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Depurination

Depurination is a fundamental type of DNA damage in which a purine base—either adenine or guanine—is spontaneously released from the deoxyribose sugar in the DNA backbone through hydrolysis of the N-glycosidic bond, leaving behind an abasic site termed an apurinic (AP) site.^[1]^[2]^[3] This non-enzymatic process represents the most common endogenous lesion in cellular DNA, occurring at an estimated rate of approximately 10,000 events per mammalian cell per day under physiological conditions.^[1]^[3] The chemical mechanism of depurination involves an acid-catalyzed hydrolysis where protonation at the N7 position of the purine ring generates an oxocarbenium ion intermediate, facilitating cleavage of the glycosidic bond and subsequent reaction with water to release the free base and form the AP site.^[2] This reaction is influenced by several factors, including low pH (with rates increasing as pH decreases, showing strong dependence above pH 2.5 and weakening below pH 2.5), elevated temperature (following Arrhenius kinetics with activation energies of 107–112 kJ/mol), and DNA sequence context (e.g., faster in thymine-rich regions like poly(dA-dT) compared to poly(dA)).^[2] Spontaneous depurination arises from thermal fluctuations and nucleophilic attack by water in the cellular environment, but it can be accelerated by exogenous stressors such as heat exposure or acidic conditions encountered in biological compartments like lysosomes or gastric fluid.^[1]^[2]^[3] If left unrepaired, AP sites pose significant threats to genomic stability, as they destabilize the DNA helix and can lead to single-strand breaks or mutagenic base insertions during replication—often resulting in transversions or deletions opposite the abasic site.^[1]^[3] Cells mitigate these risks primarily through base excision repair (BER), where AP endonucleases recognize and incise the abasic site, followed by excision of the damaged sugar-phosphate residue, gap filling by DNA polymerase, and sealing by ligase using the complementary strand as a template.^[1] Depurination's prevalence underscores its role in spontaneous mutagenesis, aging, and carcinogenesis, highlighting the critical need for efficient DNA repair pathways to maintain cellular integrity.^[2]^[3]

Introduction

Definition and Process

Depurination is a fundamental type of DNA damage characterized by the hydrolytic cleavage of the N-glycosidic bond that connects a purine base—specifically adenine or guanine—to the C1' carbon of the deoxyribose sugar in the DNA backbone. This reaction results in the release of the purine base and the formation of an apurinic (AP) site, also known as an abasic site, where the sugar-phosphate backbone remains intact but lacks the nitrogenous base essential for normal DNA structure and function.^[4]^[5] The structure of an AP site features a deoxyribose residue without its attached base, rendering the site highly reactive and prone to further degradation; this absence disrupts hydrogen bonding with the complementary strand and weakens base stacking interactions, thereby destabilizing the DNA double helix by up to 11 kcal/mol per lesion.^[6] In double-stranded DNA, the unpaired sugar moiety adopts a flexible conformation, often flipping out of the helix, which compromises the overall integrity of the genome. Depurination is distinct from depyrimidination, the analogous loss of pyrimidine bases (cytosine or thymine), as the N-glycosidic bonds of purines are significantly weaker and more susceptible to hydrolysis, leading to depurination occurring approximately 100 times more frequently than depyrimidination under physiological conditions.^[3] This disparity arises from the chemical instability of purine-deoxyribose linkages compared to their pyrimidine counterparts.^[4] In mammalian cells, depurination proceeds spontaneously at a substantial rate, with an estimated 10,000 events per cell per day, underscoring its role as one of the most common endogenous DNA lesions that cells must contend with to maintain genomic stability.^[7] These lesions are typically addressed through base excision repair pathways to prevent mutagenic consequences.^[8]

Biological Significance

Depurination represents the most common form of endogenous DNA damage involving base loss, occurring at a rate of approximately 10,000 events per mammalian cell per day and accounting for the majority of spontaneous base losses due to the higher susceptibility of purine N-glycosidic bonds to hydrolysis compared to pyrimidines.^[3]^[9] This prevalence underscores its role as a primary challenge to DNA integrity under physiological conditions, far exceeding the frequency of environmentally induced lesions such as those from UV radiation in non-exposed cells.^[9] Unrepaired apurinic (AP) sites resulting from depurination pose significant threats to genomic stability by stalling replication forks and promoting translesion synthesis, which can introduce base substitutions or frameshift mutations during DNA replication.^[3] If processing of these sites by nucleases occurs without proper repair, they may progress to single-strand breaks via β-elimination, potentially leading to double-strand breaks or cell death if unresolved, thereby contributing to mutagenesis and cellular dysfunction.^[3]^[9] The inherently high spontaneous rate of depurination highlights the evolutionary pressure it exerted on early life forms, driving the development of robust base excision repair pathways to mitigate its mutagenic potential and preserve genetic fidelity across generations.^[9] This ongoing DNA instability, as detailed in seminal work by Lindahl, implies that depurination-influenced mutagenesis rates have shaped evolutionary processes by balancing genome stability with adaptive variation.^[9] In comparison to other DNA damages, depurination is more frequent than UV-induced cyclobutane pyrimidine dimers, which occur at rates orders of magnitude lower in the absence of significant solar exposure, yet it is generally less cytotoxic than double-strand breaks, as AP sites can often be repaired without catastrophic genome fragmentation.^[9]^[10]

