1
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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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Ghosh D, Raghavan SC. Nonhomologous end joining: new accessory factors fine tune the machinery. Trends Genet 2021; 37:582-599. [PMID: 33785198 DOI: 10.1016/j.tig.2021.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major DNA double-strand break (DSB) repair pathways in eukaryotes. The well-known critical proteins involved in NHEJ include Ku70/80, DNA-PKcs, Artemis, DNA pol λ/μ, DNA ligase IV-XRCC4, and XLF. Recent studies have added a number of new proteins to the NHEJ repertoire namely paralog of XRCC4 and XLF (PAXX), modulator of retroviral infection (MRI)/ cell cycle regulator of NHEJ (CYREN), transactivation response DNA-binding protein (TARDBP) of 43 kDa (TDP-43), intermediate filament family orphan (IFFO1), ERCC excision repair 6 like 2 (ERCC6L2), and RNase H2. PAXX acts as a stabilizing factor for the main NHEJ components. MRI/CYREN seems to play a dual role stimulating NHEJ in the G1 phase of the cell cycle, while inhibiting the pathway in the S and G2 phases. TDP-43 can recruit the ligase IV-XRCC4 complex to the DSB sites and stimulate ligation in neuronal cells. RNase H2 excises out the ribonucleotides inserted during repair by DNA polymerase μ/TdT. This review provides a brief glimpse into how these new partners were discovered and their contribution to the mechanism and regulation of NHEJ.
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Affiliation(s)
- Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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3
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Bell M, Kumar A, Sevilla MD. Electron-Induced Repair of 2'-Deoxyribose Sugar Radicals in DNA: A Density Functional Theory (DFT) Study. Int J Mol Sci 2021; 22:ijms22041736. [PMID: 33572317 PMCID: PMC7916153 DOI: 10.3390/ijms22041736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of DNA. The calculation predicted the relative stability of sugar radicals in the order C4′• > C1′• > C5′• > C3′• > C2′•. The Boltzmann distribution populations based on the relative stability of the sugar radicals were not those found for ionizing radiation or OH-radical attack and are good evidence the kinetic mechanisms of the processes drive the products formed. The adiabatic electron affinities of these sugar radicals were in the range 2.6–3.3 eV which is higher than the canonical DNA bases. The sugar radicals reduction potentials (E°) without protonation (−1.8 to −1.2 V) were also significantly higher than the bases. Thus the sugar radicals will be far more readily reduced by solvated electrons than the DNA bases. In the aqueous phase, these one-electron reduced sugar radicals (anions) are protonated from solvent and thus are efficiently repaired via the “electron-induced proton transfer mechanism”. The calculation shows that, in comparison to efficient repair of sugar radicals by the electron-induced proton transfer mechanism, the repair of the cyclopurine lesion, 5′,8-cyclo-2′-dG, would involve a substantial barrier.
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4
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Nakamura J, Nakamura M. DNA-protein crosslink formation by endogenous aldehydes and AP sites. DNA Repair (Amst) 2020; 88:102806. [PMID: 32070903 DOI: 10.1016/j.dnarep.2020.102806] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/19/2022]
Abstract
Covalent binding between proteins and a DNA strand produces DNA-protein crosslinks (DPC). DPC are one of the most deleterious types of DNA damage, leading to the blockage of DNA replication and transcription. Both DNA lesions and endogenous products with carbonyl functional groups can produce DPC in genomic DNA under normal physiological conditions. For example, formaldehyde, the most abundant endogenous human carcinogen, and apurinic/apyrimidinic (AP) sites, the most common type of endogenous DNA lesions, has been shown to crosslink proteins and/or DNA through their carbonyl functional groups. Unfortunately, compared to other types of DNA damage, DPC have been less studied and understood. However, a recent advancement has allowed researchers to determine accurate yields of various DNA lesions including formaldehyde-derived DPC with high sensitivity and specificity, paving the way for new developments in this field of research. Here, we review the current literature and remaining unanswered questions on DPC formation by endogenous formaldehyde and various aldehydic 2-deoxyribose lesions.
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Affiliation(s)
- Jun Nakamura
- Laboratory of Laboratory Animal Science, Graduate School of Life and Environmental Biosciences, Osaka Prefecture University, Izumisano, Osaka, Japan.
| | - Mai Nakamura
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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5
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Gerin I, Bury M, Baldin F, Graff J, Van Schaftingen E, Bommer GT. Phosphoglycolate has profound metabolic effects but most likely no role in a metabolic DNA response in cancer cell lines. Biochem J 2019; 476:629-643. [PMID: 30670572 PMCID: PMC6380167 DOI: 10.1042/bcj20180435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 12/19/2022]
Abstract
Repair of a certain type of oxidative DNA damage leads to the release of phosphoglycolate, which is an inhibitor of triose phosphate isomerase and is predicted to indirectly inhibit phosphoglycerate mutase activity. Thus, we hypothesized that phosphoglycolate might play a role in a metabolic DNA damage response. Here, we determined how phosphoglycolate is formed in cells, elucidated its effects on cellular metabolism and tested whether DNA damage repair might release sufficient phosphoglycolate to provoke metabolic effects. Phosphoglycolate concentrations were below 5 µM in wild-type U2OS and HCT116 cells and remained unchanged when we inactivated phosphoglycolate phosphatase (PGP), the enzyme that is believed to dephosphorylate phosphoglycolate. Treatment of PGP knockout cell lines with glycolate caused an up to 500-fold increase in phosphoglycolate concentrations, which resulted largely from a side activity of pyruvate kinase. This increase was much higher than in glycolate-treated wild-type cells and was accompanied by metabolite changes consistent with an inhibition of phosphoglycerate mutase, most likely due to the removal of the priming phosphorylation of this enzyme. Surprisingly, we found that phosphoglycolate also inhibits succinate dehydrogenase with a Ki value of <10 µM. Thus, phosphoglycolate can lead to profound metabolic disturbances. In contrast, phosphoglycolate concentrations were not significantly changed when we treated PGP knockout cells with Bleomycin or ionizing radiation, which are known to lead to the release of phosphoglycolate by causing DNA damage. Thus, phosphoglycolate concentrations due to DNA damage are too low to cause major metabolic changes in HCT116 and U2OS cells.
