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Event: 1634

Key Event Title

A descriptive phrase which defines a discrete biological change that can be measured. More help

Increase, Oxidative damage to DNA

Short name
The KE short name should be a reasonable abbreviation of the KE title and is used in labelling this object throughout the AOP-Wiki. More help
Increase, Oxidative DNA damage
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Biological Context

Structured terms, selected from a drop-down menu, are used to identify the level of biological organization for each KE. More help
Level of Biological Organization

Cell term

The location/biological environment in which the event takes place.The biological context describes the location/biological environment in which the event takes place.  For molecular/cellular events this would include the cellular context (if known), organ context, and species/life stage/sex for which the event is relevant. For tissue/organ events cellular context is not applicable.  For individual/population events, the organ context is not applicable.  Further information on Event Components and Biological Context may be viewed on the attached pdf. More help
Cell term
eukaryotic cell

Organ term

The location/biological environment in which the event takes place.The biological context describes the location/biological environment in which the event takes place.  For molecular/cellular events this would include the cellular context (if known), organ context, and species/life stage/sex for which the event is relevant. For tissue/organ events cellular context is not applicable.  For individual/population events, the organ context is not applicable.  Further information on Event Components and Biological Context may be viewed on the attached pdf. More help
Organ term

Key Event Components

The KE, as defined by a set structured ontology terms consisting of a biological process, object, and action with each term originating from one of 14 biological ontologies (Ives, et al., 2017; Biological process describes dynamics of the underlying biological system (e.g., receptor signalling).Biological process describes dynamics of the underlying biological system (e.g., receptor signaling).  The biological object is the subject of the perturbation (e.g., a specific biological receptor that is activated or inhibited). Action represents the direction of perturbation of this system (generally increased or decreased; e.g., ‘decreased’ in the case of a receptor that is inhibited to indicate a decrease in the signaling by that receptor).  Note that when editing Event Components, clicking an existing Event Component from the Suggestions menu will autopopulate these fields, along with their source ID and description.  To clear any fields before submitting the event component, use the 'Clear process,' 'Clear object,' or 'Clear action' buttons.  If a desired term does not exist, a new term request may be made via Term Requests.  Event components may not be edited; to edit an event component, remove the existing event component and create a new one using the terms that you wish to add.  Further information on Event Components and Biological Context may be viewed on the attached pdf. More help
Process Object Action
regulation of response to reactive oxygen species reactive oxygen species occurrence

Key Event Overview

AOPs Including This Key Event

All of the AOPs that are linked to this KE will automatically be listed in this subsection. This table can be particularly useful for derivation of AOP networks including the KE.Clicking on the name of the AOP will bring you to the individual page for that AOP. More help
AOP Name Role of event in AOP Point of Contact Author Status OECD Status
Oxidative DNA damage, chromosomal aberrations and mutations MolecularInitiatingEvent Carole Yauk (send email) Open for comment. Do not cite WPHA/WNT Endorsed
Energy deposition leading to population decline via DNA oxidation and follicular atresia KeyEvent You Song (send email) Under development: Not open for comment. Do not cite
Energy deposition leading to population decline via DNA oxidation and oocyte apoptosis KeyEvent You Song (send email) Under development: Not open for comment. Do not cite
Deposition of energy leading to cataracts KeyEvent Vinita Chauhan (send email) Open for citation & comment

Taxonomic Applicability

Latin or common names of a species or broader taxonomic grouping (e.g., class, order, family) that help to define the biological applicability domain of the KE.In many cases, individual species identified in these structured fields will be those for which the strongest evidence used in constructing the AOP was available in relation to this KE. More help
Term Scientific Term Evidence Link
human and other cells in culture human and other cells in culture Moderate NCBI
yeast Saccharomyces cerevisiae Low NCBI
mouse Mus musculus High NCBI
rat Rattus norvegicus Low NCBI
bovine Bos taurus Low NCBI
human Homo sapiens High NCBI
rabbit Oryctolagus cuniculus Low NCBI

