, Department of Clinical Biochemistry, University of Leicester, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, LE2 7LX, UK
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31
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Ishchenko AA, Sanz G, Privezentzev CV, Maksimenko AV, Saparbaev M. Characterisation of new substrate specificities of Escherichia coli and Saccharomyces cerevisiae AP endonucleases. Nucleic Acids Res 2003; 31:6344-53. [PMID: 14576322 PMCID: PMC275454 DOI: 10.1093/nar/gkg812] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite the progress in understanding the base excision repair (BER) pathway it is still unclear why known mutants deficient in DNA glycosylases that remove oxidised bases are not sensitive to oxidising agents. One of the back-up repair pathways for oxidative DNA damage is the nucleotide incision repair (NIR) pathway initiated by two homologous AP endonucleases: the Nfo protein from Escherichia coli and Apn1 protein from Saccharomyces cerevisiae. These endonucleases nick oxidatively damaged DNA in a DNA glycosylase-independent manner, providing the correct ends for DNA synthesis coupled to repair of the remaining 5'-dangling nucleotide. NIR provides an advantage compared to DNA glycosylase-mediated BER, because AP sites, very toxic DNA glycosylase products, do not form. Here, for the first time, we have characterised the substrate specificity of the Apn1 protein towards 5,6-dihydropyrimidine, 5-hydroxy-2'-deoxyuridine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine deoxynucleotide. Detailed kinetic comparisons of Nfo, Apn1 and various DNA glycosylases using different DNA substrates were made. The apparent K(m) and kcat/K(m) values of the reactions suggest that in vitro DNA glycosylase/AP lyase is somewhat more efficient than the AP endonuclease. However, in vivo, using cell-free extracts from paraquat-induced E.coli and from S.cerevisiae, we show that NIR is one of the major pathways for repair of oxidative DNA base damage.
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Affiliation(s)
- Alexander A Ishchenko
- Groupe Réparation de l'ADN, UMR 8113 CNRS, LBPA ENS Cachan, Institut Gustave Roussy, 94805 Villejuif Cedex, France
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32
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Dou H, Mitra S, Hazra TK. Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2. J Biol Chem 2003; 278:49679-84. [PMID: 14522990 DOI: 10.1074/jbc.m308658200] [Citation(s) in RCA: 277] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Repair of oxidatively damaged bases in the genome via the base excision repair pathway is initiated with excision of these lesions by DNA glycosylases with broad substrate range. The newly discovered human DNA glycosylases, NEIL1 and NEIL2, are distinct in structural features and reaction mechanism from the previously characterized NTH1 and OGG1 but act on many of the same substrates. However, NEIL2 shows a unique preference for excising lesions from a DNA bubble, whereas NTH1 and OGG1 are only active with duplex DNA. NEIL1 also excises efficiently 5-hydroxyuracil, an oxidation product of cytosine, from the bubble and single-stranded DNA but does not have strong activity toward 8-oxoguanine in the bubble. The dichotomy in the activity of NEILs versus NTH1/OGG1 for bubble versus duplex DNA substrates is consistent with higher affinity of the NEILs for the bubble structures of both damaged and undamaged DNA relative to duplex structure. These observations suggest that the NEILs are functionally distinct from OGG1/NTH1 in vivo. OGG1/NTH1-independent repair of oxidized bases in the transcribed sequences supports the possibility that NEILs are preferentially involved in repair of lesions in DNA bubbles generated during transcription and/or replication.
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Affiliation(s)
- Hong Dou
- Sealy Center for Molecular Science and Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas 77555, USA
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33
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Abstract
Oxidative DNA damage is an inevitable consequence of cellular metabolism, with a propensity for increased levels following toxic insult. Although more than 20 base lesions have been identified, only a fraction of these have received appreciable study, most notably 8-oxo-2'deoxyguanosine. This lesion has been the focus of intense research interest and been ascribed much importance, largely to the detriment of other lesions. The present work reviews the basis for the biological significance of oxidative DNA damage, drawing attention to the multiplicity of proteins with repair activities along with a number of poorly considered effects of damage. Given the plethora of (often contradictory) reports describing pathological conditions in which levels of oxidative DNA damage have been measured, this review critically addresses the extent to which the in vitro significance of such damage has relevance for the pathogenesis of disease. It is suggested that some shortcomings associated with biomarkers, along with gaps in our knowledge, may be responsible for the failure to produce consistent and definitive results when applied to understanding the role of DNA damage in disease, highlighting the need for further studies.
