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Wang S, Song Y, Wang Y, Li X, Fu B, Liu Y, Wang J, Wei L, Tian T, Zhou X. The m 6A methylation perturbs the Hoogsteen pairing-guided incorporation of an oxidized nucleotide. Chem Sci 2017; 8:6380-6388. [PMID: 29308175 PMCID: PMC5628602 DOI: 10.1039/c7sc02340e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/05/2017] [Indexed: 01/23/2023] Open
Abstract
This study describes the structural implications and properties of m6A in reducing the incorporation of an oxidized nucleotide into DNA.
Natural nucleic acid bases can form Watson–Crick (WC) or Hoogsteen (HG) base pairs. Importantly, 8-oxo-2′-deoxyguanosine (8-oxo-dG) in DNA or 8-oxo-dG 5′-triphosphate (8-oxo-dGTP) favors a syn conformation because of the steric repulsion between O8 and O4′ of the deoxyribose ring. 8-oxo-dGTP can be incorporated into DNA opposite the templating adenine (A) using HG pairing as the dominant mechanism. Both RNA and DNA can be methylated at the N6 position of A to form N6-methyladenine (m6A). It has been found that certain viral infections may trigger an increase in the production of both 8-oxo-dGTP and m6A. The current study aims to systematically explore the effects of m6A methylation on HG base pairs and the consequent nucleotide incorporation. Our thermodynamic melting study shows that the m6A·8-oxo-dG is significantly less stable than the A·8-oxo-dG base pair in the paired region of a DNA duplex. Moreover, we have used pre-steady-state kinetics to examine the incorporation of 8-oxo-dGTP opposite m6A relative to A by a variety of reverse transcriptase (RT) enzymes and DNA polymerase (DNA pol) enzymes such as the human immunodeficiency virus type 1 (HIV-1) RT and human DNA pol β. The results demonstrate that all of these enzymes incorporate 8-oxo-dGTP less efficiently opposite m6A relative to A. Considering the steric bulk of the purine–purine pair between 8-oxo-dG and A, m6A methylation may affect the HG pairing to a great extent. Hence, it will be unfavorable to incorporate 8-oxo-dGTP into the growing strand opposite m6A. Moreover, the impeded incorporation of 8-oxo-dGTP opposite m6A has been extended to determine m6A at pre-defined positions in human rRNA. Our study may provide new insights into the roles of m6A in reducing the mutagenic potential of cellular 8-oxo-dGTP.
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Affiliation(s)
- Shaoru Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Yanyan Song
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Yafen Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Xin Li
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Boshi Fu
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Yinong Liu
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Jiaqi Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Lai Wei
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Tian Tian
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , Wuhan University , Wuhan , Hubei 430072 , P. R. China . ; ; ; Tel: +86-27-68756663
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Ande A, McArthur C, Ayuk L, Awasom C, Achu PN, Njinda A, Sinha N, Rao PSS, Agudelo M, Nookala AR, Simon S, Kumar A, Kumar S. Effect of mild-to-moderate smoking on viral load, cytokines, oxidative stress, and cytochrome P450 enzymes in HIV-infected individuals. PLoS One 2015; 10:e0122402. [PMID: 25879453 PMCID: PMC4399877 DOI: 10.1371/journal.pone.0122402] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/21/2015] [Indexed: 01/05/2023] Open
Abstract
Mild-to-moderate tobacco smoking is highly prevalent in HIV-infected individuals, and is known to exacerbate HIV pathogenesis. The objective of this study was to determine the specific effects of mild-to-moderate smoking on viral load, cytokine production, and oxidative stress and cytochrome P450 (CYP) pathways in HIV-infected individuals who have not yet received antiretroviral therapy (ART). Thirty-two human subjects were recruited and assigned to four different cohorts as follows: a) HIV negative non-smokers, b) HIV positive non-smokers, c) HIV negative mild-to-moderate smokers, and d) HIV positive mild-to-moderate smokers. Patients were recruited in Cameroon, Africa using strict selection criteria to exclude patients not yet eligible for ART and not receiving conventional or traditional medications. Those with active tuberculosis, hepatitis B or with a history of substance abuse were also excluded. Our results showed an increase in the viral load in the plasma of HIV positive patients who were mild-to-moderate smokers compared to individuals who did not smoke. Furthermore, although we did not observe significant changes in the levels of most pro-inflammatory cytokines, the cytokine IL-8 and MCP-1 showed a significant decrease in the plasma of HIV-infected patients and smokers compared with HIV negative non-smokers. Importantly, HIV-infected individuals and smokers showed a significant increase in oxidative stress compared with HIV negative non-smoker subjects in both plasma and monocytes. To examine the possible pathways involved in increased oxidative stress and viral load, we determined the mRNA levels of several antioxidant and cytochrome P450 enzymes in monocytes. The results showed that the levels of most antioxidants are unaltered, suggesting their inability to counter oxidative stress. While CYP2A6 was induced in smokers, CYP3A4 was induced in HIV and HIV positive smokers compared with HIV negative non-smokers. Overall, the findings suggest a possible association of oxidative stress and perhaps CYP pathway with smoking-mediated increased viral load in HIV positive individuals.