Chemical Mechanism

Hydrolytic Reaction

The hydrolytic reaction underlying depurination is the spontaneous cleavage of the N-glycosidic bond linking a purine base (adenine or guanine) to the C1' carbon of the deoxyribose sugar in the DNA backbone. This process releases the purine as a free base and generates an apurinic (AP) site, where the sugar-phosphate backbone remains intact but lacks the base. The overall reaction proceeds according to the equation:

\text{Purine-N-glycoside} + \ce{H2O} \rightarrow \text{AP site} + \text{Purine}

This hydrolysis is a key source of endogenous DNA damage under physiological conditions.^[3] The mechanism follows an SN1-like pathway characterized by a rate-determining departure of the purine base, forming a carbocation intermediate. Initial protonation of the purine ring—often at the N7 position—occurs in equilibrium, rendering the base a better leaving group by neutralizing its electron density. This is followed by heterolytic scission of the C1'-N9 (for purines) glycosidic bond, yielding the neutral purine base and an oxocarbenium ion (a resonance-stabilized carbocation) at the C1' of deoxyribose. Subsequently, water serves as the nucleophile, attacking the electrophilic C1' carbon of the carbocation, with the resulting protonated intermediate rapidly deprotonating to form the ring-opened AP site.^[3]^[2] The energy barrier for this bond cleavage is substantial, reflecting the stability of the native DNA structure. Activation energies are typically in the range of 25-30 kcal/mol for adenine depurination, while guanine exhibits a slightly higher barrier (around 27 kcal/mol) owing to stronger base-stacking interactions that further stabilize the double helix and impede base extrusion. These values are derived from kinetic studies on oligonucleotide models under controlled conditions.^[3]^[11] The reaction exhibits pH dependence, occurring spontaneously at neutral physiological pH but accelerating under mildly acidic conditions (pH 4-5) due to enhanced protonation of the purine, which lowers the activation barrier for bond cleavage. At neutral pH, the process remains viable, contributing to baseline DNA lesion rates in cells.^[3]^[2]

Influencing Factors

The rate of depurination exhibits a strong temperature dependence, approximately doubling with every 10°C increase, consistent with Arrhenius kinetics observed in hydrolytic reactions of DNA.^[12] Under physiological conditions (pH 7.4, 37°C), the half-life of the N-glycosidic bond in double-stranded DNA is approximately 200 years, though this shortens dramatically at elevated temperatures—for instance, to hours or days above 70°C—highlighting the thermal vulnerability of genomic integrity.^[12] Sequence context modulates depurination susceptibility through variations in base stacking interactions. Purines flanked by pyrimidines, as in alternating AT-rich sequences, undergo depurination more rapidly than those in purine homopolymers like poly(dA), owing to weaker stacking stabilization that facilitates glycosidic bond cleavage; for example, the half-life for poly(dA) is about 16-fold longer than for AT15 oligomers at acidic pH. Ionic strength influences depurination by affecting DNA helix stability, with higher salt concentrations (e.g., 50 mM NaCl versus 5 mM) reducing the rate by up to 10% through enhanced electrostatic shielding and base pairing. Similarly, divalent cations like Mg²⁺ mimic high monovalent salt effects, further slowing the reaction. Organic solvents accelerate depurination by lowering the dielectric constant and destabilizing the DNA structure, promoting hydrolysis in non-aqueous environments commonly encountered in synthetic or extraction protocols. Steric effects from DNA secondary structure significantly impact depurination kinetics, with single-stranded DNA depurinating 10-100 times faster than double-stranded forms due to reduced base stacking and hydrogen bonding protection that exposes the glycosidic bond to nucleophilic attack. This disparity is particularly pronounced under neutral pH, where double-stranded conformation provides a protective barrier against spontaneous hydrolysis.^[12]