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Affiliation(s)
- Marcus S Cooke
- Oxidative Stress Group, Department of Clinical Biochemistry, University of Leicester, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, LE2 7LX, UK.
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Kamiya H. Mutagenic potentials of damaged nucleic acids produced by reactive oxygen/nitrogen species: approaches using synthetic oligonucleotides and nucleotides: survey and summary. Nucleic Acids Res 2003; 31:517-31. [PMID: 12527759 PMCID: PMC140503 DOI: 10.1093/nar/gkg137] [Citation(s) in RCA: 215] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA and DNA precursors (deoxyribonucleotides) suffer damage by reactive oxygen/nitrogen species. They are important mutagens for organisms, due to their endogenous formation. Damaged DNA and nucleotides cause alterations of the genetic information by the mispairing properties of the damaged bases, such as 8-hydroxyguanine (7,8-dihydro-8-oxoguanine) and 2-hydroxyadenine. Here, the author reviews the mutagenic potentials of damaged bases in DNA and of damaged DNA precursors formed by reactive oxygen/nitrogen species, focusing on the results obtained with synthetic oligonucleotides and 2'-deoxyribonucleoside 5'-triphosphates.
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Affiliation(s)
- Hiroyuki Kamiya
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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Guetens G, De Boeck G, Highley M, van Oosterom AT, de Bruijn EA. Oxidative DNA damage: biological significance and methods of analysis. Crit Rev Clin Lab Sci 2002; 39:331-457. [PMID: 12385502 DOI: 10.1080/10408360290795547] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
All forms of aerobic life are subjected constantly to oxidant pressure from molecular oxygen and also reactive oxygen species (ROS), produced during the biochemical utilization of O2 and prooxidant stimulation of O2 metabolism. ROS are thought to influence the development of human cancer and more than 50 other human diseases. To prevent oxidative DNA damage (protection) or to reverse damage, thereby preventing mutagenesis and cancer (repair), the aerobic cell possesses antioxidant defense systems and DNA repair mechanisms. During the last 20 years, many analytical techniques have been developed to monitor oxidative DNA base damage. High-performance liquid chromatography-electrochemical detection and gas chromatography-mass spectrometry are the two pioneering contributions to the field. Currently, the arsenal of methods available include the promising high-performance liquid chromatography-tandem mass spectrometry technique, capillary electrophoresis, 32P-postlabeling, fluorescence postlabeling, 3H-postlabeling, antibody-base immunoassays, and assays involving the use of DNA repair glycosylases such as the comet assay, the alkaline elution assay, and the alkaline unwinding method. Recently, the use of liquid chromatography-mass spectrometry has been introduced for the measurement of a number of modified nucleosides in oxidatively damaged DNA. The bulk of available chromatographic methods aimed at measuring individual DNA base lesions require either chemical hydrolysis or enzymatic digestion of oxidized DNA, following extraction from cells or tissues. The effect of experimental conditions (DNA isolation, hydrolysis, and/or derivatization) on the levels of oxidatively modified bases in DNA is enormous and has been studied intensively in the last 10 years.
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36
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Whiteman M, Hong HS, Jenner A, Halliwell B. Loss of oxidized and chlorinated bases in DNA treated with reactive oxygen species: implications for assessment of oxidative damage in vivo. Biochem Biophys Res Commun 2002; 296:883-9. [PMID: 12200130 DOI: 10.1016/s0006-291x(02)02018-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Oxidative damage to DNA has been reported to occur in a wide variety of disease states. The most widely used "marker" for oxidative DNA damage is 8-hydroxyguanine. However, the use of only one marker has limitations. Exposure of calf thymus DNA to an .OH-generating system (CuCl(2), ascorbate, H(2)O(2)) or to hypochlorous acid (HOCl), led to the extensive production of multiple oxidized or chlorinated DNA base products, as measured by gas chromatography-mass spectrometry. The addition of peroxynitrite (ONOO(-)) (<200 microM) or SIN-1 (1mM) to oxidized DNA led to the extensive loss of 8-hydroxyguanine, 5-hydroxycytosine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, 2-hydroxyadenine, 8-hydroxyadenine, and 4,6-diamino-5-formamidopyrimidine were lost at higher ONOO(-) concentrations (>200 microM). Exposure of DNA to HOCl led to the generation of 5-Cl uracil and 8-Cl adenine and addition of ONOO(-) (<200 microM) or SIN-1 (1mM) led to an extensive loss of 8-Cl adenine and a small loss of 5-Cl uracil at higher concentrations (>500 microM). An .OH-generating system (CuCl(2)/ascorbate/H(2)O(2)) could also destroy these chlorinated species. Treatment of oxidized or chlorinated DNA with acidified nitrite (NO(2)(-), pH 3) led to substantial loss of various base lesions, in particular 8-OH guanine, 5-OH cytosine, thymine glycol, and 8-Cl adenine. Our data indicate the possibility that when ONOO(-), nitrite in regions of low pH or .OH are produced at sites of inflammation, levels of certain damaged DNA bases could represent an underestimate of ongoing DNA damage. This study emphasizes the need to examine more than one modified DNA base when assessing the role of reactive species in human disease.