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Affiliation(s)
- Isabelle Gerin
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200 Bruxelles, Belgium
| | - Marina Bury
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200 Bruxelles, Belgium
| | - Francesca Baldin
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200 Bruxelles, Belgium
| | - Julie Graff
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200 Bruxelles, Belgium
| | - Emile Van Schaftingen
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200 Bruxelles, Belgium
| | - Guido T Bommer
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200 Bruxelles, Belgium
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6
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Yao W, Ma X, Li S, Gao Y, Nian F, Zhou L. Theoretical study of mechanism and kinetics for the reaction of hydroxyl radical with 2′-deoxycytidine. Struct Chem 2018. [DOI: 10.1007/s11224-018-1122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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7
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Kawale AS, Akopiants K, Valerie K, Ruis B, Hendrickson EA, Huang SYN, Pommier Y, Povirk LF. TDP1 suppresses mis-joining of radiomimetic DNA double-strand breaks and cooperates with Artemis to promote optimal nonhomologous end joining. Nucleic Acids Res 2018; 46:8926-8939. [PMID: 30113698 PMCID: PMC6158748 DOI: 10.1093/nar/gky694] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/18/2018] [Accepted: 07/29/2018] [Indexed: 01/04/2023] Open
Abstract
The Artemis nuclease and tyrosyl-DNA phosphodiesterase (TDP1) are each capable of resolving protruding 3'-phosphoglycolate (PG) termini of DNA double-strand breaks (DSBs). Consequently, both a knockout of Artemis and a knockout/knockdown of TDP1 rendered cells sensitive to the radiomimetic agent neocarzinostatin (NCS), which induces 3'-PG-terminated DSBs. Unexpectedly, however, a knockdown or knockout of TDP1 in Artemis-null cells did not confer any greater sensitivity than either deficiency alone, indicating a strict epistasis between TDP1 and Artemis. Moreover, a deficiency in Artemis, but not TDP1, resulted in a fraction of unrepaired DSBs, which were assessed as 53BP1 foci. Conversely, a deficiency in TDP1, but not Artemis, resulted in a dramatic increase in dicentric chromosomes following NCS treatment. An inhibitor of DNA-dependent protein kinase, a key regulator of the classical nonhomologous end joining (C-NHEJ) pathway sensitized cells to NCS, but eliminated the sensitizing effects of both TDP1 and Artemis deficiencies. These results suggest that TDP1 and Artemis perform different functions in the repair of terminally blocked DSBs by the C-NHEJ pathway, and that whereas an Artemis deficiency prevents end joining of some DSBs, a TDP1 deficiency tends to promote DSB mis-joining.
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Affiliation(s)
- Ajinkya S Kawale
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Konstantin Akopiants
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Kristoffer Valerie
- Department of Radiation Oncology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Brian Ruis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Shar-yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, MD 20892-4255, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, MD 20892-4255, USA
| | - Lawrence F Povirk
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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8
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Hammoud A, Nshimyumuremyi J, Bourotte J, Lucaccioni F, Robeyns K, Dîrtu MM, Garcia Y, Singleton ML. Cooperative Interactions in the Second Coordination Sphere of Pyridazine/Pyridine Containing Polyazaheterocyclic Iron(II) Complexes Favor Protonation. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ahmad Hammoud
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
| | - Jean‐Boris Nshimyumuremyi
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
| | - Jérémie Bourotte
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
| | - Fabio Lucaccioni
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
| | - Koen Robeyns
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
| | - Marinela M. Dîrtu
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
| | - Yann Garcia
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
| | - Michael L. Singleton
- Institute of Condensed Mater and Nanosciences Molecules Solids and Reactivity (IMCN/MOST) Université catholique de Louvain Place L. Pasteur 1 1348 Louvain‐la‐Neuve Belgium
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9
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Murray V, Chen JK, Chung LH. The Interaction of the Metallo-Glycopeptide Anti-Tumour Drug Bleomycin with DNA. Int J Mol Sci 2018; 19:E1372. [PMID: 29734689 PMCID: PMC5983701 DOI: 10.3390/ijms19051372] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/17/2022] Open
Abstract
The cancer chemotherapeutic drug, bleomycin, is clinically used to treat several neoplasms including testicular and ovarian cancers. Bleomycin is a metallo-glycopeptide antibiotic that requires a transition metal ion, usually Fe(II), for activity. In this review, the properties of bleomycin are examined, especially the interaction of bleomycin with DNA. A Fe(II)-bleomycin complex is capable of DNA cleavage and this process is thought to be the major determinant for the cytotoxicity of bleomycin. The DNA sequence specificity of bleomycin cleavage is found to at 5′-GT* and 5′-GC* dinucleotides (where * indicates the cleaved nucleotide). Using next-generation DNA sequencing, over 200 million double-strand breaks were analysed, and an expanded bleomycin sequence specificity was found to be 5′-RTGT*AY (where R is G or A and Y is T or C) in cellular DNA and 5′-TGT*AT in purified DNA. The different environment of cellular DNA compared to purified DNA was proposed to be responsible for the difference. A number of bleomycin analogues have been examined and their interaction with DNA is also discussed. In particular, the production of bleomycin analogues via genetic manipulation of the modular non-ribosomal peptide synthetases and polyketide synthases in the bleomycin gene cluster is reviewed. The prospects for the synthesis of bleomycin analogues with increased effectiveness as cancer chemotherapeutic agents is also explored.
