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Ferrasi AC, Puttini R, Galvani AF, Hamamoto Filho PT, Delafiori J, Argente VD, de Oliveira AN, Dias-Audibert FL, Catharino RR, Silva OC, Zanini MA, Kurokawa GA, Lima EO. Metabolomics Approach Reveals Important Glioblastoma Plasma Biomarkers for Tumor Biology. Int J Mol Sci 2023; 24:8813. [PMID: 37240159 PMCID: PMC10218163 DOI: 10.3390/ijms24108813] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Glioblastoma (GB) is the most aggressive and frequent primary malignant tumor of the central nervous system and is associated with poor overall survival even after treatment. To better understand tumor biochemical alterations and broaden the potential targets of GB, this study aimed to evaluate differential plasma biomarkers between GB patients and healthy individuals using metabolomics analysis. Plasma samples from both groups were analyzed via untargeted metabolomics using direct injection with an electrospray ionization source and an LTQ mass spectrometer. GB biomarkers were selected via Partial Least Squares Discriminant and Fold-Change analyses and were identified using tandem mass spectrometry with in silico fragmentation, consultation of metabolomics databases, and a literature search. Seven GB biomarkers were identified, some of which were unprecedented biomarkers for GB, including arginylproline (m/z 294), 5-hydroxymethyluracil (m/z 143), and N-acylphosphatidylethanolamine (m/z 982). Notably, four other metabolites were identified. The roles of all seven metabolites in epigenetic modulation, energy metabolism, protein catabolism or folding processes, and signaling pathways that activate cell proliferation and invasion were elucidated. Overall, the findings of this study highlight new molecular targets to guide future investigations on GB. These molecular targets can also be further evaluated to derive their potential as biomedical analytical tools for peripheral blood samples.
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Affiliation(s)
- Adriana C. Ferrasi
- Laboratory of Molecular Analysis and Neuro-Oncology, Department of Internal Medicine, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (A.C.F.); (R.P.); (A.F.G.); (V.D.A.); (O.C.S.); (G.A.K.)
| | - Ricardo Puttini
- Laboratory of Molecular Analysis and Neuro-Oncology, Department of Internal Medicine, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (A.C.F.); (R.P.); (A.F.G.); (V.D.A.); (O.C.S.); (G.A.K.)
| | - Aline F. Galvani
- Laboratory of Molecular Analysis and Neuro-Oncology, Department of Internal Medicine, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (A.C.F.); (R.P.); (A.F.G.); (V.D.A.); (O.C.S.); (G.A.K.)
| | - Pedro T. Hamamoto Filho
- Department of Neurology, Psychology and Psychiatry, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (P.T.H.F.); (M.A.Z.)
| | - Jeany Delafiori
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas 13.083-877, Brazil; (J.D.); (A.N.d.O.); (F.L.D.-A.); (R.R.C.)
| | - Victoria D. Argente
- Laboratory of Molecular Analysis and Neuro-Oncology, Department of Internal Medicine, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (A.C.F.); (R.P.); (A.F.G.); (V.D.A.); (O.C.S.); (G.A.K.)
| | - Arthur N. de Oliveira
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas 13.083-877, Brazil; (J.D.); (A.N.d.O.); (F.L.D.-A.); (R.R.C.)
| | - Flávia L. Dias-Audibert
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas 13.083-877, Brazil; (J.D.); (A.N.d.O.); (F.L.D.-A.); (R.R.C.)
| | - Rodrigo R. Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas 13.083-877, Brazil; (J.D.); (A.N.d.O.); (F.L.D.-A.); (R.R.C.)
| | - Octavio C. Silva
- Laboratory of Molecular Analysis and Neuro-Oncology, Department of Internal Medicine, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (A.C.F.); (R.P.); (A.F.G.); (V.D.A.); (O.C.S.); (G.A.K.)
| | - Marco A. Zanini
- Department of Neurology, Psychology and Psychiatry, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (P.T.H.F.); (M.A.Z.)
| | - Gabriel A. Kurokawa
- Laboratory of Molecular Analysis and Neuro-Oncology, Department of Internal Medicine, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (A.C.F.); (R.P.); (A.F.G.); (V.D.A.); (O.C.S.); (G.A.K.)
| | - Estela O. Lima
- Laboratory of Molecular Analysis and Neuro-Oncology, Department of Internal Medicine, Botucatu Medical School, São Paulo State University, Botucatu 18.618-687, Brazil; (A.C.F.); (R.P.); (A.F.G.); (V.D.A.); (O.C.S.); (G.A.K.)
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Kladova OA, Tyugashev TE, Mikushina ES, Kuznetsov NA, Novopashina DS, Kuznetsova AA. The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain. Cells 2023; 12:cells12091300. [PMID: 37174699 PMCID: PMC10177036 DOI: 10.3390/cells12091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
To maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes themselves (whose primary function is the recognition and removal of damaged bases) are subject to amino acid substitutions owing to natural single-nucleotide polymorphisms (SNPs). One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA with complementary dNMPs. It is known that many SNPs can cause an amino acid substitution in this enzyme and a significant decrease in the enzymatic activity. In this study, the activity of four natural variants of Polβ, containing substitution E154A, G189D, M236T, or R254I in the transferase domain, was analyzed using molecular dynamics simulations and pre-steady-state kinetic analyses. It was shown that all tested substitutions lead to a significant reduction in the ability to form a complex with DNA and with incoming dNTP. The G189D substitution also diminished Polβ catalytic activity. Thus, a decrease in the activity of studied mutant forms may be associated with an increased risk of damage to the genome.
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Affiliation(s)
- Olga A Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Daria S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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3
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Kladova OA, Tyugashev TE, Mikushina ES, Soloviev NO, Kuznetsov NA, Novopashina DS, Kuznetsova AA. Human Polβ Natural Polymorphic Variants G118V and R149I Affects Substate Binding and Catalysis. Int J Mol Sci 2023; 24:ijms24065892. [PMID: 36982964 PMCID: PMC10051265 DOI: 10.3390/ijms24065892] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
DNA polymerase β (Polβ) expression is essential for the cell's response to DNA damage that occurs during natural cellular processes. Polβ is considered the main reparative DNA polymerase, whose role is to fill the DNA gaps arising in the base excision repair pathway. Mutations in Polβ can lead to cancer, neurodegenerative diseases, or premature aging. Many single-nucleotide polymorphisms have been identified in the POLB gene, but the consequences of these polymorphisms are not always clear. It is known that some polymorphic variants in the Polβ sequence reduce the efficiency of DNA repair, thereby raising the frequency of mutations in the genome. In the current work, we studied two polymorphic variants (G118V and R149I separately) of human Polβ that affect its DNA-binding region. It was found that each amino acid substitution alters Polβ's affinity for gapped DNA. Each polymorphic variant also weakens its binding affinity for dATP. The G118V variant was found to greatly affect Polβ's ability to fill gapped DNA and slowed the catalytic rate as compared to the wild-type enzyme. Thus, these polymorphic variants seem to decrease the ability of Polβ to maintain base excision repair efficiency.
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Affiliation(s)
- Olga A Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena S Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nikita O Soloviev
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Daria S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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4
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Kladova OA, Kuznetsov NA, Fedorova OS. Initial stages of DNA Base Excision Repair in Nucleosomes. Mol Biol 2021. [DOI: 10.1134/s0026893321020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Kandlur A, Satyamoorthy K, Gangadharan G. Oxidative Stress in Cognitive and Epigenetic Aging: A Retrospective Glance. Front Mol Neurosci 2020; 13:41. [PMID: 32256315 PMCID: PMC7093495 DOI: 10.3389/fnmol.2020.00041] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/02/2020] [Indexed: 12/17/2022] Open
Abstract
Brain aging is the critical and common factor among several neurodegenerative disorders and dementia. Cellular, biochemical and molecular studies have shown intimate links between oxidative stress and cognitive dysfunction during aging and age-associated neuronal diseases. Brain aging is accompanied by oxidative damage of nuclear as well as mitochondrial DNA, and diminished repair. Recent studies have reported epigenetic alterations during aging of the brain which involves reactive oxygen species (ROS) that regulates various systems through distinct mechanisms. However, there are studies which depict differing roles of reactive oxidant species as a major factor during aging. In this review, we describe the evidence to show how oxidative stress is intricately linked to age-associated cognitive decline. The review will primarily focus on implications of age-associated oxidative damage on learning and memory, and the cellular events, with special emphasis on associated epigenetic machinery. A comprehensive understanding of these mechanisms may provide a perspective on the development of potential therapeutic targets within the oxidative system.
