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DNA oxidation

DNA oxidation is the process by which (ROS), such as anion, , and , chemically modify the structure of DNA, primarily targeting nucleobases and the sugar-phosphate backbone, leading to lesions that impair genetic fidelity and cellular function. This oxidative damage arises as a byproduct of aerobic metabolism and environmental exposures, representing a major endogenous and exogenous threat to genomic stability in living organisms. The primary causes of DNA oxidation include endogenous sources from normal cellular processes, such as mitochondrial activity during , which generates ROS at rates sufficient to produce thousands of oxidative events per daily. Exogenous factors exacerbate this damage, including , light, air pollutants, , and certain chemicals that elevate ROS levels. Among the most prevalent lesions is 8-oxoguanine (8-oxoG), formed by the oxidation of at the C8 position due to its low , occurring at an estimated frequency of about 0.5 lesions per million base pairs in cells. Other notable modifications include thymine glycol, 5-hydroxymethyluracil, strand breaks, and DNA-protein crosslinks, which collectively contribute to clustered damage sites that are particularly challenging for repair. Cells counteract DNA oxidation through sophisticated repair pathways, predominantly base excision repair (BER), where enzymes like 8-oxoguanine DNA glycosylase (OGG1) recognize and excise 8-oxoG, creating an abasic site that is processed by apurinic/apyrimidinic endonuclease (APE1) and filled by DNA polymerase β. Additional mechanisms involve nucleotide excision repair (NER) for bulky adducts and sanitation enzymes like MUTYH to prevent misincorporation of oxidized nucleotides during replication. Defects in these systems, such as OGG1 mutations, heighten susceptibility to unrepaired lesions. Unrepaired oxidative DNA damage promotes G-to-T transversion mutations during replication, as 8-oxoG pairs preferentially with , driving genomic instability, , and accelerated aging. It is also implicated in neurodegenerative disorders like Alzheimer's and Parkinson's through neuronal and , as well as chronic conditions such as and via persistent inflammation and . Beyond mutagenesis, emerging evidence highlights 8-oxoG's role in epigenetic regulation, where it influences by modulating transcription factors like and interacting with DNA demethylation enzymes such as TET1, potentially linking oxidation to adaptive cellular responses or pathological remodeling.

Fundamentals of DNA Oxidation

Definition and Sources

DNA oxidation refers to the chemical modification of DNA molecules resulting from reactions between (ROS) and DNA components, including bases, sugars, or the phosphodiester backbone, which can produce lesions that disrupt , transcription, and overall genomic stability. These modifications arise inevitably during cellular metabolism and can be exacerbated by external factors, leading to a range of oxidative lesions. Endogenous sources of ROS contributing to DNA oxidation primarily stem from normal cellular processes, such as mitochondrial respiration, where the generates anion (O₂•⁻) as a during ATP . Enzymatic reactions, including those mediated by during inflammation and immune responses, also produce and other ROS that can diffuse to nuclear DNA. Additionally, metabolic like those from in cell membranes release reactive aldehydes and peroxides that indirectly promote DNA oxidation. Exogenous sources introduce ROS through environmental and therapeutic exposures, including ionizing radiation, which generates hydroxyl radicals (•OH) via water radiolysis to directly attack DNA. Ultraviolet (UV) light, particularly UVA, induces ROS formation through photosensitization reactions involving cellular chromophores. Environmental pollutants such as cigarette smoke contain numerous oxidants and free radical precursors that elevate ROS levels and cause DNA damage. Chemotherapeutic agents, including anthracyclines and platinum compounds, further generate ROS as part of their mechanism, leading to oxidative DNA lesions in target cells. Key chemical reactions in DNA oxidation involve the highly reactive hydroxyl radical (•OH), which adds to the C8 position of DNA bases—such as —to form products like (8-oxoG), a prevalent that can pair erroneously during replication. (¹O₂), often generated by UV exposure, reacts with bases like to produce thymine glycol through oxidation of the 5,6-double bond.