Sources and Causes

Spontaneous Occurrence

Spontaneous depurination arises from the inherent thermal fluctuations within cellular environments that destabilize the N-glycosidic bond linking purine bases (adenine or guanine) to the deoxyribose sugar in DNA, driven by the bond's intrinsic chemical lability under physiological conditions. This hydrolytic process occurs without external agents, primarily through protonation at the N7 position of the purine base, generating an oxocarbenium ion intermediate, followed by nucleophilic attack by water, generating an apurinic (AP) site. In human cells, these endogenous events produce an estimated 10,000 to 20,000 AP sites per cell per day, representing a significant baseline level of DNA damage that must be managed by cellular repair systems.^[8] The frequency of spontaneous depurination exhibits a strong dependence on organismal physiology, particularly body temperature, as the reaction rate accelerates exponentially with rising thermal energy. Warm-blooded endotherms, maintaining core temperatures around 37°C, experience notably higher depurination rates compared to poikilothermic organisms at ambient temperatures, underscoring temperature as a key modulator of this spontaneous process. This temperature sensitivity aligns with the Arrhenius equation's prediction for bond-breaking reactions, where each 10°C increase roughly doubles the rate.^[13] Genomically, spontaneous depurination is not uniformly distributed but occurs more frequently in AT-rich sequences, where the absence of positively charged guanines reduces electrostatic shielding of the glycosidic bond, facilitating hydrolysis. These AT-rich motifs, often found in promoter regions and other accessible chromatin areas associated with gene-rich loci, thus contribute to localized hotspots of AP site formation. Such sequence-specific preferences highlight how intrinsic DNA structure influences the spatial patterning of endogenous damage.^[2]^[14] Over time, the burden of spontaneous depurination accumulates with age, exacerbated by chronic oxidative stress that indirectly promotes glycosidic bond instability and overwhelms repair pathways. This age-related escalation elevates the steady-state levels of AP sites, fostering a higher baseline mutation load that correlates with declining genomic stability in aging cells. Studies in mammalian models confirm that AP site abundance rises progressively from young to senescent stages, linking endogenous depurination dynamics to longevity.^[15]^[16]

Environmental and Chemical Induction

Depurination can be significantly accelerated by external chemical agents, particularly alkylating compounds that target the N7 position of guanine, forming unstable adducts prone to hydrolysis of the glycosidic bond. Methyl methanesulfonate (MMS), a monofunctional alkylating agent, methylates the N7 atom of guanine to produce 7-methylguanine, which depurinates spontaneously at rates up to several thousand times higher than unmodified DNA under physiological conditions, leading to apurinic sites that contribute to cytotoxicity and mutagenesis.^[17] This enhanced depurination is a key mechanism of MMS-induced DNA damage, often used in experimental models to study repair pathways.^[18] Ionizing radiation induces depurination indirectly through the generation of reactive oxygen species (ROS), such as hydroxyl radicals, which oxidize DNA bases and destabilize the N-glycosidic bond, promoting purine loss. These ROS-mediated modifications, including base oxidation and strand breaks, result in clustered lesions where apurinic sites form as intermediates during damage processing, exacerbating genomic instability in irradiated cells.^[19] In cellular environments, this process is amplified by water radiolysis products that initiate oxidative cascades, with depurination contributing to the overall mutagenic burden beyond direct ionization events.^[20] Elevated temperatures and extreme pH levels further promote depurination by altering the chemical stability of the DNA backbone. Hyperthermia, often applied in cancer therapy at 42–45°C, can modestly accelerate hydrolytic depurination rates by increasing molecular kinetic energy, sensitizing tumor cells to DNA damage without directly breaking strands at moderate intensities. Acidic environments, common in hypoxic tumor microenvironments with pH as low as 6.0–6.5, protonate purine bases and enhance glycosidic bond lability, leading to up to 100-fold increases in depurination compared to neutral pH.^[2] These conditions synergize with endogenous hydrolysis, amplifying apurinic site formation in pathological tissues.^[4] Certain environmental toxins, including mycotoxins and endocrine disruptors, catalyze depurination through reactive metabolites that form unstable DNA adducts. Aflatoxin B1 (AFB1), produced by Aspergillus fungi, is metabolically activated to an epoxide that binds the N7 position of guanine, yielding AFB1-N7-guanine adducts that rapidly depurinate (half-life ~4 hours at 37°C), generating promutagenic apurinic sites responsible for its hepatocarcinogenic effects.^[21] Similarly, metabolites of bisphenol A (BPA), such as BPA-3,4-quinone, react with N7 positions of guanine and adenine to produce depurinating adducts, releasing free bases and leaving abasic sites that link BPA exposure to genotoxicity.^[22] These toxin-induced processes highlight depurination as a critical pathway in environmentally driven DNA damage.