Life Stages

An indication of the the relevant life stage(s) for this KE. More help
Life stage Evidence
All life stages High

Sex Applicability

An indication of the the relevant sex for this KE. More help
Term Evidence
Unspecific Moderate

Key Event Description

A description of the biological state being observed or measured, the biological compartment in which it is measured, and its general role in the biology should be provided. More help

The nitrogenous bases of DNA are susceptible to oxidation in the presence of oxidizing agents. Oxidative adducts form mainly on C5 and to a lesser degree on C6 of thymine and cytosine, and on C8 of guanine and adenine. Guanine is most prone to oxidation due to its low oxidation potential (Jovanovic and Simic, 1986). Indeed, 8-oxo-2’-deoxyguanosine (8-oxodG)/8-hydroxy-2’-deoxyguanosine (8-OHdG) is the most abundant and well-studied oxidative DNA lesion in the cell (Swenberg et al., 2011). It causes an A(anti):8-oxo-G(syn) mispair instead of the normal C(anti):8-oxo-G(syn) pair. This pairing does not cause large structural changes to the DNA backbone, and therefore remains undetected by the polymerase’s proofreading mechanism. Consequently, one of the daughter strands will have an AT pair instead of the correct GC pair after replication (Markkanen, 2017). 

Formamidopyrimidine lesions on guanine and adenine (FaPyG and FaPyA), 8-hydroxy-2'-deoxyadenine (8-oxodA), and thymidine glycol (Tg) are other common oxidative lesions. We refer the reader to reviews on this topic to see the full set of potential oxidative DNA lesions (Whitaker et al., 2017). Oxidative DNA lesions are present in the cell at a steady state due to endogenous redox processes (Swenberg et al., 2010). Under normal conditions, cells are able to withstand the baseline level of oxidized bases through efficient repair and regulation of free radicals in the cell. However, direct chemical insult from specific compounds, exposure to various forms of radiation, or induction of reactive oxygen species (ROS) from the reduction of endogenous molecules, as well as through the release of inflammatory cell-derived oxidants, can lead to increased DNA oxidation, a state known as oxidative stress (Turner et al., 2002; Schoenfeld et al., 2012; Tangvarasittichai and Tangvarasittichai, 2019). It is worth noting that ROS must be generated near the DNA to cause damage, otherwise, if ROS was produced more distantly, then it can be removed by the cell (Nilsson & Liu, 2020). Furthermore, although cells do possess repair mechanisms to deal with oxidative DNA damage, sometimes the repair intermediates can interfere with genome function or decrease stability of the genome. This creates a balancing act between when it is best to repair damage and when it is best to leave it (Poetsch, 2020a). 

This KE describes an increase in oxidative lesions of a broad spectrum (ie. superoxide radical (O2•−), hydroxyl radical (OH), peroxyl radical (RO22), single oxygen (1O2 ) in the nuclear DNA above the steady-state level. Oxidative DNA damage can occur in any cell type with nuclear DNA under oxidative stress.

How It Is Measured or Detected

A description of the type(s) of measurements that can be employed to evaluate the KE and the relative level of scientific confidence in those measurements.These can range from citation of specific validated test guidelines, citation of specific methods published in the peer reviewed literature, or outlines of a general protocol or approach (e.g., a protein may be measured by ELISA). Do not provide detailed protocols. More help