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Affiliation(s)
- Vincent Murray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Jon K Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Long H Chung
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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10
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Pannunzio NR, Watanabe G, Lieber MR. Nonhomologous DNA end-joining for repair of DNA double-strand breaks. J Biol Chem 2017; 293:10512-10523. [PMID: 29247009 DOI: 10.1074/jbc.tm117.000374] [Citation(s) in RCA: 314] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nonhomologous DNA end-joining (NHEJ) is the predominant double-strand break (DSB) repair pathway throughout the cell cycle and accounts for nearly all DSB repair outside of the S and G2 phases. NHEJ relies on Ku to thread onto DNA termini and thereby improve the affinity of the NHEJ enzymatic components consisting of polymerases (Pol μ and Pol λ), a nuclease (the Artemis·DNA-PKcs complex), and a ligase (XLF·XRCC4·Lig4 complex). Each of the enzymatic components is distinctive for its versatility in acting on diverse incompatible DNA end configurations coupled with a flexibility in loading order, resulting in many possible junctional outcomes from one DSB. DNA ends can either be directly ligated or, if the ends are incompatible, processed until a ligatable configuration is achieved that is often stabilized by up to 4 bp of terminal microhomology. Processing of DNA ends results in nucleotide loss or addition, explaining why DSBs repaired by NHEJ are rarely restored to their original DNA sequence. Thus, NHEJ is a single pathway with multiple enzymes at its disposal to repair DSBs, resulting in a diversity of repair outcomes.
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Affiliation(s)
- Nicholas R Pannunzio
- From the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology, Section of Molecular and Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Go Watanabe
- From the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology, Section of Molecular and Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Michael R Lieber
- From the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology, Section of Molecular and Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
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11
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Cadet J, Davies KJA, Medeiros MH, Di Mascio P, Wagner JR. Formation and repair of oxidatively generated damage in cellular DNA. Free Radic Biol Med 2017; 107:13-34. [PMID: 28057600 PMCID: PMC5457722 DOI: 10.1016/j.freeradbiomed.2016.12.049] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/27/2016] [Accepted: 12/31/2016] [Indexed: 12/18/2022]
Abstract
In this review article, emphasis is placed on the critical survey of available data concerning modified nucleobase and 2-deoxyribose products that have been identified in cellular DNA following exposure to a wide variety of oxidizing species and agents including, hydroxyl radical, one-electron oxidants, singlet oxygen, hypochlorous acid and ten-eleven translocation enzymes. In addition, information is provided about the generation of secondary oxidation products of 8-oxo-7,8-dihydroguanine and nucleobase addition products with reactive aldehydes arising from the decomposition of lipid peroxides. It is worth noting that the different classes of oxidatively generated DNA damage that consist of single lesions, intra- and interstrand cross-links were unambiguously assigned and quantitatively detected on the basis of accurate measurements involving in most cases high performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. The reported data clearly show that the frequency of DNA lesions generated upon severe oxidizing conditions, including exposure to ionizing radiation is low, at best a few modifications per 106 normal bases. Application of accurate analytical measurement methods has also allowed the determination of repair kinetics of several well-defined lesions in cellular DNA that however concerns so far only a restricted number of cases.
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Affiliation(s)
- Jean Cadet
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4.
| | - Kelvin J A Davies
- Leonard Davis School of Gerontology of the Ethel Percy Andrus Gerontology Center, The University of Southern California, Los Angeles, CA 90089-0191, United States; Division of Molecular & Computational Biology, Department of Biological Sciences of the Dornsife College of Letters, Arts, and Sciences, The University of Southern California, Los Angeles, CA 90089-0191, United States
| | - Marisa Hg Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508 000 São Paulo, SP, Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508 000 São Paulo, SP, Brazil
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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12
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Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 2017; 18:495-506. [PMID: 28512351 DOI: 10.1038/nrm.2017.48] [Citation(s) in RCA: 975] [Impact Index Per Article: 139.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks (DSBs) are the most dangerous type of DNA damage because they can result in the loss of large chromosomal regions. In all mammalian cells, DSBs that occur throughout the cell cycle are repaired predominantly by the non-homologous DNA end joining (NHEJ) pathway. Defects in NHEJ result in sensitivity to ionizing radiation and the ablation of lymphocytes. The NHEJ pathway utilizes proteins that recognize, resect, polymerize and ligate the DNA ends in a flexible manner. This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations. In this Review, we discuss the most recent findings regarding the relative involvement of the different NHEJ proteins in the repair of various DNA-end configurations. We also discuss the shunting of DNA-end repair to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA) and the relevance of these different pathways to human disease.