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Affiliation(s)
- Matthew Whiteman
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore.
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Hazra TK, Kow YW, Hatahet Z, Imhoff B, Boldogh I, Mokkapati SK, Mitra S, Izumi T. Identification and characterization of a novel human DNA glycosylase for repair of cytosine-derived lesions. J Biol Chem 2002; 277:30417-20. [PMID: 12097317 DOI: 10.1074/jbc.c200355200] [Citation(s) in RCA: 250] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Two candidate human orthologs of Escherichia coli MutM/Nei were recently identified in the human genome database, and one of these, NEH1, was characterized earlier (Hazra, T. K., Izumi, T., Boldogh, I., Imhoff, B., Kow, Y. W., Jaruga, P., and Dizdaroglu, M. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 3523-3528). Here we report characterization of the second protein, originally named NEH2 and now renamed NEIL2 (Nei-like). The 37-kDa wild-type NEIL2 expressed in and purified from E. coli has DNA glycosylase/AP lyase activity, primarily for excising oxidative products of cytosine, with highest activity for 5-hydroxyuracil, one of the most abundant and mutagenic lesions induced by reactive oxygen species, and with lower activity for 5,6-dihydrouracil and 5-hydroxycytosine. It has negligible or undetectable activity with 8-oxoguanine, thymine glycol, 2-hydroxyadenine, hypoxanthine, and xanthine. NEIL2 is similar to NEIL1 in having N-terminal Pro as the active site. However, unlike NEIL1, its expression was independent of the cell cycle stage in fibroblasts, and its highest expression was observed in the testes and skeletal muscle. Despite the absence of a putative nuclear localization signal, NEIL2 was predominantly localized in the nucleus. These results suggest that NEIL2 is involved in global genome repair mainly for removing oxidative products of cytosine.
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Affiliation(s)
- Tapas K Hazra
- Department of Human Biological Chemistry and Genetics, Sealy Center for Molecular Science, University of Texas Medical Branch, 6.136 Medical Research Building, Rte 1079, Galveston, TX 77555, USA.
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38
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Dizdaroglu M, Jaruga P, Birincioglu M, Rodriguez H. Free radical-induced damage to DNA: mechanisms and measurement. Free Radic Biol Med 2002; 32:1102-15. [PMID: 12031895 DOI: 10.1016/s0891-5849(02)00826-2] [Citation(s) in RCA: 610] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Free radicals are produced in cells by cellular metabolism and by exogenous agents. These species react with biomolecules in cells, including DNA. The resulting damage to DNA, which is also called oxidative damage to DNA, is implicated in mutagenesis, carcinogenesis, and aging. Mechanisms of damage involve abstractions and addition reactions by free radicals leading to carbon-centered sugar radicals and OH- or H-adduct radicals of heterocyclic bases. Further reactions of these radicals yield numerous products. Various analytical techniques exist for the measurement of oxidative damage to DNA. Techniques that employ gas chromatography (GC) or liquid chromatography (LC) with mass spectrometry (MS) simultaneously measure numerous products, and provide positive identification and accurate quantification. The measurement of multiple products avoids misleading conclusions that might be drawn from the measurement of a single product, because product levels vary depending on reaction conditions and the redox status of cells. In the past, GC/MS was used for the measurement of modified sugar and bases, and DNA-protein cross-links. Recently, methodologies using LC/tandem MS (LC/MS/MS) and LC/MS techniques were introduced for the measurement of modified nucleosides. Artifacts might occur with the use of any of the measurement techniques. The use of proper experimental conditions might avoid artifactual formation of products in DNA. This article reviews mechanistic aspects of oxidative damage to DNA and recent developments in the measurement of this type of damage using chromatographic and mass spectrometric techniques.