Relative Quantification of Oxidative DNA Lesions

  • Comet assay (single cell gel electrophoresis) with Fpg and hOGG1 modifications (Smith et al., 2006; Platel et al., 2011)
    • Oxoguanine glycosylase (hOGG1) and formamidopyrimidine-DNA glycosylase (Fpg) are base excision repair (BER) enzymes in eukaryotic and prokaryotic cells, respectively
    • Both enzymes are bi-functional; the glycosylase function cleaves the glycosidic bond between the ribose and the oxidized base, giving rise to an abasic site, and the apurinic/apymidinic (AP) site lyase function cleaves the phosphodiester bond via β-elimination reaction and creates a single strand break
    • Treatment of DNA with either enzyme prior to performing the electrophoresis step of the comet assay allows detection of oxidative lesions by measuring the increase in comet tail length when compared against untreated samples.
  • Enzyme-linked immunosorbant assay (ELISA) (Dizdaroglu et al., 2002; Breton et al., 2003; Xu et al., 2008; Zhao et al. 2017)
    • 8-oxodG can be detected using immunoassays, such as ELISA, that use antibodies against 8-oxodG lesions. It has been noted that immunodetection of 8-oxodG can be interfered by certain compounds in biological samples.

Absolute Quantification of Oxidative DNA Lesions

  • Quantification of 8-oxodG using HPLC-EC  (Breton et al., 2003; Chepelev et al., 2015)
    • 8-oxodG can be separated from digested DNA and precisely quantified using high performance liquid chromatography (HPLC) with electrochemical detection
  • Mass spectrometry LC-MRM/MS (Mangal et al., 2009)
    • Liquid chromatography can also be coupled with multiple reaction monitoring/ mass spectrometry to detect and quantify oxidative lesions. Correlation between lesions measured by hOGG1-modified comet assay and LC-MS has been reported

Gas chromatography-mass spectrometry (GC-MS) 

  • DNA is hydrolyzed to release either free bases or nucleosides and then undergoes derivatization in order to increase their volatility. Finally, samples run through a gas chromatograph and then a mass spectrometer. The mass spectrometer results are used to determine oxidative DNA damage by identifying modified bases or nucleosides (Dizdaroglu, 1994). 

Sequencing assays 

  • Various markers are used to detect and highlight sites of DNA damage; the result is then processed and sequenced. This category encompasses a wide range of assays such as snAP-seq, OGG1-AP-seq, oxiDIP-seq, OG-seq, and click-code-seq (Yun et al., 2017; Wu et al., 2018; Amente et al., 2019; Poetsch, 2020b). 
  • We note that other types of oxidative lesions can be quantified using the methods described above.

Domain of Applicability

A description of the scientific basis for the indicated domains of applicability and the WoE calls (if provided).  More help

Taxonomic applicability: Theoretically, DNA oxidation can occur in any cell type, in any organism. Oxidative DNA lesions have been measured in mammalian cells (human, mouse, calf, rat) in vitro and in vivo, and in prokaryotes.

Life stage applicability: This key event is not life stage specific (Mesa & Bassnett, 2013; Suman et al., 2019). 

Sex applicability: This key event is not sex specific (Mesa & Bassnett, 2013). 

Evidence for Perturbation by Prototypic Stressor: H2O2 and KBrO3 – A concentration-dependent increase in oxidative lesions was observed in both Fpg- and hOGG1-modified comet assays of TK6 cells treated with increasing concentrations of glucose oxidase (an enzyme that generates H2O2) and potassium bromate for 4 h (Platel et al., 2011).  

Evidence indicates that oxidative DNA damage is also induced by X-rays (Bahia et al., 2018), 60Co γ-rays, 12C ions, α particles, electrons (Georgakilas, 2013), UVB (Mesa and Bassnett, 2013), γ-rays, 56Fe ions (Datta et al., 2012), and protons (Suman et al., 2019).  


List of the literature that was cited for this KE description. More help

Amente, S. et al. (2019), “Genome-wide mapping of 8-oxo-7,8-dihydro-2’-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells”, Nucleic Acids Research 2019, Vol. 47/1, Oxford University Press, England, 

Bahia, S. et al. (2018), “Oxidative and nitrative stress-related changes in human lens epithelial cells following exposure to X-rays”, International journal of radiation biology, Vol. 94/4, England, 

Breton J, Sichel F, Bainchini F, Prevost V. (2003). Measurement of 8-Hydroxy-2′-Deoxyguanosine by a Commercially Available ELISA Test: Comparison with HPLC/Electrochemical Detection in Calf Thymus DNA and Determination in Human Serum. Anal Lett 36:123-134.