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Affiliation(s)
| | | | - Gireesh Gangadharan
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
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6
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Kumari B, Sinha KK, DAS P. Complex interplay of lesion-specific DNA repair enzyme on bistranded clustered DNA damage harboring Tg:G mismatch in nucleosome core particles. J Biosci 2018; 43:575-583. [PMID: 30207305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
5,6-Dihydroxy-5,6-dihydrothymine (thymine glycol) and 7,8-dihydro-8-oxo-20-deoxyguanosine (8-oxodG) are major DNA damage lesions produced by endogenous oxidative stress, as well as inflicted by carcinogens and ionizing radiation. The processing of Tg:G mismatch and 8-oxodG in close proximity of each other in a bistranded clustered environment in DNA oligomer duplexes as well as in a nucleosome core particle (NCP) model are reported here. The processing of the lesions was evaluated by purified enzyme cocktails of hNTH1 and hOGG1 as well as with a HeLa cell extract. Interestingly, the yield of double-strand breaks (DSBs) resulting from the processing of the bistranded lesions are appreciably lower when the DNA is treated with the HeLa cell extract compared with the relevant purified enzyme cocktail in both models. Clustered bistranded lesions become more repair refractive when reconstituted as an NCP. This indicates a complex interplay between the repair enzymes that influence the processing of the bistranded cluster damage positively to avoid the formation of DSBs under cellular conditions. In addition to position and orientation of the lesions, the type of the lesions in the cluster environment in DNA along with the relative abundance of the lesion-specific enzymes in the cells strongly prevents the processing of the oxidized nucleobases.
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Affiliation(s)
- Bhavini Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, Bihar 801 103, India
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7
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Complex interplay of lesion-specific DNA repair enzyme on bistranded clustered DNA damage harboring Tg:G mismatch in nucleosome core particles. J Biosci 2018. [DOI: 10.1007/s12038-018-9786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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8
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9
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Carell T, Kurz MQ, Müller M, Rossa M, Spada F. Non-canonical Bases in the Genome: The Regulatory Information Layer in DNA. Angew Chem Int Ed Engl 2018; 57:4296-4312. [DOI: 10.1002/anie.201708228] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Carell
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Matthias Q. Kurz
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Markus Müller
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Martin Rossa
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Fabio Spada
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
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10
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Kumari B, Jha P, Sinha KK, Das P. Vicinal abasic site impaired processing of a Tg:G mismatch and 8-oxoguanine lesions in three-component bistranded clustered DNA damage. RSC Adv 2018; 8:17921-17926. [PMID: 35542077 PMCID: PMC9080475 DOI: 10.1039/c8ra01992d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/03/2018] [Indexed: 11/23/2022] Open
Abstract
The occurrence of 7,8-dihydro-8-oxo-2′deoxyguanosine (8-oxodG), thymine glycol:guanine (Tg:G) mismatch and abasic site DNA damage lesions in close proximity induce repair refractive multicomponent clustered DNA damage. Herein, the influence of abasic sites in the processing of 8-oxodG lesion and Tg:G mismatch bistranded cluster is evaluated. Abasic sites are found to impart conformational destabilization that appreciably hinders the repair activity of the other lesions whenever present in a cluster combination. The repair process reduces the formation of double strand breaks (DSBs) and renders this three-lesion combination a non-DSB forming cluster. The stability of the DNA duplex harbouring these three lesions is highly compromised due to altered base helicity and base stacking phenomena leading to impaired repair. The occurrence of 7,8-dihydro-8-oxo-2′deoxyguanosine (8-oxodG), thymine glycol:guanine (Tg:G) mismatch and abasic site DNA damage lesions in close proximity induce repair refractive non-DSB cluster.![]()
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Affiliation(s)
| | - Pravin Jha
- Department of Biotechnology
- NIPER Hajipur
- India
| | | | - Prolay Das
- Department of Chemistry
- IIT Patna
- Patna-801103
- India
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11
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Wu G, Lei L, Schöler HR. Totipotency in the mouse. J Mol Med (Berl) 2017; 95:687-694. [PMID: 28102431 PMCID: PMC5487595 DOI: 10.1007/s00109-017-1509-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/20/2016] [Accepted: 01/12/2017] [Indexed: 12/31/2022]
Abstract
In mammals, the unicellular zygote starts the process of embryogenesis and differentiates into all types of somatic cells, including both fetal and extraembryonic lineages-in a highly organized manner to eventually give rise to an entire multicellular organism comprising more than 200 different tissue types. This feature is referred to as totipotency. Upon fertilization, oocyte maternal factors epigenetically reprogram the genomes of the terminally differentiated oocyte and spermatozoon and turn the zygote into a totipotent cell. Today, we still do not fully understand the molecular properties of totipotency. In this review, we discuss recent findings on the molecular signature and mechanism of transcriptional regulation networks in the totipotent mouse embryo.
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Affiliation(s)
- Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
| | - Lei Lei
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Department of Histology and Embryology, Harbin Medical University, 194 Xuefu Road, Nangang District, Harbin, 150081, China
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.
- Medical Faculty, University of Münster, Domagkstr. 3, 48149, Münster, Germany.
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12
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Yu Y, Cui Y, Niedernhofer LJ, Wang Y. Occurrence, Biological Consequences, and Human Health Relevance of Oxidative Stress-Induced DNA Damage. Chem Res Toxicol 2016; 29:2008-2039. [PMID: 27989142 DOI: 10.1021/acs.chemrestox.6b00265] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A variety of endogenous and exogenous agents can induce DNA damage and lead to genomic instability. Reactive oxygen species (ROS), an important class of DNA damaging agents, are constantly generated in cells as a consequence of endogenous metabolism, infection/inflammation, and/or exposure to environmental toxicants. A wide array of DNA lesions can be induced by ROS directly, including single-nucleobase lesions, tandem lesions, and hypochlorous acid (HOCl)/hypobromous acid (HOBr)-derived DNA adducts. ROS can also lead to lipid peroxidation, whose byproducts can also react with DNA to produce exocyclic DNA lesions. A combination of bioanalytical chemistry, synthetic organic chemistry, and molecular biology approaches have provided significant insights into the occurrence, repair, and biological consequences of oxidatively induced DNA lesions. The involvement of these lesions in the etiology of human diseases and aging was also investigated in the past several decades, suggesting that the oxidatively induced DNA adducts, especially bulky DNA lesions, may serve as biomarkers for exploring the role of oxidative stress in human diseases. The continuing development and improvement of LC-MS/MS coupled with the stable isotope-dilution method for DNA adduct quantification will further promote research about the clinical implications and diagnostic applications of oxidatively induced DNA adducts.
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Affiliation(s)
| | | | - Laura J Niedernhofer
- Department of Metabolism and Aging, The Scripps Research Institute Florida , Jupiter, Florida 33458, United States
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13
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Minetti CASA, Remeta DP, Iden CR, Johnson F, Grollman AP, Breslauer KJ. Impact of thymine glycol damage on DNA duplex energetics: Correlations with lesion-induced biochemical and structural consequences. Biopolymers 2016; 103:491-508. [PMID: 25991500 DOI: 10.1002/bip.22680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 11/08/2022]
Abstract
The magnitude and nature of lesion-induced energetic perturbations empirically correlate with mutagenicity/cytotoxicity profiles and can be predictive of lesion outcomes during polymerase-mediated replication in vitro. In this study, we assess the sequence and counterbase-dependent energetic impact of the Thymine glycol (Tg) lesion on a family of deoxyoligonucleotide duplexes. Tg damage arises from thymine and methyl-cytosine exposure to oxidizing agents or radiation-generated free-radicals. The Tg lesion blocks polymerase-mediated DNA replication in vitro and the unrepaired site elicits cytotoxic lethal consequences in vivo. Our combined calorimetric and spectroscopic characterization correlates Tg -induced energetic perturbations with biological and structural properties. Specifically, we incorporate a 5R-Tg isomer centered within the tridecanucleotide sequence 5'-GCGTACXCATGCG-3' (X = Tg or T) which is hybridized with the corresponding complementary sequence 5'-CGCATGNGTACGC-3' (N = A, G, T, C) to generate families of Tg -damaged (Tg ·N) and lesion-free (T·N) duplexes. We demonstrate that the magnitude and nature of the Tg destabilizing impact is dependent on counterbase identity (i.e., A ∼ G < T < C). The observation that a Tg lesion is less destabilizing when positioned opposite purines suggests that favorable counterbase stacking interactions may partially compensate lesion-induced perturbations. Moreover, the destabilizing energies of Tg ·N duplexes parallel their respective lesion-free T·N mismatch counterparts (i.e., G < T < C). Elucidation of Tg-induced destabilization relative to the corresponding undamaged mismatch energetics allows resolution of lesion-specific and sequence-dependent impacts. The Tg-induced energetic perturbations are consistent with its replication blocking properties and may serve as differential recognition elements for discrimination by the cellular repair machinery.