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Affiliation(s)
- Anusha Ande
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Carole McArthur
- Department of Oral and Craniofacial Science, School of Dentistry, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Leo Ayuk
- Regional Hospital, Box 818, Bamenda, North West Province, Cameroon
| | - Charles Awasom
- Regional Hospital, Box 818, Bamenda, North West Province, Cameroon
| | - Paul Ngang Achu
- Mezam Polyclinic HIV/AIDS Treatment Center, Bamenda, Cameroon
| | - Annette Njinda
- Mezam Polyclinic HIV/AIDS Treatment Center, Bamenda, Cameroon
| | - Namita Sinha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - P. S. S. Rao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Marisela Agudelo
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Anantha Ram Nookala
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Stephen Simon
- Department of Medical Informatics, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Anil Kumar
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Santosh Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail:
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Reactive oxygen species hydrogen peroxide mediates Kaposi's sarcoma-associated herpesvirus reactivation from latency. PLoS Pathog 2011; 7:e1002054. [PMID: 21625536 PMCID: PMC3098240 DOI: 10.1371/journal.ppat.1002054] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 03/16/2011] [Indexed: 01/17/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) establishes a latent
infection in the host following an acute infection. Reactivation from latency
contributes to the development of KSHV-induced malignancies, which include
Kaposi's sarcoma (KS), the most common cancer in untreated AIDS patients,
primary effusion lymphoma and multicentric Castleman's disease. However,
the physiological cues that trigger KSHV reactivation remain unclear. Here, we
show that the reactive oxygen species (ROS) hydrogen peroxide
(H2O2) induces KSHV reactivation from latency through
both autocrine and paracrine signaling. Furthermore, KSHV spontaneous lytic
replication, and KSHV reactivation from latency induced by oxidative stress,
hypoxia, and proinflammatory and proangiogenic cytokines are mediated by
H2O2. Mechanistically, H2O2
induction of KSHV reactivation depends on the activation of mitogen-activated
protein kinase ERK1/2, JNK, and p38 pathways. Significantly,
H2O2 scavengers N-acetyl-L-cysteine (NAC), catalase
and glutathione inhibit KSHV lytic replication in culture. In a mouse model of
KSHV-induced lymphoma, NAC effectively inhibits KSHV lytic replication and
significantly prolongs the lifespan of the mice. These results directly relate
KSHV reactivation to oxidative stress and inflammation, which are physiological
hallmarks of KS patients. The discovery of this novel mechanism of KSHV
reactivation indicates that antioxidants and anti-inflammation drugs could be
promising preventive and therapeutic agents for effectively targeting KSHV
replication and KSHV-related malignancies. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of all
clinical forms of Kaposi's sarcoma (KS) and several other malignancies. The
life cycle of KSHV consists of latent and lytic phases. While establishment of
viral latency is essential for KSHV to evade host immune surveillances, viral
lytic replication promotes KSHV-induced malignancies. In this study, we show
that the reactive oxygen species (ROS) hydrogen peroxide
(H2O2) induces KSHV reactivation from latency.
Furthermore, induction of KSHV reactivation by oxidative stress, hypoxia, and
proinflammatory and proangiogenic cytokines, which are physiological hallmarks
in all clinical forms of KS patients, is mediated by H2O2.
Significantly, antioxidants inhibit H2O2-induced KSHV
lytic replication in culture and in a mouse model of KSHV-induced lymphoma.
These results show that ROS is likely an important physiological cue that
triggers KSHV replication. The discovery of this novel mechanism of KSHV
reactivation indicates that antioxidants and anti-inflammation drugs might be
promising preventive and therapeutic agents for effectively targeting KSHV
replication and KSHV-related malignancies.