Structural and Cellular Consequences

Formation of Apurinic Sites

Depurination occurs through the hydrolysis of the N-glycosidic bond linking the purine base (adenine or guanine) to the C1' carbon of the deoxyribose sugar in the DNA backbone, resulting in the release of the free purine base and the formation of an apurinic (AP) site. This lesion leaves the sugar-phosphate backbone intact but exposes the anomeric C1' carbon of the deoxyribose, rendering it highly electrophilic and susceptible to nucleophilic attack by water or other molecules. The reactivity of this C1' carbon predisposes the AP site to β-elimination, a process in which the 3'-phosphodiester bond breaks, generating a 3'-unsaturated aldehyde and a 5'-phosphate terminus, potentially leading to single-strand breaks if unrepaired.^[3]^[23] The structural characteristics of an AP site significantly distort the DNA double helix. Molecular modeling studies reveal that the abasic deoxyribose adopts a flexible conformation, often in an open-chain or furanose ring form, causing a localized kink or bend in the helix of 20–30° at the lesion site due to the loss of base-stacking interactions and hydrogen bonding with the complementary strand. This distortion disrupts the regular B-form helical geometry, increasing flexibility in the surrounding DNA and exposing the phosphodiester backbone to further chemical instability.^[6] AP sites represent non-coding lesions, as they lack a base to pair with during replication or transcription, and they potently block the progression of replicative DNA polymerases such as polymerase δ, halting synthesis until repair intervenes. In vitro, under physiological conditions (pH 7.4, 37°C), AP sites exhibit a half-life of approximately 200 hours before undergoing spontaneous β-elimination and strand cleavage, highlighting their relative instability compared to intact DNA.^[24] The intermediates of depurination formation can be detected through the liberation of free purine bases, which are released intact and identifiable via high-performance liquid chromatography (HPLC) or mass spectrometry based on their distinct molecular signatures. Concurrently, alterations in the sugar-phosphate backbone, such as the opening of the deoxyribose ring or the formation of β-elimination products, manifest as changes in DNA mobility during gel electrophoresis or as fragmented species in sequencing analyses, providing evidence of the lesion's progression.^[2] Unlike AP sites in RNA, which benefit from greater stability owing to the 2'-hydroxyl group on ribose that sterically and electronically impedes β-elimination (resulting in cleavage rates 15–17 times slower than in DNA under comparable conditions), DNA AP sites are more labile due to the deoxyribose sugar's lack of this protective hydroxyl, facilitating faster backbone cleavage.^[25]

Effects on DNA Integrity

Depurination generates apurinic (AP) sites in DNA, which compromise structural integrity by facilitating spontaneous cleavage of the phosphodiester backbone. These sites undergo β-elimination under physiological conditions, where the 3'-phosphodiester bond breaks, resulting in a single-strand break (SSB) with a 3'-unsaturated aldehyde and a 5'-phosphate terminus.^[3] This process occurs slowly but steadily, with a half-life of approximately 200 hours at neutral pH and 37°C, meaning a significant fraction of unrepaired AP sites progress to SSBs before enzymatic intervention.^[24] Such breaks weaken the DNA helix and create nicks that, if clustered or during replication, exacerbate fragility. AP sites severely disrupt DNA replication by stalling the replication fork. DNA polymerases cannot efficiently bypass the abasic lesion, halting nucleotide incorporation and triggering activation of cell cycle checkpoints, such as the ATR-mediated response, to stabilize the fork and prevent collapse into double-strand breaks.^[26] This stalling is strand-specific: leading-strand AP sites block progression directly, while lagging-strand sites induce gaps that recruit repair factors, but both activate signaling to delay S-phase completion.^[27] Consequently, persistent stalling increases the risk of genomic instability if repair is delayed. Transcription is similarly impaired by AP sites, which cause RNA polymerase II (Pol II) to pause or stall at the lesion. Pol II encounters the abasic site as a non-instructive template, leading to transcriptional arrest after incorporation of a few non-template nucleotides, thereby reducing overall gene expression levels.^[28] This interference is particularly pronounced in actively transcribed regions, where unresolved pauses can propagate downstream effects on mRNA production and chromatin dynamics.^[29] Clustered depurinations, frequently induced by reactive oxygen species (ROS), further threaten DNA integrity by generating multiple AP sites within one or two helical turns. Such clusters overwhelm base excision repair, leading to opposing SSBs that convert into double-strand breaks (DSBs) during attempted processing.^[30]^[31] These DSBs are highly cytotoxic and mutagenic, as they sever both DNA strands and challenge homology-directed repair pathways.^[32]