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Affiliation(s)
- Conceição A S A Minetti
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ, 08854
| | - David P Remeta
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ, 08854
| | - Charles R Iden
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY, 11794
| | - Francis Johnson
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY, 11794
| | - Arthur P Grollman
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY, 11794
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ, 08854.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901
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14
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Jin L, Zhao C, Zhang T, Wang Z, Min S, Wang W, Wei Y. Effects of an acid–alkaline environment on the reactivity of 5-carboxycytosine with hydroxyl radicals. RSC Adv 2015. [DOI: 10.1039/c5ra17393k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The addition of ˙OH to C5C6 double bond and abstraction of H5 from 5-caCyt are more favourable in neutral, acidic and alkaline conditions.
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Affiliation(s)
- Lingxia Jin
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Caibin Zhao
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Tianlei Zhang
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Zhiyin Wang
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Suotian Min
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Yawen Wei
- Institute of Publication Science
- Chang’an University
- Xi’an 710064
- China
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15
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Perevozchikova SA, Trikin RM, Heinze RJ, Romanova EA, Oretskaya TS, Friedhoff P, Kubareva EA. Is thymidine glycol containing DNA a substrate of E. coli DNA mismatch repair system? PLoS One 2014; 9:e104963. [PMID: 25133614 PMCID: PMC4136841 DOI: 10.1371/journal.pone.0104963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/15/2014] [Indexed: 11/18/2022] Open
Abstract
The DNA mismatch repair (MMR) system plays a crucial role in the prevention of replication errors and in the correction of some oxidative damages of DNA bases. In the present work the most abundant oxidized pyrimidine lesion, 5,6-dihydro-5,6-dihydroxythymidine (thymidine glycol, Tg) was tested for being recognized and processed by the E. coli MMR system, namely complex of MutS, MutL and MutH proteins. In a partially reconstituted MMR system with MutS-MutL-MutH proteins, G/Tg and A/Tg containing plasmids failed to provoke the incision of DNA. Tg residue in the 30-mer DNA duplex destabilized double helix due to stacking disruption with neighboring bases. However, such local structural changes are not important for E. coli MMR system to recognize this lesion. A lack of repair of Tg containing DNA could be due to a failure of MutS (a first acting protein of MMR system) to interact with modified DNA in a proper way. It was shown that Tg in DNA does not affect on ATPase activity of MutS. On the other hand, MutS binding affinities to DNA containing Tg in G/Tg and A/Tg pairs are lower than to DNA with a G/T mismatch and similar to canonical DNA. Peculiarities of MutS interaction with DNA was monitored by Förster resonance energy transfer (FRET) and fluorescence anisotropy. Binding of MutS to Tg containing DNAs did not result in the formation of characteristic DNA kink. Nevertheless, MutS homodimer orientation on Tg-DNA is similar to that in the case of G/T-DNA. In contrast to G/T-DNA, neither G/Tg- nor A/Tg-DNA was able to stimulate ADP release from MutS better than canonical DNA. Thus, Tg residue in DNA is unlikely to be recognized or processed by the E. coli MMR system. Probably, the MutS transformation to active “sliding clamp” conformation on Tg-DNA is problematic.
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Affiliation(s)
- Svetlana A. Perevozchikova
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Roman M. Trikin
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Roger J. Heinze
- Institute for Biochemistry, Justus Liebig University, Giessen, Germany
| | - Elena A. Romanova
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana S. Oretskaya
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Peter Friedhoff
- Institute for Biochemistry, Justus Liebig University, Giessen, Germany
| | - Elena A. Kubareva
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
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Stimulation of N--glycoside transfer in deoxythymidine glycol: mechanism of the initial step in base excision repair. J Mol Model 2014; 20:2168. [PMID: 24595719 DOI: 10.1007/s00894-014-2168-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
Abstract
Thymine glycol (Tg), a toxic oxidative DNA lesion, is preferentially removed by endonuclease III (Endo III). To investigate the glycosylase activity of Endo III, the N--glycoside transfer mechanism in deoxythymidine glycol (dTg) is examined in this theoretical study based on the BHandHLYP/6-311++G(d,p) level of theory. Two controversial mechanisms were characterized, i.e., the displacement and endocyclic mechanisms. For each mechanism, three types of reaction models were established, including the direct reaction, local microhydration and protonated models. The calculated results indicate that (i) all three reaction models favor the displacement mechanism more than the endocyclic mechanism; (ii) the local microhydration model allows for discrete proton transfer and contributes to the reduction of activation energies, nevertheless, large activation energies are still involved; (iii) the O4'-protonated endocyclic model can efficiently promote the nucleophilic attack of lysine residue and an amino acid residue other than the nucleophilic lysine should be responsible for the opening of the sugar ring; (iv) the O2-protonated displacement model facilitates the leaving group (Tg) stabilization and therefore is the preferred mechanism for the N--glycoside transfer of dTg, whose activation energy of 17.7 kcal mol⁻¹ is in good agreement with the experimental estimate of 19.0 kcal mol⁻¹. As a result, the protonation of nucleobase plays a significant role in predicting the preferred glycosylase mechanism. Our findings can propose appropriate mechanisms for future large-scale enzymatic modeling of Endo III and provide more fundamental information about the important residues that may be included in the enzyme-catalyzed reactions.
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Adhikary A, Kumar A, Palmer BJ, Todd AD, Heizer AN, Sevilla MD. Reactions of 5-methylcytosine cation radicals in DNA and model systems: thermal deprotonation from the 5-methyl group vs. excited state deprotonation from sugar. Int J Radiat Biol 2014; 90:433-45. [PMID: 24428230 DOI: 10.3109/09553002.2014.884293] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To study the formation and subsequent reactions of the 5-methyl-2'-deoxycytidine cation radical (5-Me-2'-dC•(+)) in nucleosides and DNA-oligomers and compare to one-electron oxidized thymidine. MATERIALS AND METHODS Employing electron spin resonance (ESR), cation radical formation and its reactions were investigated in 5-Me-2'-dC, thymidine (Thd) and their derivatives, in fully double-stranded (ds) d[GC*GC*GC*GC*](2) and in the 5-Me-C/A mismatched, d[GGAC*AAGC:CCTAATCG], where C* = 5-Me-C. RESULTS We report 5-Me-2'-dC•(+) production by one-electron oxidation of 5-Me-2'-dC by Cl(2)•- via annealing in the dark at 155 K. Progressive annealing of 5-Me-2'-dC•(+) at 155 K produces the allylic radical (C-CH(2)•). However, photoexcitation of 5-Me-2'-dC•(+) by 405 nm laser or by photoflood lamp leads to only C3'• formation. Photoexcitation of N3-deprotonated thyminyl radical in Thd and its 5'-nucleotides leads to C3'• formation but not in 3'-TMP which resulted in the allylic radical (U-CH(2)•) and C5'• production. For excited 5-Me-2',3'-ddC•(+), absence of the 3'-OH group does not prevent C3'• formation. For d[GC*GC*GC*GC*](2) and d[GGAC*AAGC:CCTAATCG], intra-base paired proton transferred form of G cation radical (G(N1-H)•: C(+ H(+))) is found with no observable 5-Me-2'-dC•(+) formation. Photoexcitation of (G(N1-H)•:C(+ H(+))) in d[GC*GC*GC*GC*](2) produced only C1'• and not the expected photoproducts from 5-Me-2'-dC•(+). However, photoexcitation of (G(N1-H)•:C(+ H(+))) in d[GGAC*AAGC:CCTAATCG] led to C5'• and C1'• formation. CONCLUSIONS C-CH(2)• formation from 5-Me-2'-dC•(+) occurs via ground state deprotonation from C5-methyl group on the base. In the excited 5-Me-2'-dC•(+) and 5-Me-2',3'-ddC•(+), spin and charge localization at C3' followed by deprotonation leads to C3'• formation. Thus, deprotonation from C3' in the excited cation radical is kinetically controlled and sugar C-H bond energies are not the only controlling factors in these deprotonations.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, MI , USA
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18
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Lan L, Nakajima S, Wei L, Sun L, Hsieh CL, Sobol RW, Bruchez M, Van Houten B, Yasui A, Levine AS. Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin. Nucleic Acids Res 2013; 42:2330-45. [PMID: 24293652 PMCID: PMC3936713 DOI: 10.1093/nar/gkt1233] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Reactive oxygen species (ROS)-induced DNA damage is repaired by the base excision repair pathway. However, the effect of chromatin structure on BER protein recruitment to DNA damage sites in living cells is poorly understood. To address this problem, we developed a method to specifically produce ROS-induced DNA damage by fusing KillerRed (KR), a light-stimulated ROS-inducer, to a tet-repressor (tetR-KR) or a transcription activator (TA-KR). TetR-KR or TA-KR, bound to a TRE cassette (∼90 kb) integrated at a defined genomic locus in U2OS cells, was used to induce ROS damage in hetero- or euchromatin, respectively. We found that DNA glycosylases were efficiently recruited to DNA damage in heterochromatin, as well as in euchromatin. PARP1 was recruited to DNA damage within condensed chromatin more efficiently than in active chromatin. In contrast, recruitment of FEN1 was highly enriched at sites of DNA damage within active chromatin in a PCNA- and transcription activation-dependent manner. These results indicate that oxidative DNA damage is differentially processed within hetero or euchromatin.