Types of Oxidative Lesions

Oxidative lesions in DNA encompass a range of chemical modifications to nucleobases, the deoxyribose sugar, and the phosphodiester backbone, primarily induced by reactive oxygen species (ROS) such as the hydroxyl radical (•OH) generated from endogenous sources like mitochondrial respiration. These lesions compromise DNA integrity by altering base structures, leading to helical distortions and errors in replication or transcription. Major categories include modified purine and pyrimidine bases, abasic sites, strand breaks, and crosslinks or adducts. Purine lesions are among the most prevalent oxidative modifications, with 8-oxo-7,8-dihydroguanine (8-oxoG) and 8-oxo-7,8-dihydroadenine (8-oxoA) being prominent examples. 8-oxoG arises mainly from •OH addition to the C8 position of , forming a hydroxyl that undergoes further oxidation, , and tautomerization, or through one-electron oxidation pathways involving guanine radical cations. Similarly, 8-oxoA forms via one-electron oxidation of , generating an adenine radical cation that reacts with water to yield the oxidized product. These lesions exhibit significant mutagenic potential; 8-oxoG adopts a syn conformation that enables Hoogsteen base pairing with adenine, resulting in G:C to T:A transversions during if not repaired. 8-oxoA can likewise promote A:T to C:G transitions by mispairing with . Pyrimidine lesions include , 5-hydroxycytosine (5-ohC), and uracil glycol, which form through •OH addition to the 5,6-double bond of or via photosensitization processes involving . , a ring-saturated product from , features hydroxyl groups at C5 and C6, rendering it non-planar and helix-distorting. 5-ohC results from •OH attack on at C5, potentially leading to and formation of 5-hydroxyluracil, while uracil glycol is an analogous hydrated product from uracil oxidation. These modifications are mutagenic: primarily blocks replicative polymerases, stalling fork progression and risking deletions or frameshifts upon bypass, whereas 5-ohC induces C:G to T:A transitions through mispairing with . Uracil glycol similarly promotes cytosine-like misincorporations, contributing to point mutations. Abasic sites and strand breaks stem from oxidative assault on the deoxyribose moiety, where •OH generates C4'-centered radicals that cleave the sugar ring, yielding apurinic/apyrimidinic (AP) sites or single-strand breaks (SSBs) with damaged termini such as 3'-phosphoglycolate. AP sites lack a base but retain the sugar-phosphate backbone, while SSBs involve phosphodiester hydrolysis, often clustered in scenarios. Both are highly mutagenic, as AP sites can cause base deletions or transversions depending on translesion synthesis, and SSBs may convert to double-strand breaks during replication, amplifying genomic instability. Crosslinks and adducts, such as DNA-protein crosslinks and interstrand crosslinks, often originate from secondary ROS products like (), a byproduct that reacts with exocyclic amines of to form the promutagenic cyclic M1dG (a pyrimidopurinone). Other byproducts, such as 4-hydroxy-2-nonenal (HNE), form adducts like γ-hydroxy-1,N²-propanodeoxyguanosine. These structures covalently link DNA strands or tether proteins, severely impeding replication and transcription; their mutagenic effects include strong blocking lesions that, if bypassed, lead to deletions, insertions, or crosslink-induced rearrangements.