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13
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Identification of a mammalian glycerol-3-phosphate phosphatase: Role in metabolism and signaling in pancreatic β-cells and hepatocytes. Proc Natl Acad Sci U S A 2016; 113:E430-9. [PMID: 26755581 DOI: 10.1073/pnas.1514375113] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Obesity, and the associated disturbed glycerolipid/fatty acid (GL/FA) cycle, contribute to insulin resistance, islet β-cell failure, and type 2 diabetes. Flux through the GL/FA cycle is regulated by the availability of glycerol-3-phosphate (Gro3P) and fatty acyl-CoA. We describe here a mammalian Gro3P phosphatase (G3PP), which was not known to exist in mammalian cells, that can directly hydrolyze Gro3P to glycerol. We identified that mammalian phosphoglycolate phosphatase, with an uncertain function, acts in fact as a G3PP. We found that G3PP, by controlling Gro3P levels, regulates glycolysis and glucose oxidation, cellular redox and ATP production, gluconeogenesis, glycerolipid synthesis, and fatty acid oxidation in pancreatic islet β-cells and hepatocytes, and that glucose stimulated insulin secretion and the response to metabolic stress, e.g., glucolipotoxicity, in β-cells. In vivo overexpression of G3PP in rat liver lowers body weight gain and hepatic glucose production from glycerol and elevates plasma HDL levels. G3PP is expressed at various levels in different tissues, and its expression varies according to the nutritional state in some tissues. As Gro3P lies at the crossroads of glucose, lipid, and energy metabolism, control of its availability by G3PP adds a key level of metabolic regulation in mammalian cells, and G3PP offers a potential target for type 2 diabetes and cardiometabolic disorders.
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Li MD, Dang L, Liu M, Du L, Zheng X, Phillips DL. Ultrafast Time Resolved Spectroscopic Studies on the Generation of the Ketyl-Sugar Biradical by Intramolecular Hydrogen Abstraction among Ketoprofen and Purine Nucleoside Dyads. J Org Chem 2015; 80:3462-70. [DOI: 10.1021/acs.joc.5b00047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ming-De Li
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
| | - Li Dang
- Department
of Chemistry, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Mingyue Liu
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
| | - Lili Du
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
| | - Xuming Zheng
- Department
of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - David Lee Phillips
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
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15
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Shuck SC, Wauchope OR, Rose KL, Kingsley PJ, Rouzer CA, Shell SM, Sugitani N, Chazin WJ, Zagol-Ikapitte I, Boutaud O, Oates JA, Galligan JJ, Beavers WN, Marnett LJ. Protein modification by adenine propenal. Chem Res Toxicol 2014; 27:1732-42. [PMID: 25211669 PMCID: PMC4203390 DOI: 10.1021/tx500218g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Base propenals are products of the
reaction of DNA with oxidants
such as peroxynitrite and bleomycin. The most reactive base propenal,
adenine propenal, is mutagenic in Escherichia coli and reacts with DNA to form covalent adducts; however, the reaction
of adenine propenal with protein has not yet been investigated. A
survey of the reaction of adenine propenal with amino acids revealed
that lysine and cysteine form adducts, whereas histidine and arginine
do not. Nε-Oxopropenyllysine, a
lysine–lysine cross-link, and S-oxopropenyl
cysteine are the major products. Comprehensive profiling of the reaction
of adenine propenal with human serum albumin and the DNA repair protein,
XPA, revealed that the only stable adduct is Nε-oxopropenyllysine. The most reactive sites for modification
in human albumin are K190 and K351. Three sites of modification of
XPA are in the DNA-binding domain, and two sites are subject to regulatory
acetylation. Modification by adenine propenal dramatically reduces
XPA’s ability to bind to a DNA substrate.
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Affiliation(s)
- Sarah C Shuck
- A. B. Hancock Jr. Memorial Laboratory for Cancer Research, Departments of Biochemistry, ‡Chemistry, and §Pharmacology, ∥Mass Spectrometry Research Center, ⊥Center in Molecular Toxicology, #Center for Structural Biology, ∇Department of Medicine, Vanderbilt Institute of Chemical Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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16
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Bajacan JEV, Hong IS, Penning TM, Penning TW, Greenberg MM. Quantitative detection of 8-Oxo-7,8-dihydro-2'-deoxyguanosine using chemical tagging and qPCR. Chem Res Toxicol 2014; 27:1227-35. [PMID: 24932862 PMCID: PMC4106692 DOI: 10.1021/tx500120p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
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8-Oxo-7,8-dihydro-2′-deoxyguanosine
(8-oxodGuo) is a commonly
formed DNA lesion that is useful as a biomarker for oxidative stress.
Although methods for selective quantification of 8-oxodGuo exist,
there is room for additional methods that are sensitive and utilize
instrumentation that is widely available. We previously took advantage
of the reported reactivity of 8-oxodGuo to develop a method for detecting
the lesion by selectively covalently tagging it with a molecule equipped
with a biotin label that can be used subsequently with a reporting
method (XueL., and GreenbergM. M. (2007) 129, 701017497789). We now report a method that can
detect as little as 14 amol of 8-oxodGuo by tagging DNA with a reagent
containing a disulfide that reduces background due to nonspecific
binding. The reagent also contains biotin that enables capturing target
DNA on streptavidin-coated magnetic beads. The captured DNA is quantified
using quantitative PCR. The method is validated by comparing the amount
of 8-oxodGuo detected as a function of Fe2+/H2O2/ascorbate-dose to that reported previously using mass
spectrometry.