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Affiliation(s)
- Li Lan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA, School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, People's Republic of China, Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA, Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15213, USA, Department of Chemistry and Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA and Division of Dynamic Proteome, Institute of Development, Aging, and Cancer, Tohoku University, Seiryomachi 4-1, Sendai 980-8575, Japan
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Navarro-Whyte L, Kellie JL, Lenz SAP, Wetmore SD. Hydrolysis of the damaged deoxythymidine glycol nucleoside and comparison to canonical DNA. Phys Chem Chem Phys 2013; 15:19343-52. [DOI: 10.1039/c3cp53217h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Chen CC, Wang KY, Shen CKJ. The mammalian de novo DNA methyltransferases DNMT3A and DNMT3B are also DNA 5-hydroxymethylcytosine dehydroxymethylases. J Biol Chem 2012; 287:33116-21. [PMID: 22898819 PMCID: PMC3460417 DOI: 10.1074/jbc.c112.406975] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 08/15/2012] [Indexed: 12/14/2022] Open
Abstract
For cytosine (C) demethylation of vertebrate DNA, it is known that the TET proteins could convert 5-methyl C (5-mC) to 5-hydroxymethyl C (5-hmC). However, DNA dehydroxymethylase(s), or enzymes able to directly convert 5-hmC to C, have been elusive. We present in vitro evidence that the mammalian de novo DNA methyltransferases DNMT3A and DNMT3B, but not the maintenance enzyme DNMT1, are also redox-dependent DNA dehydroxymethylases. Significantly, intactness of the C methylation catalytic sites of these de novo enzymes is also required for their 5-hmC dehydroxymethylation activity. That DNMT3A and DNMT3B function bidirectionally both as DNA methyltransferases and as dehydroxymethylases raises intriguing and new questions regarding the structural and functional aspects of these enzymes and their regulatory roles in the dynamic modifications of the vertebrate genomes during development, carcinogenesis, and gene regulation.
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Affiliation(s)
- Chun-Chang Chen
- From the Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan and
- the Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Keh-Yang Wang
- From the Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan and
| | - Che-Kun James Shen
- From the Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan and
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21
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Dolinnaya NG, Kubareva EA, Romanova EA, Trikin RM, Oretskaya TS. Thymidine glycol: the effect on DNA molecular structure and enzymatic processing. Biochimie 2012; 95:134-47. [PMID: 23000318 DOI: 10.1016/j.biochi.2012.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/12/2012] [Indexed: 12/18/2022]
Abstract
Thymine glycol (Tg) in DNA is a biologically active oxidative damage caused by ionizing radiation or oxidative stress. Due to chirality of C5 and C6 atoms, Tg exists as a mixture of two pairs of cis and trans diastereomers: 5R cis-trans pair (5R,6S; 5R,6R) and 5S cis-trans pair (5S,6R; 5S,6S). Of all the modified pyrimidine lesions that have been studied to date, only thymine glycol represents a strong block to high-fidelity DNA polymerases in vitro and is lethal in vivo. Here we describe the preparation of thymine glycol-containing oligonucleotides and the influence of the oxidized residue on the structure of DNA in different sequence contexts, thymine glycol being paired with either adenine or guanine. The effect of thymine glycol on biochemical processing of DNA, such as biosynthesis, transcription and repair in vitro and in vivo, is also reviewed. Special attention is paid to stereochemistry and 5R cis-trans epimerization of Tg, and their relation to the structure of DNA double helix and enzyme-mediated DNA processing. Described here are the comparative structure and properties of other forms of pyrimidine base oxidation, as well as the role of Tg in tandem lesions.
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Affiliation(s)
- Nina G Dolinnaya
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russia
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22
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Onizuka K, Yeo J, David SS, Beal PA. NEIL1 binding to DNA containing 2'-fluorothymidine glycol stereoisomers and the effect of editing. Chembiochem 2012; 13:1338-48. [PMID: 22639086 DOI: 10.1002/cbic.201200139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Indexed: 11/06/2022]
Abstract
Thymine glycol (Tg), one of the oxidized bases formed in DNA by reactive oxygen species, is repaired by the DNA glycosylases such as NEIL1, NTH1 and Endo III. In our recent studies, we showed that NEIL1's catalytic efficiency and lesion specificity are regulated by an RNA-editing adenosine deamination reaction. In this study, we synthesized oligodeoxynucleotides containing 2'-fluorothymidine glycol with either ribo or arabino configuration and investigated the binding of these modified DNAs with the unedited and edited forms of human NEIL1 along with E. coli Endo III. For the two forms of hNEIL1, binding affinities to FTg-containing DNA were similar indicating that the editing effect is more subtle than to simply alter substrate affinity. While the NEIL1-binding to FTg-containing DNAs was largely insensitive to C5 and 2' stereochemistry, a preference was observed for the FTg-G pair over the FTg-A pair. In addition, we found that optimal binding is observed with Endo III and duplex DNA with riboFTg(5S) paired with dG. The modified DNAs reported here will provide useful tools for further characterizing the interaction between DNA repair glycosylases and thymine glycol containing DNA.
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Affiliation(s)
- Kazumitsu Onizuka
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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23
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Abstract
Cancer initiation and progression is controlled by both genetic and epigenetic events. The complexity of carcinogenesis cannot be accounted for by genetic alterations alone but also involves epigenetic changes. Epigenetics refers to the study of mechanisms that alter gene expression without altering the primary DNA sequence. Epigenetic mechanisms are heritable and reversible, and include changes in DNA methylation, histone modifications and small noncoding microRNAs (miRNA). Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications probably occur at a very early stage in neoplastic development, and they are widely described as essential players in cancer progression. Recent advances in epigenetics offer a better understanding of the underlying mechanism(s) of carcinogenesis and provide insight into the discovery of putative cancer biomarkers for early detection, disease monitoring, prognosis, and risk assessment. In this review, we summarize the current literature on epigenetic changes causing genetic alterations that are thought to contribute to cancer, and discuss the potential impact of epigenetics future research.