Mechanisms of Repair

Base Excision Repair

Base excision repair (BER) serves as the primary enzymatic pathway for excising oxidative DNA lesions, such as (8-oxoG) and oxidized pyrimidines, thereby preserving genomic integrity against reactive oxygen species-induced damage. This multistep process begins with the recognition and removal of the damaged base by specific , creating an abasic (. The bifunctional glycosylase OGG1 specifically targets 8-oxoG paired with , cleaving the N-glycosidic bond to release the free base and leaving an , while also exhibiting weak β-lyase activity to nick the DNA backbone. Similarly, NTH1 acts on a range of oxidized pyrimidines, including thymine glycol and 5-hydroxycytosine, through a comparable glycosylase/lyase mechanism to generate the . These enzymes ensure lesion-specific initiation, with OGG1 demonstrating high affinity for 8-oxoG. Following base removal, the AP endonuclease APE1 incises the phosphodiester backbone immediately 5' to the via , producing a single-strand break with a 3'-hydroxyl (3'-OH) end for downstream extension and a 5'-deoxyribose (5'-dRP) blocking moiety. This step is crucial for preventing stalled replication forks and is highly efficient, with APE1 processing at rates of approximately 300-800 min⁻¹ on free substrates under physiological conditions. Subsequent gap-filling occurs primarily through short-patch BER, where DNA polymerase β (Pol β) incorporates a single opposite the undamaged template and removes the 5'-dRP via its lyase activity, achieving near-complete repair in mammalian cells. In long-patch BER, which handles more complex lesions, Pol δ or Pol ε, in coordination with PCNA and , synthesizes 2-10 , displacing the 5'-dRP-containing strand for degradation by FEN1 or APE1. The process concludes with ligation: XRCC1 scaffolded with DNA ligase IIIα seals short-patch nicks, while DNA ligase I handles long-patch junctions, ensuring seamless restoration of the DNA strand. BER coordination involves poly(ADP-ribose) polymerase 1 (), which is rapidly recruited to oxidative damage sites to synthesize poly(ADP-ribose) chains, signaling the assembly of repair factors like XRCC1 and enhancing lesion processing efficiency. Recent studies from 2023-2025 have revealed OGG1's functions beyond repair, including its role in facilitating recruitment and modulating at oxidative stress-responsive promoters, independent of glycosylase activity. For instance, OGG1 coordinates with transcription factors like to modulate inflammatory following 8-oxoG recognition. Recent studies (2023-2025) have also explored OGG1 inhibitors for modulating its non-repair functions in and cancer. Efficiency in BER is influenced by lesion specificity and pathway redundancy; while OGG1 excels at isolated 8-oxoG, the NEIL family glycosylases (NEIL1, NEIL2, NEIL3) provide backup for clustered oxidative damage, excising lesions in close proximity (e.g., 3'-proximal sites resistant to OGG1 or NTH1) to mitigate replication stress in densely damaged regions. This redundancy ensures robust repair, with NEIL1 demonstrating up to 10-fold higher activity on clustered lesions compared to monofunctional glycosylases.

Backup and Alternative Pathways

While (BER) serves as the primary pathway for most oxidative DNA lesions, alternative mechanisms are essential for addressing more complex or clustered damage that BER cannot fully resolve. (NER) provides a critical backup for bulky oxidative adducts, such as cyclopurine lesions (e.g., 5',8-cyclopurine-2'-deoxynucleosides), which distort the DNA helix and are generated by attack on the sugar. NER operates through two subpathways: global genome NER (GG-NER), which scans the entire genome for lesions using the XPC-RAD23B complex to recognize distortions, and transcription-coupled NER (TC-NER), which prioritizes actively transcribed strands via and CSB proteins that detect stalled . Both pathways recruit the TFIIH complex for helicase-mediated unwinding and excision of a 24-32 oligonucleotide containing the lesion, followed by gap filling and . These mechanisms are particularly important for cyclopurine lesions, which are repaired by NER with relatively low compared to UV-induced photoproducts, leading to their accumulation in aging tissues. For double-strand breaks (DSBs) arising from clustered oxidative lesions—such as closely spaced single-strand breaks or bifunctional alkylating agent effects— and serve as key alternatives. , active primarily in S/G2 phases, uses a homologous template (e.g., ) for accurate repair, with and facilitating strand invasion and Rad51-mediated homology search to restore the original sequence. In contrast, NHEJ predominates throughout the and directly ligates broken ends via the Ku70/Ku80 heterodimer, which recruits , , and ligase IV, though this process is error-prone and can introduce small insertions or deletions. Oxidative stress-induced DSBs, often from overwhelming BER, are repaired preferentially by NHEJ in non-proliferating cells, but HR ensures fidelity in dividing ones. Translesion synthesis (TLS) acts as a during replication, allowing bypass of oxidative lesions like (8-oxoG) to prevent fork collapse, though it introduces mutagenic risk. Specialized Y-family DNA polymerases, such as polymerase η (Pol η) and polymerase ι (Pol ι), insert nucleotides opposite the lesion: Pol η accurately inserts opposite 8-oxoG in an anti conformation, minimizing G-to-T transversions, while Pol ι shows lower fidelity but contributes to extension past the lesion. TLS is regulated by ubiquitination of PCNA via Rad6/Rad18, recruiting these polymerases transiently. Defects in Pol η, as in variant, elevate mutagenesis from oxidative damage. In mitochondria, where oxidative damage is prevalent due to proximity to the , specialized variants of BER enzymes like mitochondrial OGG1 (mtOGG1) and APE1 process 8-oxoG and abasic sites, respectively, though the compact mtDNA structure limits full BER cascades. Recent studies highlight mtOGG1's role in mitigating age-related mtDNA oxidation, with elevated expression reducing and preserving in aging models. However, mitochondrial repair is less efficient than BER for oxidative single-strand breaks, contributing to mtDNA mutations over time. Overall, these backup pathways exhibit limitations in handling oxidative single-strand breaks compared to BER, often due to lower specificity or higher error rates, underscoring their role as complementary rather than primary defenses.