Biological Impacts

Mutagenic Outcomes

Unrepaired apurinic (AP) sites arising from depurination pose a significant threat to genomic fidelity during DNA replication, as they block high-fidelity replicative polymerases and necessitate bypass via translesion synthesis (TLS) mediated by specialized low-fidelity DNA polymerases. In TLS, these polymerases, such as DNA polymerase ζ in eukaryotes or Pol V in bacteria, accommodate the non-instructional AP site in their active site, often leading to erroneous nucleotide insertion. A key mechanism is the "A-rule," where adenine is preferentially incorporated opposite the AP site due to its minimal steric hindrance and ability to maintain base-pair geometry, as observed across prokaryotic and eukaryotic systems.^[33]^[34] This preferential adenine insertion results in specific base substitution mutations. For instance, if depurination removes a guanine from a G:C base pair, the resulting AP site opposite cytosine prompts TLS insertion of adenine, yielding an A:C mismatch. Upon subsequent replication, this mismatch resolves into a T:A pair, causing a G:C to T:A transversion—the most common outcome of AP site bypass. Similar transversions occur at adenine sites (A:T to T:A), though at lower rates, with overall base substitutions accounting for approximately 60-70% of depurination-induced mutations in model systems like bacteriophage and yeast.^[33]^[35] In addition to substitutions, AP sites can induce frameshift mutations during TLS, particularly through polymerase slippage or template-independent deletion at the lesion. These typically manifest as -1 base deletions, where the AP site facilitates misalignment of the primer terminus, leading to loss of a nucleotide during extension; such events comprise about 5-6% of depurination-induced mutants in viral and bacterial assays. Frameshifts are more prevalent when the AP site is in repetitive or flexible sequence contexts that promote strand slippage.^[33]^[36] The overall mutation frequency from unrepaired AP sites is estimated at 1-5% per lesion in mammalian and yeast shuttle vector systems, reflecting the balance between accurate and error-prone bypass pathways. This rate escalates significantly in cells deficient in base excision repair (BER), such as those lacking AP endonuclease or Rev1, where spontaneous mutation frequencies can increase 3- to 10-fold due to reliance on TLS without repair intervention.^[37]^[38]^[8] Sequence context influences AP site mutagenicity, with AT-rich regions exhibiting hypermutability owing to their structural flexibility, which facilitates purine base extrusion and accelerates non-enzymatic depurination rates compared to GC-rich areas. In such motifs, the ease of base flipping exposes the N-glycosidic bond to hydrolysis, increasing local AP site formation and subsequent TLS errors by up to several-fold in synthetic oligonucleotides.^[2]

Associations with Disease and Aging

Depurination contributes to cancer progression through the accumulation of unrepaired apurinic (AP) sites in hypoxic tumor microenvironments, where oxygen deprivation impairs base excision repair (BER) pathways responsible for processing these lesions.^[39] Chronic hypoxia downregulates BER protein expression, leading to persistent DNA damage that promotes genomic instability and mutations in critical genes such as the tumor suppressor p53.^[40] For instance, unrepaired AP sites can stall replication forks, resulting in error-prone bypass and oncogenic mutations, including those in p53, which are observed in over 50% of human cancers and exacerbate tumor aggressiveness.^[41] In neurodegenerative diseases like Alzheimer's, oxidative stress accelerates the formation and accumulation of AP sites in neuronal DNA, overwhelming repair capacities and contributing to cellular dysfunction.^[42] Elevated reactive oxygen species in affected brain regions generate base modifications that lead to glycosylase-initiated BER intermediates, including AP sites, which persist due to impaired enzymatic processing and correlate with amyloid-beta plaque formation and tau pathology.^[43] This accumulation disrupts mitochondrial function and promotes neuronal apoptosis, linking depurination-derived damage to the progressive cognitive decline observed in Alzheimer's disease.^[44] Aging is associated with a decline in BER efficiency, resulting in the progressive buildup of AP sites and heightened somatic mutation rates that underlie senescence. Basal levels of AP sites in human fibroblasts and leukocytes from older individuals are elevated compared to younger ones, with repair kinetics slowing significantly in senescent cells.^[45] Studies indicate approximately a 2-fold increase in AP site accumulation by advanced age (equivalent to around 70 years in humans), driven by reduced expression of repair enzymes like APE1, which fosters mutagenesis and contributes to age-related pathologies such as frailty and increased cancer risk.^[46] Therapeutically, agents that induce depurination, such as temozolomide, are employed in chemotherapy to overwhelm BER in cancer cells, generating cytotoxic AP sites that trigger apoptosis.^[47] Temozolomide methylates guanine bases, leading to spontaneous depurination and AP site formation, particularly effective against gliomas where mismatch repair deficiencies amplify the damage; this mechanism underpins its role as a standard treatment, though resistance can emerge from upregulated repair pathways.^[48]