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Affiliation(s)
- R Kanwal
- Department of Urology, Case Western Reserve University, Case Comprehensive Cancer Center, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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24
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Saitou M, Kagiwada S, Kurimoto K. Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells. Development 2012; 139:15-31. [PMID: 22147951 DOI: 10.1242/dev.050849] [Citation(s) in RCA: 298] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetic modifications are crucial for the identity and stability of cells, and, when aberrant, can lead to disease. During mouse development, the genome-wide epigenetic states of pre-implantation embryos and primordial germ cells (PGCs) undergo extensive reprogramming. An improved understanding of the epigenetic reprogramming mechanisms that occur in these cells should provide important new information about the regulation of the epigenetic state of a cell and the mechanisms of induced pluripotency. Here, we discuss recent findings about the potential mechanisms of epigenetic reprogramming, particularly genome-wide DNA demethylation, in pre-implantation mouse embryos and PGCs.
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Affiliation(s)
- Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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25
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Abstract
Methylation of DNA and histones in chromatin has been implicated in numerous biological processes. For many years, methylation has been recognized as static and stable modification, as compared with other covalent modifications of chromatin. Recently, however, several mechanisms have been demonstrated to be involved in demethylation of chromatin, suggesting that chromatin methylation is more dynamically regulated. One chemical reaction that mediates demethylation of both DNA and histones is hydroxylation, catalysed by Fe(II) and α-ketoglutarate (KG)-dependent hydroxylase/dioxygenase. Given that methylation of chromatin is an important epigenetic mark involved in fundamental biological processes such as cell fate determination, understanding how chromatin methylation is dynamically regulated has implications for human diseases and regenerative medicine.
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Affiliation(s)
- Yu-ichi Tsukada
- Division of Molecular Immunology, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
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26
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Abstract
Cancer initiation and progression is controlled by both genetic and epigenetic events. The complexity of carcinogenesis cannot be accounted for by genetic alterations alone but also involves epigenetic changes. Epigenetics refers to the study of mechanisms that alter gene expression without altering the primary DNA sequence. Epigenetic mechanisms are heritable and reversible, and include changes in DNA methylation, histone modifications and small noncoding microRNAs (miRNA). Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications probably occur at a very early stage in neoplastic development, and they are widely described as essential players in cancer progression. Recent advances in epigenetics offer a better understanding of the underlying mechanism(s) of carcinogenesis and provide insight into the discovery of putative cancer biomarkers for early detection, disease monitoring, prognosis, and risk assessment. In this review, we summarize the current literature on epigenetic changes causing genetic alterations that are thought to contribute to cancer, and discuss the potential impact of epigenetics future research.
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Affiliation(s)
- R Kanwal
- Department of Urology, Case Western Reserve University, Case Comprehensive Cancer Center, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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27
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Analysis of urinary nucleosides as potential tumor markers in human breast cancer by high performance liquid chromatography/electrospray ionization tandem mass spectrometry. Clin Chim Acta 2011; 412:1861-6. [DOI: 10.1016/j.cca.2011.06.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 06/19/2011] [Accepted: 06/21/2011] [Indexed: 02/08/2023]
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28
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Chen ZQ, Zhang CH, Kim CK, Xue Y. Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol. Phys Chem Chem Phys 2011; 13:6471-83. [PMID: 21380473 DOI: 10.1039/c0cp02783a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.
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Affiliation(s)
- Ze Qin Chen
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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29
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Schötz U, Heuer S, Caldwell RB, Zitzelsberger H. Genetic and biochemical analysis of base excision repair complexes participating in radiation-induced ROS damage repair. RADIATION PROTECTION DOSIMETRY 2011; 143:284-288. [PMID: 21109544 DOI: 10.1093/rpd/ncq400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This work is part of the joint research project 'radiation-induced DNA damage' of the KVSF, a BMBF Initiative (maintenance of radiation biology expertise in Germany). The focus of the research is the mechanism of DNA repair, specifically damage repair aspects arising from radiation-induced reactive oxygen species production. The authors will systematically look at potential accessory proteins associated with primarily base excision repair using molecular and biochemical methods. The authors hope to gain knowledge on the initial response mechanisms to varying sources and doses of radiation. By using a highly sensitive marker system, it is intended to achieve a greater resolution of responses induced at lower doses. The work is of relevance for different human diseases caused by defects in DNA repair, e.g. spontaneous and radiation-related cancer. Beyond this, the risk of low radiation doses, for example, in the workplace is of relevance for radiation protection policy and decision-making thereof.
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Affiliation(s)
- Ulrike Schötz
- Department of Radiation Cytogenetics, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
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30
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Jiang Y, Wang Y, Wang Y. In vitro replication and repair studies of tandem lesions containing neighboring thymidine glycol and 8-oxo-7,8-dihydro-2'-deoxyguanosine. Chem Res Toxicol 2010; 22:574-83. [PMID: 19193190 DOI: 10.1021/tx8003449] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactive oxygen species can induce the formation of tandem DNA lesions. We recently showed that the treatment of calf thymus DNA with Cu2+/H2O2/ascorbate could result in the efficient formation of a tandem lesion where a 5,6-dihydroxy-5,6-dihydrothymidine (or thymidine glycol) is situated on the 5' side of an 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG). In the present study, we assessed how the 5'-Tg-(8-oxodG)-3' and 5'-(8-oxodG)-Tg-3' tandem lesions are replicated by purified DNA polymerases and how they are recognized by base excision repair enzymes. Our results revealed that the tandem lesions blocked primer extension mediated by the Klenow fragment and yeast polymerase eta more readily than when the Tg or 8-oxodG was present alone. The mutagenic properties of Tg or 8-oxodG differed while they were present alone or in tandem. Moreover, the human 8-oxoguanine-DNA glycosylase (hOGG1)-mediated cleavage of 8-oxodG was compromised considerably by the presence of a neighboring 5' Tg, whereas the presence of Tg as the adjacent 3' nucleoside enhanced 8-oxodG cleavage by hOGG1. The efficiency for the cleavage of Tg by endonuclease III was not affected by the presence of an adjoining 8-oxodG. These results supported the notion that the replication and repair of tandem single-nucleobase lesions depend on the types of lesions involved and their spatial arrangement.
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Affiliation(s)
- Yong Jiang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521-0403, USA
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31
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Yuan B, Jiang Y, Wang Y, Wang Y. Efficient formation of the tandem thymine glycol/8-oxo-7,8-dihydroguanine lesion in isolated DNA and the mutagenic and cytotoxic properties of the tandem lesions in Escherichia coli cells. Chem Res Toxicol 2010; 23:11-9. [PMID: 20014805 DOI: 10.1021/tx9004264] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Reactive oxygen species can induce the formation of not only single-nucleobase lesions, which have been extensively studied, but also tandem lesions. Herein, we report a high frequency of formation of a type of tandem lesion, where two commonly observed oxidatively induced single-nucleobase lesions, that is, thymidine glycol (Tg) and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), are vicinal to each other in calf thymus DNA upon exposure to Cu(II)/ascorbate along with H(2)O(2) or gamma-rays. We further explored how the tandem lesions perturb the efficiency and fidelity of DNA replication by assessing the replication products formed from the propagation, in Escherichia coli cells, of the single-stranded pYMV1 shuttle vectors containing two tandem lesions [5'-(8-oxodG)-Tg-3' and 5'-Tg-(8-oxodG)-3'] or an isolated Tg or 8-oxodG. The bypass efficiencies for the two tandem lesions were approximately one-half of those for the two isolated single-nucleobase lesions. The presence of an adjacent Tg could lead to significant increases in G-->T transversion at the 8-oxodG site as compared to that of a single 8-oxodG lesion; the frequencies of G-->T mutation were approximately 18, 32, and 28% for 8-oxodG that is isolated, in 5'-(8-oxodG)-Tg-3' and in 5'-Tg-(8-oxodG)-3', respectively. Moreover, both pol IV and pol V are involved, in part, in bypassing the Tg, either present alone or as part of the tandem lesions, in E. coli cells. Together, our results support that complex lesions could exert greater cytotoxic and mutagenic effects than when the composing individual lesions are present alone.