Quantification and Baseline Levels

Detection and Techniques

Detection and of oxidative DNA damage rely on a variety of techniques that target specific , such as 8-oxo-7,8-dihydroguanine (8-oxoG), or broader indicators like strand breaks. These methods must account for the low abundance of lesions —typically one to several per million bases—and minimize artifacts from . Chromatographic assays, immunological approaches, and emerging single-molecule techniques provide complementary insights into lesion identity, quantity, and genomic location. Chromatographic methods, including high-performance liquid chromatography with electrochemical detection (HPLC-EC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), enable precise quantification of oxidative lesions after enzymatic hydrolysis of DNA to nucleosides. HPLC-EC specifically detects 8-oxoG-derived 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) with high sensitivity, often achieving limits of detection around 1-10 fmol, making it suitable for cellular and tissue samples. LC-MS/MS extends this to multiple lesions, such as oxidized purines and pyrimidines, by using stable isotope dilution for accurate total levels, with protocols allowing simultaneous analysis of up to seven damage products in a single run. These techniques often involve DNA digestion with nucleases and phosphatases, followed by solid-phase extraction to isolate nucleosides before separation and detection. Immunological methods offer high-throughput options for lesion detection, particularly in biological fluids or fixed tissues. Enzyme-linked immunosorbent assay () uses monoclonal antibodies specific to 8-oxoG or thymine glycol (Tg) to quantify s in hydrolyzed DNA samples, with sensitivities reaching 0.1-1 ng/mL for 8-oxo-dG in urine or cell lysates. Immunohistochemistry (IHC) localizes 8-oxoG in tissue sections via antibody , revealing in nuclei or mitochondria, though it requires careful validation to avoid . The , employing alkaline , assesses strand breaks and alkali-labile sites from oxidative damage by embedding cells in , lysing them, and applying an electric field; DNA migration forms "comet tails" whose length correlates with damage extent, quantifiable by fluorescence microscopy. Advanced techniques provide genome-wide or single-molecule resolution for oxidative lesions. Single-molecule PCR amplifies individual DNA templates to detect mutation spectra from unrepaired 8-oxoG, such as G-to-T transversions, by comparing amplified products across replicates. Recent advances include CRISPR-enhanced assays for 8-oxoG detection, where Cas12a or Cas13a cleavages amplify signals in structure-switching aptamer systems, achieving sub-femtomolar sensitivity without enzymatic hydrolysis. Nanopore sequencing maps lesions directly by analyzing current blockages from modified bases like 8-oxo-dG in synthetic or genomic DNA, with deep learning models trained on context-variable oligos enabling strand-specific quantification at single-molecule resolution as of 2025. Artifacts from adventitious oxidation during isolation pose significant challenges, often inflating 8-oxoG levels by 10-100 fold due to trace metals catalyzing Fenton reactions. Prevention strategies include adding chelators like desferrioxamine (1-10 mM) to lysis buffers and extraction solvents, alongside using Chelex-treated water and avoiding freeze-thaw cycles; levels are normalized to total via UV or slot blot for accurate per-base estimates. For in vivo assessment, urinary 8-oxo-dG serves as a non-invasive biomarker of systemic oxidative DNA damage, reflecting repair-mediated excision from nuclear and mitochondrial genomes, with levels typically 5-20 ng/mg creatinine in healthy adults and elevated under oxidative stress. This contrasts with in vitro methods, which measure lesions in isolated DNA or cells but require controls to mimic physiological conditions.