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Ibeh BO, Obidoa O, Uzoegwu PN. High plasma activity of endogenous antioxidants protect CD4+ T-cells in HIV-serodiscordant heterosexual partners in a Nigerian population. Int J STD AIDS 2008; 19:536-40. [PMID: 18663040 DOI: 10.1258/ijsa.2008.008031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antioxidants significantly inhibit oxidative processes. The study seeks to determine the activity of endogenous antioxidants and CD4+ T-cell expression in HIV-serodiscordant-heterosexual partners. The case-control study had the following groups; A- (13 serodiscordant-seronegative subjects), B- (13 serodiscordant-seropositive subjects) and C/control- (13 healthy volunteers). CD4+ T-cell expression was determined using a FACScan (fluorescent activated cell sorting) flow cytometer. CAT (catalase), superoxide dismutase, glutathione peroxidase (GHPX) and glutathione S-transferase (GST) activities were assayed using spectrophotometer. The activities of SOD, GHPX, GST and CAT were significantly (P < 0.05) increased by 164.7% (0.090 +/- 0.032), 126% (662 +/- 96), 355.2% (22.023 +/- 1.4) and 119.1% (2.76 +/- 0.10), respectively, in group A when compared with B. The mean CD4+ T-cell (1348 +/- 142) showed a significant (P < 0.05) increase by 237% when compared with group B (400 +/- 182). Conversely, group B revealed a significant (P < 0.05) decrease in activity by 86.5% (CAT), 76.5% (SOD), 106.8% (GHPX) and 81.8% (GST) when compared with C. CD4+ T-cells in groups A and C (1390 +/- 190) did not show any significant decrease (3.11%). The antioxidant activity showed a positive correlation (P < 0.01, r = 0.89) with their respective CD4+ T-cells in groups A and C. Group B showed same positive correlation (P < 0.01, r = 0.76). These results show that high activity of endogenous antioxidants may have a protective role on CD4+ T-cells, which limits HIV infection.
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Affiliation(s)
- Bartholomew O Ibeh
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria Nsukka, Nigeria.
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Ferreira HB, Castro LAD. A preliminary survey of M. hyopneumoniae virulence factors based on comparative genomic analysis. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000200012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Aruoma OI, Spencer JP, Mahmood N. Protection against oxidative damage and cell death by the natural antioxidant ergothioneine. Food Chem Toxicol 1999; 37:1043-53. [PMID: 10566875 DOI: 10.1016/s0278-6915(99)00098-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The natural antioxidant ergothioneine (EGT) was tested for its ability to inhibit cell death caused by hydrogen peroxide (H2O2) and to inhibit DNA oxidation by peroxynitrite (ONOO-) in human neuronal hybridoma cell line (N-18-RE-105). High concentrations of EGT (5 mM) were tolerated by the N-18-RE-105 cells. N-acetylcysteine (NAC) was not well tolerated by the cells at concentrations greater than 3 mM (cell viability averaged 50%). Increasing concentrations of EGT increases cell viability in the presence of NAC. EGT at concentrations up to 2 mM weakly improved cell viability in the presence of H2O2. NAC at concentrations up to 2 mM weakly decreased, but not significantly, the viability of the cells. At a higher concentration of 5 mM, NAC weakly protected the neuronal cells against the H2O2-induced cell death. The protection was significantly enhanced by preincubation with EGT. Ergothioneine inhibited ONOO(-)-induced oxidative damage in isolated calf thymus DNA and DNA in N-18-RE-105 cells. The concentration of EGT in human and mammalian tissue has been estimated to be 1-2 mM, which suggests that EGT may serve as a non-toxic thiol buffering antioxidant in vivo and may find applications in pharmaceutical preparations where oxidative stability is desired.
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Affiliation(s)
- O I Aruoma
- Department of Biology, Imperial College of Science, Technology and Medicine, London, UK
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Peterhans E. Oxidants and antioxidants in viral diseases: disease mechanisms and metabolic regulation. J Nutr 1997; 127:962S-965S. [PMID: 9164274 DOI: 10.1093/jn/127.5.962s] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Reactive oxygen and nitrogen metabolites play a complex role in many diseases and in metabolic regulation. Because viruses replicate in living cells, such metabolites influence the growth of viruses in addition to serving as a host defense mechanism. Low levels of reactive oxygen species (ROS) play a role in mitogenic activation, and the early phase of lytic and nonlytic virus infection indeed resembles that of mitogenic cell activation. In addition to these subtle cell-activating effects shared by many viruses, influenza and paramyxoviruses activate a respiratory burst in phagocytic cells. These viruses are toxic when injected in animals. Cells lavaged from the lungs of mice infected with influenza virus are primed for enhanced superoxide generation. Moreover, xanthine oxidase is enhanced and the buffering capacity of small molecular antioxidants is decreased in the lungs, suggesting that infection leads to oxidative stress. The wide array of cytokines produced in the lungs during influenza could contribute to the systemic effects of influenza. Oxidative stress has also been shown in human immunodeficiency virus (HIV) infection in humans. Via activation of NF kappa B, ROS may activate viral replication, but oxidants are believed to contribute also to the loss of CD4 T cells by apoptosis. Antioxidants, together with agents interfering with the harmful effects of cytokines and lipid mediators, may have a role in the treatment of viral diseases. Such agents could not only alleviate disease symptoms but also decrease the long-term effects of chronic oxidative stress, which have been linked to the development of cancer in some viral infections.