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Affiliation(s)
- Bifeng Yuan
- Department of Chemistry and, Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, USA
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32
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Motorin Y, Lyko F, Helm M. 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res 2009; 38:1415-30. [PMID: 20007150 PMCID: PMC2836557 DOI: 10.1093/nar/gkp1117] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The nucleobase modification 5-methylcytosine (m5C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m5C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in RNA still remain to be elucidated. The recent development of a bisulfite sequencing approach for efficient m5C localization in various RNA molecules puts ribo-m5C in a highly privileged position as one of the few RNA modifications whose detection is amenable to PCR-based amplification and sequencing methods. Additional progress in the field also includes the characterization of several specific RNA methyltransferase enzymes in various organisms, and the discovery of a new and unexpected link between DNA and RNA m5C-methylation. Numerous putative RNA:m5C-MTases have now been identified and are awaiting characterization, including the identification of their RNA substrates and their related cellular functions. In order to bring these recent exciting developments into perspective, this review provides an ordered overview of the detection methods for RNA methylation, of the biochemistry, enzymology and molecular biology of the corresponding modification enzymes, and discusses perspectives for the emerging biological functions of these enzymes.
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Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP Faculté des Sciences et Techniques, Université Henri Poincaré, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
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Brown KL, Roginskaya M, Zou Y, Altamirano A, Basu AK, Stone MP. Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site. Nucleic Acids Res 2009; 38:428-40. [PMID: 19892827 PMCID: PMC2811006 DOI: 10.1093/nar/gkp844] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of epimers paired opposite adenine in the 5′-GTgG-3′ sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) epimer Tg and A are inserted into the helix, remaining in the Watson–Crick alignment. The Tg N3H imine and A N6 amine protons undergo increased solvent exchange. Stacking between Tg and the 3′-neighbor G•C base pair is disrupted. The solvent accessible surface and T2 relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH3 group is favored; propeller twisting of the Tg•A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3′-neighbor guanine alleviate steric clash with the 5′-neighbor base pair. Tg also destabilizes the 5′-neighbor G•C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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Affiliation(s)
- Kyle L Brown
- Department of Chemistry and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37235, USA
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Brown KL, Basu AK, Stone MP. The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA. Biochemistry 2009; 48:9722-33. [PMID: 19772348 PMCID: PMC2761728 DOI: 10.1021/bi900695e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Oxidative damage to 5-methylcytosine in DNA, followed by deamination, yields thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, mispaired with deoxyguanosine. The structure of the 5R Tg·G mismatch pair has been refined using a combination of simulated annealing and isothermal molecular dynamics calculations restrained by NMR-derived distance restraints and torsion angle restraints in 5′-d(G1T2G3C4G5Tg6G7T8T9T10G11T12)-3′·5′-d(A13C14A15A16A17C18G19C20G21C22A23C24)-3′; Tg = 5R Tg. In this duplex the cis-5R,6S:trans-5R,6R equilibrium favors the cis-5R,6S epimer [Brown, K. L., Adams, T., Jasti, V. P., Basu, A. K., and Stone, M. P. (2008) J. Am. Chem. Soc. 130, 11701−11710]. The cis-5R,6S Tg lesion is in the wobble orientation such that Tg6O2 is proximate to G19 N1H and Tg6 N3H is proximate to G19O6. Both Tg6 and the mismatched nucleotide G19 remain stacked in the helix. The Tg6 nucleotide shifts toward the major groove and stacks below the 5′-neighbor base G5, while its complement G19 stacks below the 5′-neighbor C20. In the 3′-direction, stacking between Tg6 and the G7·C18 base pair is disrupted. The solvent-accessible surface area of the Tg nucleotide increases as compared to the native Watson−Crick hydrogen-bonded T·A base pair. An increase in T2 relaxation rates for the Tg6 base protons is attributed to puckering of the Tg base, accompanied by increased disorder at the Tg·G mismatch pair. The axial vs equatorial conformation of the Tg6 CH3 group cannot be determined with certainty from the NMR data. The rMD trajectories suggest that in either the axial or equatorial conformations the cis-5R,6S Tg lesion does not form strong intrastrand hydrogen bonds with the imidazole N7 atom of the 3′-neighbor purine G7. The wobble pairing and disorder of the Tg·G mismatch correlate with the reduced thermodynamic stability of the mismatch and likely modulate its recognition by DNA base excision repair systems.
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Affiliation(s)
- Kyle L Brown
- Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
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35
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Cao H, Jiang Y, Wang Y. Kinetics of deamination and Cu(II)/H2O2/Ascorbate-induced formation of 5-methylcytosine glycol at CpG sites in duplex DNA. Nucleic Acids Res 2009; 37:6635-43. [PMID: 19706732 PMCID: PMC2770644 DOI: 10.1093/nar/gkp615] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mutation in p53 tumor suppressor gene is a hallmark of human cancers. Six major mutational hotspots in p53 contain methylated CpG (mCpG) sites, and C →T transition is the most common mutation at these sites. It was hypothesized that the formation of 5-methylcytosine glycol induced by reactive oxygen species, its spontaneous deamination to thymine glycol and the miscoding property of the latter may account, in part, for the ubiquitous C →T mutation at CpG site. Here, we assessed the kinetics of deamination for two diastereomers of 5-methylcytosine glycol in duplex DNA. Our results revealed that the half-lives for the deamination of the (5S,6S) and (5R,6R) diastereomers of 5-methylcytosine glycol in duplex DNA at 37°C were 37.4 ± 1.6 and 27.4 ± 1.0 h, respectively. The deamination rates were only slightly lower than those for the two diastereomers in mononucleosides. Next, we assessed the formation of 5-methyl-2′-deoxycytidine glycol in the form of its deaminated product, namely, thymidine glycol (Tg), in methyl-CpG-bearing duplex DNA treated with Cu(II)/H2O2/ascorbate. LC-MS/MS quantification results showed that the yield of Tg is similar as that of 5-(hydroxymethyl)-2′-deoxycytidine. Together, our data support that the formation and deamination of 5-methylcytosine glycol may contribute significantly to the C →T transition mutation at mCpG dinucleotide site.
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Affiliation(s)
- Huachuan Cao
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403, USA
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Neidigh JW, Darwanto A, Williams AA, Wall NR, Sowers LC. Cloning and characterization of Rhodotorula glutinis thymine hydroxylase. Chem Res Toxicol 2009; 22:885-93. [PMID: 19341313 DOI: 10.1021/tx8004482] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymine hydroxylase (TH) is a member of the alpha-ketoglutarate-dependent nonheme iron dioxygenase family that includes a series of DNA repair proteins including alkB. Substantial interest in this family of enzymes derives from their capacity to modify DNA bases and precursors by oxidation. Previously, a sequence has been published for cloned Rhodotorula glutinis TH. However, the minimal reported activity of this enzyme, coupled with inconsistencies with previously published mass spectrometry data, compelled us to reexamine TH. The sequence reported here differs from the previously reported sequence at two amino acid positions and is consistent with previously reported mass spectrometry data. The cloned enzyme characterized in this report displayed substantial activity, indicating that the sequence differences are critical for activity. The substrate selectivity of TH against a series of pyrimidine analogues is consistent with that reported for the wild-type enzyme and, in part, explains the mode of selection of uracil analogues. A preliminary model of the active site has been constructed for the purposes of comparing TH with other members of this family. TH and alkB share in common the capacity to oxidize N-methyl groups. However, TH has the added capacity to oxidize the 5-methyl group of thymine, a property that is potentially important for enzymes that could act on DNA and modify DNA-protein interactions.
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Affiliation(s)
- Jonathan W Neidigh
- Department of Basic Sciences, Loma Linda University School of Medicine, Alumni Hall for Basic Science, Room 101, 11021 Campus Street, Loma Linda, California 92350, USA
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Chen ZQ, Zhang CH, Xue Y. Theoretical Studies on the Thermodynamics and Kinetics of the N-Glycosidic Bond Cleavage in Deoxythymidine Glycol. J Phys Chem B 2009; 113:10409-20. [PMID: 19719287 DOI: 10.1021/jp903334j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ze-qin Chen
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, and College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, People’s Republic of China
| | - Cheng-hua Zhang
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, and College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, People’s Republic of China
| | - Ying Xue
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, and College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, People’s Republic of China
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Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009; 324:929-30. [PMID: 19372393 PMCID: PMC3263819 DOI: 10.1126/science.1169786] [Citation(s) in RCA: 1999] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite the importance of epigenetic regulation in neurological disorders, little is known about neuronal chromatin. Cerebellar Purkinje neurons have large and euchromatic nuclei, whereas granule cell nuclei are small and have a more typical heterochromatin distribution. While comparing the abundance of 5-methylcytosine in Purkinje and granule cell nuclei, we detected the presence of an unusual DNA nucleotide. Using thin-layer chromatography, high-pressure liquid chromatography, and mass spectrometry, we identified the nucleotide as 5-hydroxymethyl-2'-deoxycytidine (hmdC). hmdC constitutes 0.6% of total nucleotides in Purkinje cells, 0.2% in granule cells, and is not present in cancer cell lines. hmdC is a constituent of nuclear DNA that is highly abundant in the brain, suggesting a role in epigenetic control of neuronal function.