Repair Mechanisms

Base Excision Repair Pathway

The base excision repair (BER) pathway serves as the primary mechanism for repairing apurinic (AP) sites resulting from depurination in mammalian cells. This multi-step process addresses the AP site, which is highly reactive and cytotoxic if unrepaired. BER coordinates a series of enzymatic reactions to excise the abasic residue, fill the resulting gap, and restore DNA integrity, preventing mutations and strand breaks.^[49] Initiation of BER at AP sites is primarily mediated by apurinic/apyrimidinic endonuclease 1 (APE1), the major AP endonuclease in humans, which recognizes the abasic site and catalyzes a hydrolytic incision of the phosphodiester backbone immediately 5' to the abasic sugar residue. This cleavage generates a single-strand break (SSB) with a 3'-hydroxyl terminus suitable for polymerase extension and a 5'-deoxyribose phosphate (5'-dRP) blocking group. APE1's activity is essential, as its absence leads to accumulation of unrepaired AP sites and cellular toxicity.^[49]^[50]^[51] In the predominant short-patch BER subpathway, which repairs single-nucleotide gaps, DNA polymerase β (Pol β) subsequently binds to the 3'-OH terminus at the nick and performs dual functions: it removes the 5'-dRP moiety via its lyase activity and inserts a single correct nucleotide using available deoxyribonucleotide triphosphates (dNTPs). The final sealing of the nick is accomplished by DNA ligase III (Lig III), often in complex with XRCC1, which forms a phosphodiester bond to complete the repair patch. This short-patch mode is efficient for simple AP sites and predominates in non-proliferating cells.^[52]^[53]^[54] For more complex lesions or when the 5'-dRP is resistant to Pol β removal, BER switches to the long-patch subpathway, which replaces 2–10 nucleotides. Here, Pol β or replicative polymerases such as Pol δ/ε, stimulated by proliferating cell nuclear antigen (PCNA), extend the 3'-OH terminus beyond the lesion, displacing the downstream strand to form a 5'-flap structure. Flap endonuclease 1 (FEN1), recruited via PCNA interaction, then cleaves the flap to generate a ligatable nick, which is sealed by DNA ligase I. This variant ensures robust repair of clustered or oxidative damage-associated AP sites.^[55]^[56]^[57] BER efficiently processes the majority of endogenous AP sites, with cellular systems capable of repairing acute burdens within hours through iterative enzyme action, though exact rates vary by lesion context and enzyme availability. Deficiencies in core BER components underscore its criticality: for instance, complete APE1 knockout is embryonically lethal in mice due to unresolved SSBs and genomic instability, while Pol β or Lig III mutants exhibit hypersensitivity to alkylating agents and accumulated repair intermediates. Alternative pathways provide backup support for persistent AP sites.^[58]^[51]^[59]

Alternative Repair Processes

When base excision repair (BER) is insufficient to address apurinic/apyrimidinic (AP) sites arising from depurination, particularly in cases of clustered lesions or those causing significant helical distortion, nucleotide excision repair (NER) serves as a complementary pathway. NER recognizes these AP sites through the XPC-RAD23B complex, which binds to the resulting DNA distortion rather than the lesion itself, initiating the excision of a short oligonucleotide segment containing the damage. This process is efficient for BER-resistant AP sites, such as those mimicked by tetrahydrofuran (THF), and involves both global genome NER (GG-NER) and transcription-coupled NER (TC-NER) subpathways, with GG-NER providing the primary contribution to reducing mutagenesis from such lesions. In yeast and mammalian cells, NER's involvement is evidenced by increased mutation rates in XPC-deficient models, highlighting its role in preventing transcriptional blocks and clustered damage propagation.^[60]^[8] For double-strand breaks (DSBs) generated from unrepaired AP sites during DNA replication in S-phase, homologous recombination (HR) provides an error-free alternative repair mechanism. HR utilizes the sister chromatid as a template, with RAD51 nucleoprotein filaments facilitating strand invasion and gap filling opposite the AP-induced lesion. This pathway is particularly crucial for single-stranded DNA (ssDNA) AP sites at stalled replication forks, where fork reversal or template switching prevents collapse into DSBs. Studies in mammalian cells demonstrate that HR deficiency, such as in RAD51 mutants, leads to heightened sensitivity to AP site-inducing agents, underscoring its backup role when BER fails during active replication.^[8]^[61] In contrast, non-homologous end joining (NHEJ) handles AP site-derived strand breaks in a more error-prone manner, predominantly during G1 phase when no sister chromatid is available. NHEJ directly ligates broken ends via the Ku70/80 heterodimer and DNA-PKcs, often resulting in small insertions or deletions at the junction due to imprecise processing. This pathway is activated following APE1 incision of AP sites that inadvertently create DSBs, especially in non-dividing cells like neurons, where it collaborates with BER remnants to restore integrity despite the mutagenic risk. Evidence from neuronal models shows NHEJ's prevalence in G0/G1, with inhibition leading to persistent breaks and cell death.^[61]^[50] As a last-resort tolerance mechanism during replication, translesion synthesis (TLS) polymerases enable bypass of persistent AP sites with low fidelity. Polymerase zeta (Pol ζ), composed of Rev3 and Rev7 subunits, primarily extends from nucleotides inserted opposite the AP site by other polymerases, such as Pol δ inserting adenine, rather than performing de novo insertion. In yeast, this two-polymerase coordination results in ~64% adenine insertions opposite AP sites, with mutagenic frequencies around 10^{-4} to 10^{-5}, promoting survival but increasing mutation load. Human cells similarly rely on Pol ζ for AP bypass, as Rev3/7 deficiencies elevate sensitivity to depurination-mimicking agents, confirming its auxiliary, error-prone function.^[62]^[8]