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Affiliation(s)
- E Peterhans
- Institute of Veterinary Virology, University of Berne, Switzerland
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Abstract
Metabolites derived from superoxide (O2.-) and nitric oxide (NO.) play an important role in antimicrobial and antitumoral defense, but may also harm the host. Low levels of such metabolites can also facilitate viral replication because of their mitogenic effects on cells. Most viruses grow better in proliferating cells, and indeed, many viruses induce in their host cell changes similar to those seen early after treatment with mitogenic lectins. Influenza and paramyxo-viruses activate in phagocytes in the generation of superoxide by a mechanism involving the interaction between the viral surface glycoproteins and the phagocyte's plasma membrane. Interestingly, viruses that activate this host defense mechanism are toxic when injected in the bloodstream of animals. Mice infected with influenza virus undergo oxidative stress. In addition, a wide array of cytokines are formed in the lung, contributing to the systemic effects of influenza. Oxidative stress is seen also in chronic viral infections, such as AIDS and viral hepatitis. Oxidant production in viral hepatitis may contribute to the emergence of hepatocellular carcinoma, a tumor seen in patients after years of chronic inflammation of the liver. Antioxidants and agents that downregulate proinflammatory cytokines and lipid mediators may be a useful complement to specific antiviral drugs in the therapy of viral diseases.
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Affiliation(s)
- E Peterhans
- Institute of Veterinary Virology, University of Berne, Switzerland.
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Aruoma OI, Spencer JP, Rossi R, Aeschbach R, Khan A, Mahmood N, Munoz A, Murcia A, Butler J, Halliwell B. An evaluation of the antioxidant and antiviral action of extracts of rosemary and Provençal herbs. Food Chem Toxicol 1996; 34:449-56. [PMID: 8655093 DOI: 10.1016/0278-6915(96)00004-x] [Citation(s) in RCA: 161] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Extracts of herbs and spices are increasingly of interest in the food industry because they retard oxidative degradation of lipids. There is also increasing interest in the antiviral activity of plant products. A liquid, deodorized rosemary extract and an oily extract of a mixture of Provençal herbs were tested for antioxidant and antiviral action in vitro. The rosemary extract (Herbor 025) and the extract of Provençal herbs (Spice Cocktail) inhibited peroxidation of phospholipid liposomes with 50% inhibition concentration values of 0.0009% (v/v) and 0.0035% (v/v), respectively. Herbor 025 and the spice cocktail (at 0.2%, v/v) reacted with trichloromethylperoxyl radical with calculated rates of 2.7 x 10(4) s-1 and 1.5 x 10(3) s-1, respectively. The main active components in the herbal preparations, carnosol and carnosic acid, at 0.05% (v/v) react with rate constants of (1-3) x 10(6) M-1 sec-1 and 2.7 x 10(7) M-1 sec-1, respectively. Both extracts show good antioxidant activity in the Rancimat test, especially in lard. Herbor 025 and the spice cocktail inhibited human immunodeficiency virus (HIV) infection at very low concentrations which were also cytotoxic. However, purified carnosol exhibited definite anti-HIV activity at a concentration (8 microM) which was not cytotoxic. Both preparations promoted some DNA damage in the copper-phenanthroline and the bleomycin-iron systems. The two herbal preparations possess antioxidant properties that may make them useful in the food matrix.
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Affiliation(s)
- O I Aruoma
- Pharmacology Group, University of London King's College, UK
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Spencer JP, Jenner A, Chimel K, Aruoma OI, Cross CE, Wu R, Halliwell B. DNA strand breakage and base modification induced by hydrogen peroxide treatment of human respiratory tract epithelial cells. FEBS Lett 1995; 374:233-6. [PMID: 7589542 DOI: 10.1016/0014-5793(95)01117-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Treatment of human respiratory tract epithelial cells with H2O2 led to concentration-dependent DNA strand breakage that was highly-correlated with multiple chemical modifications of all four DNA bases, suggesting that damage is due to hydroxyl radical, OH. However, the major base damage occurred to adenine. Hence, conclusions made about the occurrence and the extent of oxidative DNA damage on the basis only of changes in 8-hydroxyguanine should be approached with caution.
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Affiliation(s)
- J P Spencer
- Neurodegenerative Disease Research Centre, University of London King's College, UK
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