Steady-State Levels in Cells

In mammalian cells, the steady-state levels of 8-oxoguanine (8-oxoG), a primary oxidative lesion in DNA, are maintained at approximately 1,000 to 2,000 lesions per cell in nuclear DNA under normal physiological conditions, corresponding to roughly 1 lesion per 10^6 base pairs. These levels reflect a dynamic balance between continuous production from reactive oxygen species during metabolism—estimated at about 10,000 lesions per cell per day—and efficient removal primarily via base excision repair (BER). In mitochondria, where oxidative stress is elevated due to proximity to the electron transport chain, 8-oxoG concentrations are approximately 10-fold higher per base pair compared to nuclear DNA, underscoring the organelle's vulnerability to oxidation. Several factors modulate these steady-state levels. Aging is associated with a 2- to 3-fold increase in 8-oxoG accumulation in tissues such as the liver, attributed to declining repair efficiency and rising endogenous oxidative burden over time. Similarly, acute or chronic oxidative stress, such as during inflammation, can elevate 8-oxoG levels by up to 100-fold or more in affected tissues, though repair mechanisms mitigate much of this surge in healthy cells. Tissue specificity also plays a role; metabolically active organs like the brain and liver exhibit higher baseline 8-oxoG due to their elevated oxygen consumption and ROS generation, a pattern conserved evolutionarily across mammalian species to support high-energy demands. Recent studies highlight how efficient BER contributes to low steady-state 8-oxoG in specific cell types, such as stem cells, where enhanced glycosylase activity and repair kinetics maintain levels below those in differentiated cells, preserving genomic integrity during proliferation. Dietary interventions rich in antioxidants, like or caloric restriction, can further modulate these levels by reducing oxidative input, leading to measurable decreases in 8-oxoG (e.g., up to 22% in leukocytes). Overall, this equilibrium ensures that unrepaired s represent only 0.1-1% of total generated damage, supporting cellular homeostasis through robust repair fidelity.

Health and Disease Implications

Role in Carcinogenesis

Persistent oxidative DNA damage, particularly the lesion (8-oxoG), contributes to through direct by inducing G:C to T:A transversions during , as 8-oxoG preferentially mispairs with . These mutations frequently occur in critical genes such as the KRAS, where G>T transversions activate oncogenic signaling, and the tumor suppressor TP53, where they inactivate DNA damage response pathways, promoting uncontrolled cell proliferation in cancers like adenocarcinoma. Levels of 8-oxo-dG are significantly elevated in tumor tissues compared to normal tissues, often serving as a marker of and poor in solid tumors including and cancers. Chronic inflammation exacerbates DNA oxidation in the , where (ROS) produced by immune cells such as macrophages and neutrophils sustain oxidative damage and suppress anti-tumor immunity, fostering tumor growth and progression. Deficiency in the repair enzyme OGG1, which excises 8-oxoG, accelerates tumorigenesis in models by allowing accumulation of these lesions and increasing rates, as demonstrated in studies of oxidative stress-enhanced intestinal tumor formation. Additionally, oxidative DNA damage indirectly promotes genomic instability by generating clustered lesions that lead to double-strand breaks (DSBs), which, if unrepaired, cause chromosomal aberrations and further oncogenic mutations. Oxidative lesions can also induce epigenetic alterations, such as changes in patterns at CpG islands, leading to aberrant of tumor suppressors through recruitment of methyl-binding proteins and deacetylases. In the context of , oxidative damage to endothelial cells in the vasculature increases permeability and promotes via upregulation of (VEGF), facilitating tumor cell dissemination and invasion at distant sites. Human cohort studies provide epidemiological evidence linking elevated urinary 8-oxo-dG levels—a of systemic oxidative DNA damage—to increased cancer risk; for instance, prospective analyses in never-smokers have shown a dose-dependent association with incidence, independent of status. Similar correlations have been observed in cohorts, where higher urinary 8-oxo-dG predicts tumor development and recurrence, underscoring the role of persistent oxidation in cancer initiation.