Advanced Research

Detection Methods

Depurination, resulting in apurinic (AP) sites, is a common form of DNA damage that requires sensitive detection methods to quantify in biological samples, as these sites can lead to mutations if unrepaired. Experimental techniques span biochemical labeling, chromatographic separation, sequencing-based enrichment, and imaging approaches, each offering distinct advantages in sensitivity, specificity, and applicability to in vitro or in vivo contexts. Biochemical assays, such as aldehyde-reactive probe (ARP) labeling, enable the specific detection of AP sites by exploiting the reactive aldehyde group at the abasic position. In this method, ARP—a biotinylated hydroxylamine derivative—forms a stable adduct with the aldehyde, allowing subsequent quantification through slot-blot hybridization with streptavidin-linked probes. This technique achieves high sensitivity, detecting as few as 5 AP sites per 10^6 nucleotides in genomic DNA, and has been widely used for assessing oxidative stress-induced depurination in mammalian cells. The assay's simplicity and specificity make it suitable for large-scale screening in extracted DNA samples. Chromatographic methods provide direct measurement of depurination by quantifying released purine bases (adenine and guanine) following acid hydrolysis of DNA, which accelerates glycosidic bond cleavage. High-performance liquid chromatography (HPLC) separates these free purines using reversed-phase columns with UV detection, offering reliable quantification in the range of picomoles from microgram quantities of DNA. For instance, non-enzymatic depurination rates in synthetic oligonucleotides have been precisely determined this way, revealing pH- and temperature-dependent kinetics. Complementing HPLC, liquid chromatography-mass spectrometry (LC-MS) enhances specificity by identifying purine adducts or derivatized AP sites, with ultrasensitive variants detecting sub-femtogram levels after chemical labeling, such as with O-(pyridin-3-yl-methyl) hydroxylamine, to stabilize and ionize the aldehyde for tandem MS analysis. Sequencing-based approaches allow genome-wide mapping of AP sites at single-nucleotide resolution, integrating next-generation sequencing (NGS) with enzymatic enrichment. One prominent method involves treating DNA with APE1 endonuclease, which cleaves at AP sites to generate single-strand breaks, followed by end-repair and adapter ligation for NGS library preparation; this enriches fragmented regions corresponding to depurination hotspots. Such techniques have uncovered non-random AP site distributions in mammalian genomes, with up to thousands of sites identified per cell under oxidative conditions, providing insights into damage patterns without relying on indirect proxies. These methods typically achieve >90% specificity for AP-derived breaks when combined with bioinformatic filtering. In vivo imaging techniques utilize fluorescent probes that selectively bind AP sites in living cells, enabling real-time visualization of depurination dynamics. Aminooxy-functionalized fluorophores, such as those conjugated to rhodamine or coumarin, react covalently with the AP aldehyde to produce a turn-on fluorescence signal, allowing spatial and temporal tracking within nuclei. For example, palmatine-based probes intercalate near AP sites and exhibit enhanced emission upon binding, detecting depurination in real time during cellular stress with subcellular resolution. These probes have demonstrated compatibility with live-cell microscopy, revealing AP site accumulation in response to genotoxic agents over minutes to hours.