Cabrera, M. P., R. Chihuailaf and F. Wittwer Menge (2011), “Antioxidants and the integrity of ocular tissues”, Veterinary medicine international, Vol. 2011, SAGE-Hindawi Access to Research, United States, 

Cadet, J. et al. (2012), “Oxidatively generated complex DNA damage: tandem and clustered lesions”, Cancer letters, Vol. 327/1, Elsevier Ireland Ltd, Ireland. 

Chepelev N, Kennedy D, Gagne R, White T, Long A, Yauk C, White P. (2015). HPLC Measurement of the DNA Oxidation Biomarker, 8-oxo-7,8-dihydro-2'-deoxyguanosine, in Cultured Cells and Animal Tissues. Journal of Visualized Experiments 102:e52697.

Collins, A. R. (2014), “Measuring oxidative damage to DNA and its repair with the comet assay”, Biochimica et biophysica acta. General subjects, Vol. 1840/2, Elsevier B.V., 

Datta, K. et al. (2012), “Exposure to heavy ion radiation induces persistent oxidative stress in mouse intestive”, PloS One, Vol. 7/8, Public Library of Science, United States, 

Dizdaroglu, M. (1994), “Chemical determination of oxidative DNA damage by gas chromatography-mass spectrometry”, Methods in Enzymology, Vol. 234, Elsevier Science & Technology, United States, 10.1016/0076-6879(94)34072-2 

Dizdaroglu, M. et al. (2002), “Free radical-induced damage to DNA : mechanisms and measurement”, Free radical biology & medicine, Vol. 32/11, United States, pp. 1102-1115 

Eaton, J. W. (1995), “UV-mediated cataractogenesis: a radical perspective”, Documenta ophthalmologica, Vol. 88/3-4, Springer, Dordrecht, 

Fletcher, A. E. (2010), “Free radicals, antioxidants and eye diseases: evidence from epidemiological studies on cataract and age-related macular degeneration”, Ophthalmic Research, Vol. 44/3, Karger international, Basel, 

Georgakilas, A. G et al. (2013), “Induction and repair of clustered DNA lesions: what do we know so far?”, Radiation Research, Vol. 180/1, The Radiation Research Society, United States, 

Jose, D. et al. (2009). “Spectroscopic studies of position-specific DNA “breathing” fluctuations at replication forks and primer-template junctions”, Proceedings of the National Academy of Sciences of the United States of America, Vol. 106/11, 

Jovanovic S, Simic M. (1986). One-electron redox potential of purines and pyrimidines. J Phys Chem 90:974-978.

Kruk, J., K. Kubasik-Kladna and H. Y. Aboul-Enein (2015), “The role oxidative stress in the pathogenesis of eye diseases: current status and a dual role of physical activity”, Mini-reviews in medicinal chemistry, Vol. 16/3, Bentham Science Publishers Ltd, Netherlands, 

Lee, J. et al. (2004), “Reactive oxygen species, aging, and antioxidative nutraceuticals”, Comprehensive reviews in food science and food safety, Vol. 3/1, Blackwell Publishing Ltd, Oxford, 

Mangal D, Vudathala D, Park J, Lee S, Penning T, Blair I. (2009). Analysis of 7,8-Dihydro-8-oxo-2′-deoxyguanosine in Cellular DNA during Oxidative Stress. Chem Res Toxicol 22:788-797.