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Affiliation(s)
- Skirmantas Kriaucionis
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA
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Chan MK, Ocampo-Hafalla MT, Vartanian V, Jaruga P, Kirkali G, Koenig KL, Brown S, Lloyd RS, Dizdaroglu M, Teebor GW. Targeted deletion of the genes encoding NTH1 and NEIL1 DNA N-glycosylases reveals the existence of novel carcinogenic oxidative damage to DNA. DNA Repair (Amst) 2009; 8:786-94. [PMID: 19346169 DOI: 10.1016/j.dnarep.2009.03.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 03/06/2009] [Accepted: 03/09/2009] [Indexed: 02/07/2023]
Abstract
We have generated a strain of mice lacking two DNA N-glycosylases of base excision repair (BER), NTH1 and NEIL1, homologs of bacterial Nth (endonuclease three) and Nei (endonuclease eight). Although these enzymes remove several oxidized bases from DNA, they do not remove the well-known carcinogenic oxidation product of guanine: 7,8-dihydro-8-oxoguanine (8-OH-Gua), which is removed by another DNA N-glycosylase, OGG1. The Nth1-/-Neil1-/- mice developed pulmonary and hepatocellular tumors in much higher incidence than either of the single knockouts, Nth1-/- and Neil1-/-. The pulmonary tumors contained, exclusively, activating GGT-->GAT transitions in codon 12 of K-ras of their DNA. Such transitions contrast sharply with the activating GGT-->GTT transversions in codon 12 of K-ras of the pathologically similar pulmonary tumors, which arose in mice lacking OGG1 and a second DNA N-glycosylase, MUTY. To characterize the biochemical phenotype of the knockout mice, the content of oxidative DNA base damage was analyzed from three tissues isolated from control, single and double knockout mice. The content of 8-OH-Gua was indistinguishable among all genotypes. In contrast, the content of 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) derived from adenine and guanine, respectively, were increased in some but not all tissues of Neil1-/- and Neil1-/-Nth1-/- mice. The high incidence of tumors in our Nth1-/-Neil1-/- mice together with the nature of the activating mutation in the K-ras gene of their pulmonary tumors, reveal for the first time, the existence of mutagenic and carcinogenic oxidative damage to DNA which is not 8-OH-Gua.
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Affiliation(s)
- Michael K Chan
- Department of Pathology and Cancer Institute, New York University School of Medicine, New York, NY, United States
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Abstract
The purpose of this review is to summarize the evidence that can be used to reconstruct the etiology of human cancers from mutations found in tumors. Mutational spectra of the tumor suppressor gene p53 (TP53) are tumor specific. In several cases, these mutational spectra can be linked to exogenous carcinogens, most notably for sunlight-associated skin cancers, tobacco-associated lung cancers, and aristolochic acid-related urothelial tumors. In the TP53 gene, methylated CpG dinucleotides are sequences selectively targeted by endogenous and exogenous mutagenic processes. Recent high-throughput sequencing efforts analyzing a large number of genes in cancer genomes have so far, for the most part, produced mutational spectra similar to those in TP53 but have unveiled a previously unrecognized common G to C transversion mutation signature at GpA dinucleotides in breast cancers and several other cancers. Unraveling the origin of these G to C mutations will be of importance for understanding cancer etiology.
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Radford IR, Lobachevsky PN. Clustered DNA lesion sites as a source of mutations during human colorectal tumourigenesis. Mutat Res 2008; 646:60-8. [PMID: 18824008 DOI: 10.1016/j.mrfmmm.2008.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 08/25/2008] [Accepted: 08/28/2008] [Indexed: 12/01/2022]
Abstract
The role of gene mutations in tumourigenesis is well understood, however, the mechanism(s) by which they arise are less clear. Indeed, the common assumption that tumourigenic mutations are the result of DNA replication errors is apparently contradicted by the very low division frequency of the cells from which tumours are thought to arise (i.e. deep stem cells). As a potential solution to this paradox, we tested a model whereby clustered DNA lesion sites (CLS) (where several lesions occur within a few base pairs of each other on opposing strands) could give rise to mutations in quiescent cells. We used statistical analyses to search for sets of dinucleotide sequences (designated target sequences) that are present at and in close proximity to mutation sites in four genes associated with human colorectal tumourigenesis (adenomatosis polyposis coli (APC), v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), phosphoinositide-3-kinase, catalytic, alpha polypeptide (PIK3CA), and tumour protein p53 (TP53)). The dinucleotides CG, AC-GT, TG, and GC were identified as target sequences in at least three of the genes analysed. Consistent with their designation as target sequences, these dinucleotides have all been identified as high probability sites of oxidative damage formation in in vitro studies. Our results strongly suggest a statistical association between the presence of multiple, clustered target sequences and mutational events. We propose that CLS are a major source of mutations during human tumourigenesis.
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Brown KL, Adams T, Jasti VP, Basu AK, Stone MP. Interconversion of the cis-5R,6S- and trans-5R,6R-thymine glycol lesions in duplex DNA. J Am Chem Soc 2008; 130:11701-10. [PMID: 18681438 PMCID: PMC2646635 DOI: 10.1021/ja8016544] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, is formed in DNA by the reaction of thymine with reactive oxygen species. The 5R Tg lesion was incorporated site-specifically into 5'-d(G(1)T(2)G(3)C(4)G(5)Tg(6)G(7)T(8)T(9)T(10)G(11)T(12))-3'; Tg = 5R Tg. The Tg-modified oligodeoxynucleotide was annealed with either 5'-d(A(13)C(14)A(15)A(16)A(17)C(18)A(19)C(20)G(21)C(22)A(23)C(24))-3', forming the Tg(6) x A(19) base pair, corresponding to the oxidative damage of thymine in DNA, or 5'-d(A(13)C(14)A(15)A(16)A(17)C(18)G(19)C(20)G(21)C(22)A(23)C(24))-3', forming the mismatched Tg(6) x G(19) base pair, corresponding to the formation of Tg following oxidative damage and deamination of 5-methylcytosine in DNA. At 30 degrees C, the equilibrium ratio of cis-5R,6S:trans-5R,6R epimers was 7:3 for the duplex containing the Tg(6) x A (19) base pair. In contrast, for the duplex containing the Tg(6) x G(19) base pair, the cis-5R,6S:trans-5R,6R equilibrium favored the cis-5R,6S epimer; the level of the trans-5R,6R epimer remained below the level of detection by NMR. The data suggested that Tg disrupted hydrogen bonding interactions, either when placed opposite to A(19) or G(19). Thermodynamic measurements indicated a 13 degrees C reduction of T(m) regardless of whether Tg was placed opposite dG or dA in the complementary strand. Although both pairings increased the free energy of melting by 3 kcal/mol, the melting of the Tg x G pair was more enthalpically favored than was the melting of the Tg x A pair. The observation that the position of the equilibrium between the cis-5R,6S and trans-5R,6R thymine glycol epimers in duplex DNA was affected by the identity of the complementary base extends upon observations that this equilibrium modulates the base excision repair of Tg [Ocampo-Hafalla, M. T.; Altamirano, A.; Basu, A. K.; Chan, M. K.; Ocampo, J. E.; Cummings, A., Jr.; Boorstein, R. J.; Cunningham, R. P.; Teebor, G. W. DNA Repair (Amst) 2006, 5, 444-454].
