Increase, Oxidative DNA damage

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.

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.

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).  

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