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Affiliation(s)
- Miral Dizdaroglu
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA.
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39
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Chao JI, Yang JL. Alteration of cadmium-induced mutational spectrum by catalase depletion in Chinese hamster ovary-K1 cells. Mutat Res 2001; 498:7-18. [PMID: 11673067 DOI: 10.1016/s1383-5718(01)00249-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Previously, we have demonstrated that cadmium acetate significantly induces hprt mutation frequency in Chinese hamster ovary (CHO)-K1 and that 3-amino-1,2,4-triazole (3AT), a catalase inhibitor, potentiates the mutagenicity of cadmium [Chem. Res. Toxicol. 9 (1996) 1360-1367]. In this study, we investigate the role of intracellular peroxide in the molecular nature of mutations induced by cadmium. Using 2',7'-dichlorofluorescin diacetate and fluorescence spectrophotometry, we have shown that cadmium dose-dependently increased the amounts of intracellular peroxide and the levels were significantly enhanced by 3AT. Furthermore, we have characterized and compared the hprt mutation spectra in 6-thioguanine-resistant mutants derived from CHO-K1 cells exposed to 4 microM of cadmium acetate for 4h in the absence and presence of 3AT. The mutation frequency induced by cadmium and cadmium plus 3AT was 11- and 16-fold higher than that observed in untreated populations (2.2 x 10(-6)), respectively. A total of 40 and 51 independent hprt mutants were isolated from cadmium and cadmium plus 3AT treatments for mRNA-polymerase chain reaction (PCR), genomic DNA-PCR and DNA sequencing analyses. 3AT co-administration significantly enhanced the frequency of deletions induced by cadmium. Cadmium induced more transversions than transitions. In contrast, 3AT co-administration increased the frequency of GC-->AT transitions and decreased the frequencies of TA-->AT and TA-->GC transversions. Together, the results suggest that intracellular catalase is important to prevent the formation of oxidative DNA damage as well as deletions and GC-->AT transitions upon cadmium exposure.
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Affiliation(s)
- J I Chao
- Molecular Carcinogenesis Laboratory, Department of Life Sciences, National Tsing Hua University, Hsinchu 300, Taiwan, ROC
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40
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Hong J, Kim DG, Cheong C, Paeng KJ. Damaged products of cytosine in hydroxyl radical solution under UV-irradiation. Microchem J 2001. [DOI: 10.1016/s0026-265x(00)00144-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Rehman A, Jenner A, Halliwell B. Gas chromatography-mass spectrometry analysis of DNA: optimization of protocols for isolation and analysis of DNA from human blood. Methods Enzymol 2000; 319:401-17. [PMID: 10907529 DOI: 10.1016/s0076-6879(00)19038-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- A Rehman
- Department of Pharmacology, King's College, London, United Kingdom
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42
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43
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Tremblay S, Douki T, Cadet J, Wagner JR. 2'-Deoxycytidine glycols, a missing link in the free radical-mediated oxidation of DNA. J Biol Chem 1999; 274:20833-8. [PMID: 10409624 DOI: 10.1074/jbc.274.30.20833] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
2'-Deoxycytidine glycols (5,6-dihydroxy-5, 6-dihydro-2'-deoxycytidine) are major products of the hydroxyl radical-induced oxidation of 2'-deoxycytidine resulting from either a Fenton reaction or exposure to ionizing radiation. Because of their instability, however, the glycols have not previously been characterized. Instead, the impetus has been placed on the primary decomposition products of 2'-deoxycytidine glycols, which includes 5-hydroxy-2'-deoxycytidine, 5-hydroxy-2'-deoxyuridine, and 2'-deoxyuridine glycols. Here, we have identified one of the four possible diastereomers of 2'-deoxycytidine glycols by product analyses of decomposition products, (1)H NMR, and mass spectrometry. This glycol was observed to decompose with a half-life of 50 min at 37 degrees C in buffered neutral solutions and preferentially undergo dehydration to 5-hydroxy-2'-deoxycytidine. The rate of decomposition was strongly dependent on pH (2-10) and the concentration of phosphate ion (10-300 mM). Next, we report on the deamination of cytosine glycols to uracil glycols in oxidized DNA using acid hydrolysis and high performance liquid chromatography analysis with electrochemical detection to monitor 5-hydroxycytosine and 5-hydroxyuracil. The results showed that the lifetime of cytosine glycols is greatly enhanced in DNA (34-fold; half-life, 28 h), and that deamination accounts for at least one-third of the total decomposition. The relatively long lifetime of cytosine glycols in DNA suggests that this important class of DNA oxidation products will be significantly involved in repair and mutagenesis processes.