Associations with Neurological Conditions

The exhibits heightened vulnerability to DNA oxidation due to its elevated oxygen consumption, which accounts for approximately 20% of the body's total despite comprising only 2% of body weight, coupled with comparatively low antioxidant enzyme activities such as and . This predisposition results in substantially higher steady-state levels of the oxidative lesion (8-oxoG) in neuronal DNA, reported to be elevated compared to peripheral tissues like liver or muscle. DNA oxidation has been implicated in various neurological conditions through clinical and genetic evidence. In , polymorphisms in the OGG1 gene, particularly the Ser326Cys variant, impair repair efficiency and elevate susceptibility to oxidative DNA damage, correlating with disease onset and severity. features increased mitochondrial (ROS) production during manic phases, leading to heightened DNA oxidation levels that scale with the number of manic episodes. shows correlations between hippocampal oxidative DNA lesions, including elevated 8-oxoG, and symptom severity, with postmortem analyses revealing neuronal damage in mood-regulating regions. In , 8-oxoG accumulates in dopaminergic neurons and associates with α-synuclein aggregates in Lewy bodies, exacerbating neurodegeneration. Similarly, involves 8-oxoG enrichment in and neurofibrillary tangles within the and cortex, as confirmed in recent immunohistochemical studies. Key mechanisms linking DNA oxidation to these conditions include age-related impairments in (BER), the primary pathway for removing 8-oxoG, where reduced OGG1 and polymerase β activities in the fail to process lesions efficiently, leading to persistent genomic instability. Additionally, DNA damage in s activates , the 's resident immune cells, triggering a proinflammatory cascade that amplifies through release and further ROS generation, forming a vicious cycle of and neuronal loss. Postmortem examinations of patients with these disorders consistently demonstrate 2- to 4-fold increases in 8-oxoG lesions compared to age-matched controls, particularly in vulnerable regions like the and . Animal models reinforce these findings; OGG1 knockout mice exhibit behavioral deficits, including reduced locomotor activity, anxiety-like behaviors, and cognitive impairments, alongside accelerated 8-oxoG accumulation and loss. Recent 2025 research underscores the role of DNA oxidation in early-onset neurodegeneration, with studies showing that unrepaired oxidative lesions in young neurons disrupt and initiate microglial activation, potentially accelerating progression in familial forms of Alzheimer's and Parkinson's. These advances highlight therapeutic potential in enhancing BER or mitigating microglial inflammation to intervene at preclinical stages.

Regulatory and Emerging Functions

Involvement in Gene Regulation

Controlled DNA oxidation serves as a signaling mechanism distinct from high-level oxidative damage, where low concentrations of reactive oxygen species (ROS) generate reversible lesions like 8-oxoguanine (8-oxoG) to modulate gene expression without causing mutagenesis, whereas excessive ROS lead to persistent, mutagenic adducts requiring repair. This low-level oxidation facilitates recruitment of repair enzymes such as OGG1, which, beyond initiating base excision repair, binds 8-oxoG at promoter regions to orchestrate transcriptional activation. In oxidative signaling, 8-oxoG recruits transcription factors to enhance expression of specific genes; for instance, OGG1 binding to 8-oxoG interacts with PGC-1α to upregulate genes like Nrf1 and Tfam, promoting adaptive responses to mild . Similarly, epigenetic alterations arise from ROS-induced oxidation of (5mC) to (5hmC), a process catalyzed by enzymes that respond to oxidative cues by facilitating locus-specific demethylation and for transcriptional accessibility. These TET-mediated oxidations, dependent on Fe²⁺ and α-ketoglutarate, integrate ROS signals to drive demethylation pathways without widespread genomic instability. Promoter-specific effects of localized ROS bursts further illustrate this regulatory role, particularly during , where transient production stabilizes HIF-1α and activates pathways to induce genes involved in and , such as VEGF and IL-6, through direct promoter binding and redox-sensitive modifications. Recent studies from 2023 highlight 8-oxoG accumulation in enhancer regions as a driver of ; for example, exogenous 8-oxoG enhances myoblast fusion and myogenin expression via the Ras-MEK-MyoD axis, underscoring its role in lineage commitment without repair intervention.