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Affiliation(s)
- John Ernest Vallarta Bajacan
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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17
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Kma L. Plant Extracts and Plant-Derived Compounds: Promising Players in Countermeasure Strategy Against Radiological Exposure: A Review. Asian Pac J Cancer Prev 2014; 15:2405-25. [DOI: 10.7314/apjcp.2014.15.6.2405] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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18
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Roginskaya M, Mohseni R, Moore TJ, Bernhard WA, Razskazovskiy Y. Identification of the C4′-Oxidized Abasic Site as the Most Abundant 2-Deoxyribose Lesion in Radiation-Damaged DNA Using a Novel HPLC-Based Approach. Radiat Res 2014; 181:131-7. [DOI: 10.1667/rr12993.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Marina Roginskaya
- Department of Chemistry, East Tennessee State University, Johnson City, Tennessee
| | - Reza Mohseni
- Department of Chemistry, East Tennessee State University, Johnson City, Tennessee
| | - Terence J. Moore
- Department of Chemistry, East Tennessee State University, Johnson City, Tennessee
| | - William A. Bernhard
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Yuriy Razskazovskiy
- Department of Physics and Astronomy, East Tennessee State University, Johnson City, Tennessee
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19
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Povirk LF. Processing of damaged DNA ends for double-strand break repair in mammalian cells. ISRN MOLECULAR BIOLOGY 2012; 2012. [PMID: 24236237 PMCID: PMC3825254 DOI: 10.5402/2012/345805] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Most DNA double-strand breaks (DSBs)formed in a natural environment have chemical modifications at or near the ends that preclude direct religation and require removal or other processing so that rejoining can proceed. Free radical-mediated DSBs typically bear unligatable 3'-phosphate or 3'-phosphoglycolate termini and often have oxidized bases and/or abasic sites near the break. Topoisomerase-mediated DSBs are blocked by covalently bound peptide fragments of the topoisomerase. Enzymes capable of resolving damaged ends include polynucleotide kinase/phosphatase, which restores missing 5'-phosphates and removes 3'-phosphates; tyrosyl-DNA phosphodiesterases I and II (TDP1 and TDP2), which remove peptide fragments of topoisomerases I and II, respectively, and the Artemis and Metnase endonucleases, which can trim damaged overhangs of diverse structure. TDP1 as well as APE1 can remove 3'-phosphoglycolates and other 3' blocks, while CtIP appears to provide an alternative pathway for topoisomerase II fragment removal. Ku, a core DSB joining protein, can cleave abasic sites near DNA ends. The downstream processes of patching and ligation are tolerant of residual damage, and can sometimes proceed without complete damage removal. Despite these redundant pathways for resolution, damaged ends appear to be a significant barrier to rejoining, and their resolution may be a rate-limiting step in repair of some DSBs..
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Affiliation(s)
- Lawrence F Povirk
- Department of Pharmacology and Toxicology, and Massey Cancer Center, Virginia Commonwealth University, 401 College St. Richmond, VA 23298, USA, 804-828-9640
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20
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Kumar A, Pottiboyina V, Sevilla MD. One-electron oxidation of neutral sugar radicals of 2'-deoxyguanosine and 2'-deoxythymidine: a density functional theory (DFT) study. J Phys Chem B 2012; 116:9409-16. [PMID: 22793263 DOI: 10.1021/jp3059068] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One electron oxidation of neutral sugar radicals has recently been suggested to lead to important intermediates in the DNA damage process culminating in DNA strand breaks. In this work, we investigate sugar radicals in a DNA model system to understand the energetics of sugar radical formation and oxidation. The geometries of neutral sugar radicals C(1')(•), C(2')(•), C(3')(•), C(4')(•), and C(5')(•) of 2'-deoxyguanosine (dG) and 2'-deoxythymidine (dT) were optimized in the gas phase and in solution using the B3LYP and ωB97x functionals and 6-31++G(d) basis set. Their corresponding cations (C(1')(+), C(2')(+), C(3')(+), C(4')(+), and C(5')(+)) were generated by removing an electron (one-electron oxidation) from the neutral sugar radicals, and their geometries were also optimized using the same methods and basis set. The calculation predicts the relative stabilities of the neutral sugar radicals in the order C(1')(•) > C(4')(•) > C(5')(•) > C(3')(•) > C(2')(•), respectively. Of the neutral sugar radicals, C(1')(•) has the lowest vertical ionization potential (IP(vert)), ca. 6.33 eV in the gas phase and 4.71 eV in solution. C(2')(•) has the highest IP(vert), ca. 8.02 eV, in the gas phase, and the resultant C(2') cation is predicted to undergo a barrierless hydride transfer from the C(1') site to produce the C(1') cation. One electron oxidation of C(2')(•) in dG is predicted to result in a low lying triplet state consisting of G(+•) and C(2')(•). The 5',8-cyclo-2'-deoxyguanosin-7-yl radical formed by intramolecular bonding between C(5')(•) and C(8) of guanine transfers spin density from C(5') site to guanine, and this structure has IP(vert) 6.25 and 5.48 eV in the gas phase and in solution.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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21
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Cadet J, Douki T, Ravanat JL, Wagner JR. Measurement of oxidatively generated base damage to nucleic acids in cells: facts and artifacts. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12566-012-0029-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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Mohapatra S, Kawahara M, Khan IS, Yannone SM, Povirk LF. Restoration of G1 chemo/radioresistance and double-strand-break repair proficiency by wild-type but not endonuclease-deficient Artemis. Nucleic Acids Res 2011; 39:6500-10. [PMID: 21531702 PMCID: PMC3159448 DOI: 10.1093/nar/gkr257] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Deficiency in Artemis is associated with lack of V(D)J recombination, sensitivity to radiation and radiomimetic drugs, and failure to repair a subset of DNA double-strand breaks (DSBs). Artemis harbors an endonuclease activity that trims both 5′- and 3′-ends of DSBs. To examine whether endonucleolytic trimming of terminally blocked DSBs by Artemis is a biologically relevant function, Artemis-deficient fibroblasts were stably complemented with either wild-type Artemis or an endonuclease-deficient D165N mutant. Wild-type Artemis completely restored resistance to γ-rays, bleomycin and neocarzinostatin, and also restored DSB-repair proficiency in G0/G1 phase as measured by pulsed-field gel electrophoresis and repair focus resolution. In contrast, cells expressing the D165N mutant, even at very high levels, remained as chemo/radiosensitive and repair deficient as the parental cells, as evidenced by persistent γ-H2AX, 53BP1 and Mre11 foci that slowly increased in size and ultimately became juxtaposed with promyelocytic leukemia protein nuclear bodies. In normal fibroblasts, overexpression of wild-type Artemis increased radioresistance, while D165N overexpression conferred partial repair deficiency following high-dose radiation. Restoration of chemo/radioresistance by wild-type, but not D165N Artemis suggests that the lack of endonucleolytic trimming of DNA ends is the principal cause of sensitivity to double-strand cleaving agents in Artemis-deficient cells.