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Affiliation(s)
- S Tremblay
- Institut Universitaire de Gériatrie de Sherbrooke (Pavillon d'Youville), 1036 rue Bélvédère Sud, Sherbrooke, Québec J1H 4C4, Canada
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44
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Structure and tautomeric properties of thymine derivatives generated by hydroxyl radical in anaerobic conditions. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00479-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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Structure and properties of hydroxyl radical modified nucleic acid components: tautomerism and miscoding properties of 5-hydroxycytosine. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00337-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Cysewski P, Jeziorek D, Oliński R. Structure and tautomeric properties of cytosine derivatives generated by a hydroxyl radical in aerobic conditions. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00205-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Meehan WJ, Spencer JP, Rannels DE, Welch DR, Knobbe ET, Ostrander GK. Hydrogen peroxide induces oxidative DNA damage in rat type II pulmonary epithelial cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 1999; 33:273-278. [PMID: 10398374 DOI: 10.1002/(sici)1098-2280(1999)33:4<273::aid-em3>3.0.co;2-t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Type II epithelial cells, which line the alveolar surface of the lung, are exposed to a variety of potentially mutagenic and carcinogenic insults. The purpose of this study was to determine if type II cells are susceptible to oxidative DNA damage in vitro. Treatment of cultured rat type II lung epithelial cells with hydrogen peroxide led to increased concentrations (nmol/mg DNA) of 12 of 14 monitored DNA base modifications, suggesting oxidative damage by the hydroxyl radical. These base modifications are typically associated with oxidative stress, and elevated levels have been correlated with mutagenesis and carcinogenesis. These data demonstrate that type II cells are indeed vulnerable to oxidative DNA damage.
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Affiliation(s)
- W J Meehan
- Jake Gittlen Cancer Research Institute, Penn State University College of Medicine, Hershey, Pennsylvania, USA
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48
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England TG, Jenner A, Aruoma OI, Halliwell B. Determination of oxidative DNA base damage by gas chromatography-mass spectrometry. Effect of derivatization conditions on artifactual formation of certain base oxidation products. Free Radic Res 1998; 29:321-30. [PMID: 9860047 DOI: 10.1080/10715769800300361] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
GC-MS is a widely used tool to measure oxidative DNA damage because of its ability to identify a wide range of base modification products. However, it has been suggested that the derivatization procedures required to form volatile products prior to GC-MS analysis can sometimes produce artifactual formation of certain base oxidation products, although these studies did not replicate previously-used reaction conditions, e.g. they failed to remove air from the derivatization vials. A systematic examination of this problem revealed that levels of 8-hydroxyguanine, 8-hydroxyadenine, 5-hydroxycytosine and 5-(hydroxymethyluracil) in commercial calf thymus DNA determined by GC-MS are elevated by increasing the temperature at which derivatization is performed in our laboratory. In particular, 8-hydroxyguanine levels after silylation at 140 degrees C were raised 8-fold compared to derivatization at 23 degrees C. Experiments on the derivatization of each undamaged base revealed that the artifactual oxidation of guanine, adenine, cytosine and thymine respectively was responsible. Formation of the above products was potentiated by not purging with nitrogen prior to derivatization. Increasing the temperature to 140 degrees C or allowing air to be present during derivatization did not significantly increase levels of the other oxidized bases measured. This work suggests that artifactual oxidation during derivatization is restricted to certain products (8-hydroxyguanine, 8-hydroxyadenine, 5-hydroxycytosine and 5-[hydroxymethyluracil]) and can be decreased by reducing the temperature of the derivatization reaction to 23 degrees C and excluding as much air possible. Despite some recent reports, we were easily able to detect formamidopyrimidines in acid-hydrolyzed DNA. Artifacts of derivatization are less marked than has been claimed in some papers and may vary between laboratories, depending on the experimental procedures used, in particular the efficiency of exclusion of O2 during the derivatization process.