Positive Roles in Physiology

DNA oxidation, particularly the formation of (8-oxoG), plays a beneficial role in formation within hippocampal neurons. The accumulation of 8-oxoG facilitates (LTP), a key synaptic process underlying learning and , by enabling the 8-oxoG-OGG1 complex to activate transcription factors such as CREB, which promotes neuronal plasticity and gene expression essential for synaptic strengthening. studies demonstrate that inhibition or genetic knockout of OGG1 impairs spatial learning and performance, as evidenced by reduced performance in behavioral tasks like the Morris water maze, confirming the positive physiological contribution of controlled 8-oxoG signaling in cognitive processes from 2015 to 2025. In , oxidized DNA bases, including contributions from oxidized lesions, support TET-mediated active demethylation pathways that enable . TET enzymes oxidize 5-methylcytosine to intermediates like , which, through involving processing of oxidized bases, facilitate the removal of repressive methylation marks and promote transcriptional of genes critical for and embryonic development. This process ensures dynamic epigenetic reprogramming, as shown in studies where TET and TDG activity is essential for pluripotency and lineage specification in stem cells. Therapeutically, modulating DNA oxidation pathways offers potential benefits, with OGG1 inhibitors enhancing selectively in tumor cells to and synergize with existing treatments. For instance, small-molecule OGG1 inhibitors like TH5487 induce persistent 8-oxoG lesions in cancer cells, leading to replication stress and in BRCA1-deficient tumors, as validated in preclinical models of ovarian and . In neuroprotection, small molecules that modulate (BER), such as those targeting OGG1 activity, show promise in preclinical studies for mitigating oxidative damage in neurons and reducing , as demonstrated by OGG1 inhibitors like TH5487 decreasing pro-inflammatory production in models of neurodegenerative conditions as of 2024. Controlled DNA oxidation contributes to immune responses by signaling cytokine production in immune cells. The release of 8-oxoG from oxidized DNA activates dendritic cells and macrophages, upregulating pro-inflammatory cytokines like IL-6 and TNF-α through OGG1-dependent pathways, thereby enhancing innate immunity against pathogens without excessive inflammation. From an evolutionary perspective, balanced (ROS) levels, including those inducing DNA oxidation, underpin —a adaptive response where low-dose improves cellular resilience and stress resistance. This mechanism has been conserved across to optimize life-history traits, such as and , by upregulating defenses and in response to environmental challenges.