Markkanen, E. (2017), “Not breathing is not an option: How to deal with oxidative DNA damage”, DNA repair, Vol. 59, Elsevier B.V., Netherlands, 

Mesa, R. and S. Bassnett (2013), “UV-B induced DNA damage and repair in the mouse lens”, Investigative ophthalmology & visual science, Vol. 54/10, the Association for Research in Vision and Ophthalmology, United States, 

Nilsson R. and Liu N. (2020), “Nuclear DNA damages generated by reactive oxygen molecules (ROS) under oxidative stress and their relevance to human cancers, including ionizing radiation-induced neoplasia part I: Physical, chemical and molecular biology aspects”, Radiation Medicine and Protection, Vol. 1/3(3), 

Pendergrass, W. et al. (2010), “X-ray induced cataract is preceded by LEC loss, and coincident with accumulation of cortical DNA, and ROS; similarities with age-related cataracts”, Molecular vision, Vol. 16, Molecular Vision, United States, pp. 1496-1513 

Platel A, Nesslany F, Gervais V, Claude N, Marzin D. (2011). Study of oxidative DNA damage in TK6 human lymphoblastoid cells by use of the thymidine kinase gene-mutation assay and the in vitro modified comet assay: Determination of No-Observed-Genotoxic-Effect-Levels. Mutat Res 726:151-159.

Poetsch, Anna R. (2020a), “The genomics of oxidative DNA damage, repair, and resulting mutagenesis”, Computational and structural biotechnology journal 2020, Vol. 18, Elsevier B.V., Netherlands 

Poetsch, A. R. (2020b), “AP-Seq: A method to measure apurinic sites and small base adducts genome-wide”, The Nucleus, Springer US, New York, Sacca, S. C. et al. (2009), “Gene-environment interactions in ocular diseases”, Mutation research – fundamental and molecular mechanisms of mutagenesis, Vol. 667/1-2, Elsevier, Amsterdam, 

Schoenfeld, M. P. et al. (2012), “A hypothesis on biological protection from space radiation through the use of new therapeutic gases as medical counter measures”, Medical gas research, Vol. 2/1, BioMed Central Ltd, India, 

Smith C, O'Donovan M, Martin E. (2006). hOGG1 recognizes oxidative damage using the comet assay with greater specificity than FPG or ENDOIII. Mutagenesis 21:185-190.

Stohs, S. J. (1995), “The role of free radicals in toxicity and disease”, Journal of Basic and Clinical Physiology and Pharmacology, Vol. 6/3-4, Freund Publishing House Ltd, 

Suman, S. et al. (2019), “Fractionated and acute proton radiation show differential intestinal tumorigenesis and DNA damage and repair pathway response in ApcMin/+ mice”, International Journal of Radiation Oncology, Biology, Physics, Vol. 105/3, Elsevier Inc, 

Swenberg J. et al. (2011). "Endogenous versus Exogenous DNA Adducts: Their Role in Carcinogenesis, Epidemiology, and Risk Assessment." Toxicol Sci 120:S130-S145.

Tangvarasittichai, O and S. Tangvarasittichai (2018), “Oxidative stress, ocular disease, and diabetes retinopathy”, Current Pharmaceutical Design, Vol. 24/40, Bentham Science Publishers, 

Turner, N. D. et al. (2002), “Opportunities for nutritional amelioration of radiation-induced cellular damage”, Nutrition, Vol. 18/10, Elsevier Inc, New York, 

Whitaker A, Schaich M, Smith MS, Flynn T, Freudenthal B. (2017). Base excision repair of oxidative DNA damage: from mechanism to disease. Front Biosci 22:1493-1522.

Wu, J. (2018), “Nucleotide-resolution genome-wide mapping of oxidative DNA damage by click-code-seq”, Journal of the American Chemical Society 2018, American Chemical Society, United States 

Xu, X. et al. (2008). “Fluorescence recovery assay for the detection of protein-DNA binding”, Analytical Chemistry, Vol. 80/14, 

Zhao M, Howard E, Guo Z, Parris A, Yang X. (2017). p53 pathway determines the cellular response to alcohol-induced DNA damage in MCF-7 breast cancer cells. PLoS One 12:e0175121.