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Affiliation(s)
- Susovan Mohapatra
- Department of Pharmacology and Toxicology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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23
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Zhou RZ, Akopiants K, Povirk LF. Patching and single-strand ligation in nonhomologous DNA end joining despite persistence of a closely opposed 3'-phosphoglycolate-terminated strand break. Radiat Res 2010; 174:274-9. [PMID: 20726725 DOI: 10.1667/rr2050.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Previous work showed that in human nuclear extracts, double-strand break substrates bearing partially complementary (-ACG) 3'-phosphoglycolate (PG)-terminated 3' overhangs are joined by a mechanism involving annealing of the terminal CG dinucleotides, PG removal, single-base gap filling and ligation. However, in these extracts only a minority of the breaks are rejoined, and most of the 3'-PG termini remain intact even after several hours. To determine whether the presence of a persistent 3'-PG prevents patching and ligation of the opposite strand, a substrate was constructed with two -ACG overhangs, one PG-terminated and one hydroxyl-terminated. after incubation in HeLa cell nuclear extracts, two major repair products of similar yield were formed: a fully repaired duplex and a nicked duplex in which the initial 3'-PG terminus remained intact. These results indicate that patching and ligation can proceed to completion in the unmodified strand despite persistence of the 3'-PG-terminated break in the opposite strand. The break in the PG-containing strand could then presumably be rejoined by a single-strand break repair pathway.
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Affiliation(s)
- Rui-Zhe Zhou
- Department of Pharmacology and Toxicology, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298-0035, USA
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24
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Chan W, Chen B, Wang L, Taghizadeh K, Demott MS, Dedon PC. Quantification of the 2-deoxyribonolactone and nucleoside 5'-aldehyde products of 2-deoxyribose oxidation in DNA and cells by isotope-dilution gas chromatography mass spectrometry: differential effects of gamma-radiation and Fe2+-EDTA. J Am Chem Soc 2010; 132:6145-53. [PMID: 20377226 DOI: 10.1021/ja910928n] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The oxidation of 2-deoxyribose in DNA has emerged as a critical determinant of the cellular toxicity of oxidative damage to DNA, with oxidation of each carbon producing a unique spectrum of electrophilic products. We have developed and validated an isotope-dilution gas chromatography-coupled mass spectrometry (GC-MS) method for the rigorous quantification of two major 2-deoxyribose oxidation products: the 2-deoxyribonolactone abasic site of 1'-oxidation and the nucleoside 5'-aldehyde of 5'-oxidation chemistry. The method entails elimination of these products as 5-methylene-2(5H)-furanone (5MF) and furfural, respectively, followed by derivatization with pentafluorophenylhydrazine (PFPH), addition of isotopically labeled PFPH derivatives as internal standards, extraction of the derivatives, and quantification by GC-MS analysis. The precision and accuracy of the method were validated with oligodeoxynucleotides containing the 2-deoxyribonolactone and nucleoside 5'-aldehyde lesions. Further, the well-defined 2-deoxyribose oxidation chemistry of the enediyne antibiotics, neocarzinostatin and calicheamicin gamma(1)(I), was exploited in control studies, with neocarzinostatin producing 10 2-deoxyribonolactone and 300 nucleoside 5'-aldehyde per 10(6) nt per microM in accord with its established minor 1'- and major 5'-oxidation chemistry. Calicheamicin unexpectedly caused 1'-oxidation at a low level of 10 2-deoxyribonolactone per 10(6) nt per microM in addition to the expected predominance of 5'-oxidation at 560 nucleoside 5'-aldehyde per 10(6) nt per microM. The two hydroxyl radical-mediated DNA oxidants, gamma-radiation and Fe(2+)-EDTA, produced nucleoside 5'-aldehyde at a frequency of 57 per 10(6) nt per Gy (G-value 74 nmol/J) and 3.5 per 10(6) nt per microM, respectively, which amounted to 40% and 35%, respectively, of total 2-deoxyribose oxidation as measured by a plasmid nicking assay. However, gamma-radiation and Fe(2+)-EDTA produced different proportions of 2-deoxyribonolactone at 7% and 24% of total 2-deoxyribose oxidation, respectively, with frequencies of 10 lesions per 10(6) nt per Gy (G-value, 13 nmol/J) and 2.4 lesions per 10(6) nt per microM. Studies in TK6 human lymphoblastoid cells, in which the analytical data were corrected for losses sustained during DNA isolation, revealed background levels of 2-deoxyribonolactone and nucleoside 5'-aldehyde of 9.7 and 73 lesions per 10(6) nt, respectively. Gamma-irradiation of the cells caused increases of 0.045 and 0.22 lesions per 10(6) nt per Gy, respectively, which represents a approximately 250-fold quenching effect of the cellular environment similar to that observed in previous studies. The proportions of the various 2-deoxyribose oxidation products generated by gamma-radiation are similar for purified DNA and cells. These results are consistent with solvent exposure as a major determinant of hydroxyl radical reactivity with 2-deoxyribose in DNA, but the large differences between gamma-radiation and Fe(2+)-EDTA suggest that factors other than hydroxyl radical reactivity govern DNA oxidation chemistry.