RNA Oxidation

Mechanisms and Lesion Types

RNA oxidation arises primarily from reactive oxygen species (ROS), such as hydroxyl radicals generated via Fenton chemistry or superoxide from mitochondrial respiration, mirroring the oxidative sources that damage DNA but amplified by RNA's structural vulnerabilities. Unlike the double-stranded, protein-protected DNA, RNA's single-stranded nature and lack of robust repair mechanisms render it more susceptible to base exposure and rapid oxidation, with guanine residues particularly prone due to their low redox potential. This heightened reactivity leads to widespread modifications across RNA species, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA), disrupting cellular processes like translation. Key oxidative lesions in RNA include base modifications such as (8-oxoG), which forms via and pairs aberrantly with during , and 8-oxoadenine (8-oxoA), resulting from oxidation and altering base-pairing . Another prominent , 5-hydroxyuracil, arises from or uracil oxidation and incorporates into codons, potentially misdirecting selection and compromising protein synthesis accuracy. Strand breaks occur more frequently in RNA than in DNA due to the instability of oxidized sugars, leading to fragmentation that halts ribosomal progression and exacerbates translational errors. Similar to 8-oxoG in DNA, these RNA lesions introduce miscoding risks but lack the mutagenic persistence seen in genomic contexts. These lesions profoundly impact translation fidelity; for instance, 8-oxoG in mRNA induces ribosomal stalling and miscoding, including frameshift errors that produce aberrant polypeptides, while oxidized tRNA and rRNA further reduce decoding accuracy under stress. During oxidative stress, oxidized RNAs accumulate in polysomes, forming stalled complexes that impair global protein synthesis and contribute to cellular dysfunction. In contrast to DNA oxidation, which risks heritable mutations during replication, RNA lesions evade such errors due to the transcriptome's rapid turnover via degradation pathways, though persistent damage in long-lived RNAs like mitochondrial rRNA disrupts translation of electron transport chain components, linking oxidation to energy production defects and bioenergetic failure. Recent studies also indicate that controlled RNA oxidation may play a role in modulating immune signaling during viral infections, potentially contributing to adaptive antiviral responses. Recent 2025 investigations highlight RNA oxidation's role in viral pathologies, where ROS bursts during infections like SARS-CoV-2 oxidize host and viral RNAs, amplifying replication errors, inflammatory cascades, and tissue damage to worsen disease outcomes. For example, oxidized viral genomic RNA impairs polymerase fidelity, while host mRNA modifications skew antiviral responses, underscoring oxidation as a key amplifier of infection severity.

Quality Control and Repair

Cells employ several degradation pathways to mitigate the effects of RNA oxidation, primarily targeting damaged transcripts for rapid turnover to prevent faulty and cellular dysfunction. Oxidized mRNAs, particularly those containing (8-oxoG), are recognized and degraded by exoribonucleases such as XRN1 and XRN2, which facilitate 5' to 3' exonucleolytic decay following initial . enzymes, including DCP2, play a crucial role in this process by removing the 5' cap structure of oxidized mRNAs, thereby exposing them to XRN-mediated degradation and promoting their elimination in processing bodies. Additionally, (NMD) targets frameshifted transcripts arising from oxidative lesions that disrupt reading frames during transcription or , ensuring the selective removal of aberrant mRNAs that could produce truncated or erroneous proteins. These mechanisms collectively maintain by prioritizing the decay of damaged molecules over repair. Surveillance factors further enhance the detection and clearance of oxidized RNA. RNA-binding proteins, such as Y-box binding protein 1 (YBX1), exhibit preferential affinity for 8-oxoG-modified RNAs, facilitating their recruitment to degradation pathways and preventing their incorporation into functional ribonucleoprotein complexes. This recognition helps in segregating damaged transcripts for targeted elimination. In parallel, damaged ribosomes affected by RNA oxidation undergo ubiquitin-mediated proteasomal clearance, where ubiquitination of ribosomal proteins marks them for degradation, thereby recycling components and averting translational errors from faulty rRNA or mRNA interactions. Unlike DNA, RNA lacks a canonical base excision repair (BER) pathway equivalent, relying instead predominantly on degradation for quality control due to the transient nature of most RNA molecules. While some enzymes like APE1 process oxidized RNA lesions by cleaving abasic sites, no dedicated glycosylase-mediated reversal exists for common oxidative adducts such as 8-oxoG in RNA. Hypothetical direct reversal mechanisms, such as reductases that could reduce oxidized bases back to their native form, remain speculative and unsupported by direct evidence in recent reviews. Broader cellular strategies complement degradation by promoting the rapid synthesis of new to replace damaged pools, leveraging the high turnover rate of cytoplasmic transcripts to restore functional levels under . Antioxidants, including , provide protective shielding for cytoplasmic by scavenging (ROS), thereby reducing the incidence of oxidation and preserving RNA integrity in the . Emerging research highlights potential enzymatic reversal pathways for specific RNA damages, with 2024-2025 studies identifying AlkB homolog (ALKBH) family enzymes in and eukaryotes capable of oxidative demethylation to repair certain RNA alkylations; however, direct repair mechanisms for oxidative lesions like 8-oxoG in are not established and continue to rely on degradation pathways.