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Affiliation(s)
- Kyle L Brown
- Department of Chemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
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43
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Wang W, Jin L, Wang W, Lu J, Yang J. Theoretical study on the multi-channel reaction of OH radical with 5-methylcytosine. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.07.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Cao H, Wang Y. Quantification of oxidative single-base and intrastrand cross-link lesions in unmethylated and CpG-methylated DNA induced by Fenton-type reagents. Nucleic Acids Res 2007; 35:4833-44. [PMID: 17626047 PMCID: PMC1976268 DOI: 10.1093/nar/gkm497] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methylation of cytosine at CpG sites in mammalian cells plays an important role in the epigenetic regulation of gene expression. Here, we assessed the formation of single-nucleobase lesions and intrastrand cross-link lesions (i.e. G[8-5]C, C[5-8]G, mC[5m-8]G, and G[8-5m]mC, where ‘mC’ represents 5-methylcytosine) in unmethylated and the corresponding CpG-methylated synthetic double-stranded DNA upon treatment with Fenton-type reagents [i.e. H2O2, ascorbate together with Cu(II) or Fe(II)]. Our results showed that the yields of oxidative single-nucleobase lesions were considerably higher than those of the intrastrand cross-link lesions. Although no significant differences were found for the yields of single-base lesions induced from cytosine and mC, the G[8-5m]mC cross-link was induced ∼10 times more efficiently than the G[8-5]C cross-link. In addition, the mC[5m-8]G was induced at a level that was ∼15 times less than G[8-5m]mC, whereas the corresponding C[5-8]G intrastrand cross-link lesion was not detectable. Moreover, Cu(II) is ∼10-fold as effective as Fe(II) in inducing oxidative DNA lesions. These results suggest that oxidative intrastrand cross-link lesions formed at methylated-CpG sites may account for the previously reported mCG→TT tandem double mutations induced by Fenton-type reagents.
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Affiliation(s)
| | - Yinsheng Wang
- *To whom correspondence should be addressed.+1 951 827 2700+1 951 827 4713
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Abstract
This review describes the various manifestations of the pyrimidine system (alkylated, glycosylated, benzo-annelated.). These comprise pyrimidine nucleosides as well as alkaloids and antibiotics--some of them have been discovered and isolated from natural sources already long time ago, others have been reported very recently. A short overview on pyrimidine syntheses (prebiotic synthesis, biosynthesis, and metabolism) is given. The biological activities of most of the pyrimidine analogs are briefly described, and, in some cases, syntheses are formulated.
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Affiliation(s)
- Irene M Lagoja
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven.
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46
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Politzer P, Murray JS. Chapter 8 The average local ionization energy: concepts and applications. THEORETICAL AND COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1016/s1380-7323(07)80009-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47
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Wang Y, Wang Y. Synthesis and thermodynamic studies of oligodeoxyribonucleotides containing tandem lesions of thymidine glycol and 8-oxo-2'-deoxyguanosine. Chem Res Toxicol 2006; 19:837-43. [PMID: 16780363 PMCID: PMC2533691 DOI: 10.1021/tx060032l] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymidine glycol (Tg), which is also known as 5,6-dihydroxy-5,6-dihydrothymidine, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) are two major types of DNA damage products induced by reactive oxygen species (ROS). Here, we report the synthesis of oligodeoxyribonucleotides (ODNs) containing both Tg and 8-oxodG. The dual incorporation of the two single-base lesions was achieved by using a phosphoramidite building block of 8-oxodG with ultramild base protecting group and a building block of Tg whose nucleobase hydroxyl groups were protected with acetyl functionality. The availability of ODNs carrying neighboring 8-oxodG and Tg provided authentic substrates for assessing the formation and examining the replication and repair of this kind of tandem lesions. In addition, thermodynamic parameters derived from melting temperature data revealed that tandem lesions destabilized the double helix to a greater extent than either of the two single-base lesions alone. The thermodynamic results could offer a basis for understanding the repair of the tandem base lesions.
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Affiliation(s)
- Yuesong Wang
- Department of Chemistry, University of California at Riverside, 92521-0403, USA
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48
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Abstract
5-Methylcytosine in DNA is genetically unstable. Methylated CpG (mCpG) sequences frequently undergo mutation resulting in a general depletion of this dinucleotide sequence in mammalian genomes. In human genetic disease- and cancer-relevant genes, mCpG sequences are mutational hotspots. It is an almost universally accepted dogma that these mutations are caused by random deamination of 5-methylcytosines. However, it is plausible that mCpG transitions are not caused simply by spontaneous deamination of 5-methylcytosine in double-stranded DNA but by other processes including, for example, mCpG-specific base modification by endogenous or exogenous mutagens or, alternatively, by secondary factors operating at mCpG sequences and promoting deamination. We also discuss that mCpG sequences are favored targets for specific exogenous mutagens and carcinogens. When adjacent to another pyrimidine, 5-methylcytosine preferentially undergoes sunlight-induced pyrimidine dimer formation. Certain polycyclic aromatic hydrocarbons form guanine adducts and induce G to T transversion mutations with high selectivity at mCpG sequences.
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Affiliation(s)
- G P Pfeifer
- Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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49
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Ocampo-Hafalla MT, Altamirano A, Basu AK, Chan MK, Ocampo JEA, Cummings A, Boorstein RJ, Cunningham RP, Teebor GW. Repair of thymine glycol by hNth1 and hNeil1 is modulated by base pairing and cis-trans epimerization. DNA Repair (Amst) 2006; 5:444-54. [PMID: 16446124 DOI: 10.1016/j.dnarep.2005.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 12/08/2005] [Accepted: 12/12/2005] [Indexed: 10/25/2022]
Abstract
Oxidation of thymine yields 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol. Tg) which, as cis 5S,6R and 5R,6S 2'-deoxyribonucleoside diastereoisomers (dTg1, dTg2), are in equilibrium with their trans 5S,6S and 5R,6R epimers. The stereoselective excision of Tg from DNA by the mammalian orthologs of E. coli DNA N-glycosylase/AP lyases Nth and Nei was reported using substrates in which Tg opposed adenine. Since we showed that Tg is the major product of oxidation of 5-methylcytosine, we asked if the opposing purine influenced stereospecific enzymatic excision. The human ortholog hNth1 released Tg2 much more rapidly than Tg1 regardless of the opposing purine. In contrast, hNeil1 released Tg non-stereoselectively, but the rate of excision was much greater when Tg opposed guanine. Remarkably, the kinetics of excision of Tg by hNth1 and hNeil1 were biphasic, describing a double exponential curve which yielded two rate constants. We suggest that the greater rate constant describes the rate of enzymatic excision of Tg. The smaller rate constant represents the equilibrium constant for the cis and trans epimerization of dTg1 and dTg2 in high molecular weight DNA. Thus, only one of the epimers of dTg1 and dTg2 are enzymatically processed but it is not yet known whether it is cis or trans. Thus, base excision repair of Tg in mammals is mediated by at least two DNA N-glycosylase/AP lyases which are affected by the nature of the diastereoisomer of dTg, the rate of cis-trans epimerization of each diastereoisomer, and the nature of the opposing purine.
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Wirtz M, Schumann CA, Schellenträger M, Gäb S, Vom Brocke J, Podeschwa MAL, Altenbach HJ, Oscier D, Schmitz OJ. Capillary electrophoresis-laser induced fluorescence analysis of endogenous damage in mitochondrial and genomic DNA. Electrophoresis 2005; 26:2599-607. [PMID: 15929058 DOI: 10.1002/elps.200410397] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Reactive oxygen molecules are formed in vivo as by-products of normal aerobic metabolism. All organisms dependent on oxygen are inevitably exposed to these species so that DNA damage can occur in both genomic and mitochondrial DNA (mtDNA). In order to determine endogenous DNA damage we have developed an analytical method that involves the isolation and hydrolysis of genomic DNA or mtDNA, the labeling of modified and unmodified nucleotides and micellar electrokinetic chromatography with laser-induced fluorescence detection. With this method we have found etheno-adenine, thymine glycol, uracil, hypoxanthine, and 5-methylcytosine. These were identified by the addition of internal standards to the genomic or mtDNA. There are a large number of other signals in the electropherograms of mtDNA that we have never found in genomic DNA analysis because they are at lower concentration in the genome. In the DNA of untreated patients with chronic lymphocytic leukemia (CLL), uracil and high levels of etheno-adenine were found, which can be explained by antioxidant enzyme alterations and oxidative stress in the CLL lymphocytes.
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Affiliation(s)
- Michaela Wirtz
- Department of Analytical Chemistry, University of Wuppertal, Wuppertal, Germany
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