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Affiliation(s)
- T G England
- International Antioxidant and Neurodegenerative Disease Research Centres, Pharmacology Group, University of London King's College, UK
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49
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Wang D, Kreutzer DA, Essigmann JM. Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions. Mutat Res 1998; 400:99-115. [PMID: 9685598 DOI: 10.1016/s0027-5107(98)00066-9] [Citation(s) in RCA: 369] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Oxidative DNA damage has been implicated in mutagenesis, carcinogenesis and aging. Endogenous cellular processes such as aerobic metabolism generate reactive oxygen species (ROS) that interact with DNA to form dozens of DNA lesions. If unrepaired, these lesions can exert a number of deleterious effects including the induction of mutations. In an effort to understand the genetic consequences of cellular oxidative damage, many laboratories have determined the patterns of mutations generated by the interaction of ROS with DNA. Compilation of these mutational spectra has revealed that GC-->AT transitions and GC-->TA transversions are the most commonly observed mutations resulting from oxidative damage to DNA. Since mutational spectra convey only the end result of a complex cascade of events, which includes formation of multiple adducts, repair processing, and polymerase errors, it is difficult if not impossible to assess the mutational specificity of individual DNA lesions directly from these spectra. This problem is especially complicated in the case of oxidative DNA damage owing to the multiplicity of lesions formed by a single damaging agent. The task of assigning specific features of mutational spectra to individual DNA lesions has been made possible with the advent of a technology to analyze the mutational properties of single defined adducts, in vitro and in vivo. At the same time, parallel progress in the discovery and cloning of repair enzymes has advanced understanding of the biochemical mechanisms by which cells excise DNA damage. This combination of tools has brought our understanding of DNA lesions to a new level of sophistication. In this review, we summarize the known properties of individual oxidative lesions in terms of their structure, mutagenicity and repairability.
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Affiliation(s)
- D Wang
- Division of Toxicology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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50
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Jenner A, England TG, Aruoma OI, Halliwell B. Measurement of oxidative DNA damage by gas chromatography-mass spectrometry: ethanethiol prevents artifactual generation of oxidized DNA bases. Biochem J 1998; 331 ( Pt 2):365-9. [PMID: 9531471 PMCID: PMC1219362 DOI: 10.1042/bj3310365] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Analysis of oxidative damage to DNA bases by GC-MS enables identification of a range of base oxidation products, but requires a derivatization procedure. However, derivatization at high temperature in the presence of air can cause 'artifactual' oxidation of some undamaged bases, leading to an overestimation of their oxidation products, including 8-hydroxyguanine. Therefore derivatization conditions that could minimize this problem were investigated. Decreasing derivatization temperature to 23 degrees C lowered levels of 8-hydroxyguanine, 8-hydroxyadenine, 5-hydroxycytosine and 5-(hydroxymethyl)uracil measured by GC-MS in hydrolysed calf thymus DNA. Addition of the reducing agent ethanethiol (5%, v/v) to DNA samples during trimethylsilylation at 90 degrees C also decreased levels of these four oxidized DNA bases as well as 5-hydroxyuracil. Removal of guanine from hydrolysed DNA samples by treatment with guanase, prior to derivatization, resulted in 8-hydroxyguanine levels (54-59 pmol/mg of DNA) that were significantly lower than samples not pretreated with guanase, independent of the derivatization conditions used. Only hydrolysed DNA samples that were derivatized at 23 degrees C in the presence of ethanethiol produced 8-hydroxyguanine levels (56+/-8 pmol/mg of DNA) that were as low as those of guanase-pretreated samples. Levels of other oxidized bases were similar to samples derivatized at 23 degrees C without ethanethiol, except for 5-hydroxycytosine and 5-hydroxyuracil, which were further decreased by ethanethiol. Levels of 8-hydroxyguanine, 8-hydroxyadenine and 5-hydroxycytosine measured in hydrolysed calf thymus DNA by the improved procedures described here were comparable with those reported previously by HPLC with electrochemical detection and by GC-MS with prepurification to remove undamaged base. We conclude that artifactual oxidation of DNA bases during derivatization can be prevented by decreasing the temperature to 23 degrees C, removing air from the derivatization reaction and adding ethanethiol.
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Affiliation(s)
- A Jenner
- International Antioxidant and Neurodegenerative Disease Research Centres, Pharmacology Group, University of London, King's College, Manresa Road, London. SW3 6LX, U.K.
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