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Affiliation(s)
- Wan Chan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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25
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Cadet J, Douki T, Ravanat JL. Oxidatively generated base damage to cellular DNA. Free Radic Biol Med 2010; 49:9-21. [PMID: 20363317 DOI: 10.1016/j.freeradbiomed.2010.03.025] [Citation(s) in RCA: 380] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/16/2010] [Accepted: 03/26/2010] [Indexed: 12/17/2022]
Abstract
Search for the formation of oxidatively base damage in cellular DNA has been a matter of debate for more than 40 years due to the lack of accurate methods for the measurement of the lesions. HPLC associated with either tandem mass spectrometry (MS/MS) or electrochemical detector (ECD) together with optimized DNA extraction conditions constitutes a relevant analytical approach. This has allowed the accurate measurement of oxidatively generated single and clustered base damage in cellular DNA following exposure to acute oxidative stress conditions mediated by ionizing radiation, UVA light and one-electron oxidants. In this review the formation of 11 single base lesions that is accounted for by reactions of singlet oxygen, hydroxyl radical or high intensity UVC laser pulses with nucleobases is discussed on the basis of the mechanisms available from model studies. In addition several clustered lesions were found to be generated in cellular DNA as the result of one initial radical hit on either a vicinal base or the 2-deoxyribose. Information on nucleobase modifications that are formed upon addition of reactive aldehydes arising from the breakdown of lipid hydroperoxides is also provided.
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Affiliation(s)
- Jean Cadet
- Laboratoire Lésions des Acides Nucléiques, SCIB-UMR-E (CEA/UJF) Institut Nanosciences et Cryogénie, CEA/Grenoble, F-38054 Grenoble Cedex 9, France.
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26
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Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
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27
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Macrae MX, Blake S, Jiang X, Capone R, Estes DJ, Mayer M, Yang J. A semi-synthetic ion channel platform for detection of phosphatase and protease activity. ACS NANO 2009; 3:3567-80. [PMID: 19860382 PMCID: PMC2805247 DOI: 10.1021/nn901231h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sensitive methods to probe the activity of enzymes are important for clinical assays and for elucidating the role of these proteins in complex biochemical networks. This paper describes a semi-synthetic ion channel platform for detecting the activity of two different classes of enzymes with high sensitivity. In the first case, this method uses single ion channel conductance measurements to follow the enzyme-catalyzed hydrolysis of a phosphate group attached to the C-terminus of gramicidin A (gA, an ion channel-forming peptide) in the presence of alkaline phosphatase (AP). Enzymatic hydrolysis of this phosphate group removes negative charges from the entrance of the gA pore, resulting in a product with measurably reduced single ion channel conductance compared to the original gA-phosphate substrate. This technique employs a standard, commercial bilayer setup and takes advantage of the catalytic turnover of enzymes and the amplification characteristics of ion flux through individual gA pores to detect picomolar concentrations of active AP in solution. Furthermore, this technique makes it possible to study the kinetics of an enzyme and provides an estimate for the observed rate constant (k(cat)) and the Michaelis constant (K(M)) by following the conversion of the gA-phosphate substrate to product over time in the presence of different concentrations of AP. In the second case, modification of gA with a substrate for proteolytic cleavage by anthrax lethal factor (LF) afforded a sensitive method for detection of LF activity, illustrating the utility of ion channel-based sensing for detection of a potential biowarfare agent. This ion channel-based platform represents a powerful, novel approach to monitor the activity of femtomoles to picomoles of two different classes of enzymes in solution. Furthermore, this platform has the potential for realizing miniaturized, cost-effective bioanalytical assays that complement currently established assays.
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Affiliation(s)
- Michael X. Macrae
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358
| | - Steven Blake
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358
| | - Xiayun Jiang
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Ricardo Capone
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Daniel J. Estes
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Michael Mayer
- Department of Biomedical Engineering and Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109-2110
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, CA 92093-0358
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28
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Chowdhury G, Guengerich FP. Tandem mass spectrometry-based detection of c4'-oxidized abasic sites at specific positions in DNA fragments. Chem Res Toxicol 2009; 22:1310-9. [PMID: 19496605 DOI: 10.1021/tx900115z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oxidative damage to DNA has been linked to aging, cancer, and other biological processes. Reactive oxygen species and various antitumor agents including bleomycin and ionizing radiation have been shown to cause oxidative DNA sugar damage. Detection of DNA lesions is important for understanding the toxicological or therapeutic consequences associated with such agents. C4'-oxidized abasic sites (C4-AP) are produced by the antitumor drug bleomycin and ionizing radiation. The currently available methods for the detection of C4-AP cannot provide both structural and sequence information. We have developed an LC-ESI-MS-based approach for specific detection and mapping of C4-AP from a mixture of lesions. We show using Fe-bleomycin-damaged DNA that C4-AP can be detected at cytosine and thymine sites by direct MS analysis. Our results reveal that collision-induced dissociation of C4-AP-containing oligonucleotides results in preferential fragmentation at C4-AP sites with the formation of the unique a* ions (18 amu more than the a-B ions) that allow mapping of the C4-AP sites. Various chemical modification strategies (e.g., reduction with NaBH4 and NaBD4 and derivatization with methoxyamine and hydrazine, followed by LC-MS analysis) were also used for unambiguous detection of C4-AP sites. Finally, we show that the methods described here can detect the presence of C4-AP at specific sites in a complex sample such as hydroxyl radical-damaged DNA. The LC-MS approach was also used for the simultaneous detection of the other C4'-oxidation end product, 3'-phosphoglycolate, at a specific site in hydroxyl radical-damaged DNA. Thus, LC-MS provides a rapid and direct approach for the detection and mapping of oxidative DNA lesions.
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Affiliation(s)
- Goutam Chowdhury
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, 638 Robinson Research Building, 2200 Pierce Avenue, Nashville, Tennessee 37232-0146, USA
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29
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Tyrosyl-DNA phosphodiesterase and the repair of 3'-phosphoglycolate-terminated DNA double-strand breaks. DNA Repair (Amst) 2009; 8:901-11. [PMID: 19505854 DOI: 10.1016/j.dnarep.2009.05.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 04/24/2009] [Accepted: 05/11/2009] [Indexed: 11/21/2022]
Abstract
Although tyrosyl-DNA phosphodiesterase (TDP1) is capable of removing blocked 3' termini from DNA double-strand break ends, it is uncertain whether this activity plays a role in double-strand break repair. To address this question, affinity-tagged TDP1 was overexpressed in human cells and purified, and its interactions with end joining proteins were assessed. Ku and DNA-PKcs inhibited TDP1-mediated processing of 3'-phosphoglycolate double-strand break termini, and in the absence of ATP, ends sequestered by Ku plus DNA-PKcs were completely refractory to TDP1. Addition of ATP restored TDP1-mediated end processing, presumably due to DNA-PK-catalyzed phosphorylation. Mutations in the 2609-2647 Ser/Thr phosphorylation cluster of DNA-PKcs only modestly affected such processing, suggesting that phosphorylation at other sites was important for rendering DNA ends accessible to TDP1. In human nuclear extracts, about 30% of PG termini were removed within a few hours despite very high concentrations of Ku and DNA-PKcs. Most such removal was blocked by the DNA-PK inhibitor KU-57788, but approximately 5% of PG termini were removed in the first few minutes of incubation even in extracts preincubated with inhibitor. The results suggest that despite an apparent lack of specific recruitment of TDP1 by DNA-PK, TDP1 can gain access to and can process blocked 3' termini of double-strand breaks before ends are fully sequestered by DNA-PK, as well as at a later stage after DNA-PK autophosphorylation. Following cell treatment with calicheamicin, which specifically induces double-strand breaks with protruding 3'-PG termini, TDP1-mutant SCAN1 (spinocerebellar ataxia with axonal neuropathy) cells exhibited a much higher incidence of dicentric chromosomes, as well as higher incidence of chromosome breaks and micronuclei, than normal cells. This chromosomal hypersensitivity, as well as a small but reproducible enhancement of calicheamicin cytotoxicity following siRNA-mediated TDP1 knockdown, suggests a role for TDP1 in repair of 3'-PG double-strand breaks in vivo.
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30
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Hawkins AJ, Subler MA, Akopiants K, Wiley JL, Taylor SM, Rice AC, Windle JJ, Valerie K, Povirk LF. In vitro complementation of Tdp1 deficiency indicates a stabilized enzyme-DNA adduct from tyrosyl but not glycolate lesions as a consequence of the SCAN1 mutation. DNA Repair (Amst) 2009; 8:654-63. [PMID: 19211312 DOI: 10.1016/j.dnarep.2008.12.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 12/19/2008] [Accepted: 12/21/2008] [Indexed: 11/17/2022]
Abstract
A homozygous H493R mutation in the active site of tyrosyl-DNA phosphodiesterase (TDP1) has been implicated in hereditary spinocerebellar ataxia with axonal neuropathy (SCAN1), an autosomal recessive neurodegenerative disease. However, it is uncertain how the H493R mutation elicits the specific pathologies of SCAN1. To address this question, and to further elucidate the role of TDP1 in repair of DNA end modifications and general physiology, we generated a Tdp1 knockout mouse and carried out detailed behavioral analyses as well as characterization of repair deficiencies in extracts of embryo fibroblasts from these animals. While Tdp1(-/-) mice appear phenotypically normal, extracts from Tdp1(-/-) fibroblasts exhibited deficiencies in processing 3'-phosphotyrosyl single-strand breaks and 3'-phosphoglycolate double-strand breaks (DSBs), but not 3'-phosphoglycolate single-strand breaks. Supplementing Tdp1(-/-) extracts with H493R TDP1 partially restored processing of 3'-phosphotyrosyl single-strand breaks, but with evidence of persistent covalent adducts between TDP1 and DNA, consistent with a proposed intermediate-stabilization effect of the SCAN1 mutation. However, H493R TDP1 supplementation had no effect on phosphoglycolate (PG) termini on 3' overhangs of double-strand breaks; these remained completely unprocessed. Altogether, these results suggest that for 3'-phosphoglycolate overhang lesions, the SCAN1 mutation confers loss of function, while for 3'-phosphotyrosyl lesions, the mutation uniquely stabilizes a reaction intermediate.
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Affiliation(s)
- Amy J Hawkins
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
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Affiliation(s)
- Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, NE47-277, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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