Sequence-Specific Depurination

Sequence-specific depurination refers to a non-random form of DNA damage where purine bases, particularly guanine, are lost at elevated rates due to a self-catalyzed mechanism involving structural extrusion of single-stranded loops in double-stranded DNA. This process was first identified in the mid-2000s through studies on gene sequences prone to mutation, such as those in the human β-globin gene. Unlike general spontaneous depurination, which occurs uniformly across the genome at a baseline rate of approximately 3 × 10⁻⁹ min⁻¹ under physiological conditions, sequence-specific depurination is facilitated by the spontaneous formation of stem-loop or cruciform structures that position a purine base for protonation and subsequent hydrolysis of the N-glycosyl bond, leading to an apurinic (AP) site via an SN1-type reaction without requiring enzymes or external agents.^[13] The mechanism relies on specific consensus sequences that promote loop extrusion, primarily G-rich motifs such as 5′-G[A/T]GG-3′ (G-loop) or 5′-GAGA-3′ (A-loop), where the 5′ purine in the loop is selectively vulnerable. These sequences require a stable stem of at least four base pairs, often with a T·A or G·C pair at the first stem position, and are enhanced in negatively supercoiled DNA contexts that favor cruciform formation. Depurination rates at these hotspots range from 10⁻⁶ to 4 × 10⁻⁵ min⁻¹, representing 10³ to 10⁵ times the random rate, as demonstrated in vitro using supercoiled plasmids and confirmed under physiological pH (6.9–7.4) and temperature (37°C). This site-specificity arises from the loop's single-stranded nature, which lowers the activation energy for base protonation and departure, generating promutagenic AP sites prone to error during repair.^[63]^[13] Biologically, sequence-specific depurination contributes to somatic mutation generation and genetic diversity, particularly in immune cells where it supports antibody diversification. These hotspots are overrepresented in immunoglobulin genes and other antibody function-related loci, potentially aiding adaptive evolution by introducing targeted variability through error-prone base excision repair of the resulting AP sites, which can lead to transitions, transversions, or small indels. For instance, the mutation hotspot at codon 6 of the human β-globin gene (GAG → GTG, substituting valine for glutamic acid and causing sickle cell anemia) exemplifies how such depurination adjacent to the site can drive clinically relevant changes, with similar patterns observed in immune gene clusters. This process links to broader evolutionary dynamics, as the ~50,000 predicted sites in the human genome suggest a physiological role in creating sequence diversity beyond random damage.^[13] Recent post-2020 analyses of cancer genomes have highlighted sequence-specific depurination hotspots as contributors to oncogenic mutations, with elevated AP site accumulation at G-rich regions correlating with tumor progression. Studies using whole-genome sequencing across thousands of samples have identified these sites as recurrent mutational foci in various cancers, underscoring their role in genomic instability and potential as therapeutic targets.^[64]

References

[1]
DNA Repair - Molecular Biology of the Cell - NCBI Bookshelf
Depurination, which is by far the most frequent type of damage suffered by DNA, also leaves a deoxyribose sugar with a missing base. Depurinations are directly ...
[2]
Non-Enzymatic Depurination of Nucleic Acids: Factors and ... - PMC
Dec 29, 2014 · Depurination, the release of purine bases from nucleic acids by the hydrolysis of N-glycosidic bonds, has aroused considerable interest for a ...
[3]
An Overview of Chemical Processes That Damage Cellular DNA
DNA damage can trigger changes in gene expression, inhibit cell division, or trigger cell death (7-9). In addition, attempts to replicate damaged DNA can ...
[4]
Depurination - an overview | ScienceDirect Topics
Depurination refers to the loss of purine bases (adenine and guanine) from DNA, resulting from hydrolysis of the N-glycosyl bond to deoxyribose, which leaves an ...
[5]
Mechanisms for enzymatic cleavage of the N-glycosidic bond in DNA
Monofunctional glycosylases catalyze hydrolysis of the N-glycosidic bond, yielding an apurinic/apyrimidinic (AP) or abasic site in the DNA (scheme 1).
[6]
New insights into the structure of abasic DNA from molecular ...
A single abasic site has a surprisingly strong destabilizing effect (up to 11 kcal/mol) in DNA double helices as determined by spectroscopic and calorimetric ...
[7]
Interstrand DNA–DNA Cross-Link Formation Between Adenine ...
Feb 7, 2014 · The loss of a coding nucleobase from the structure of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an ...
[8]
https://pmc.ncbi.nlm.nih.gov/articles/PMC7299775/
[9]
New Insights into Abasic Site Repair and Tolerance - PMC
Apr 30, 2020 · Although the mechanism of base loss is similar for purines and pyrimidines, the rate of depyrimidination is 1/20th the rate for depurination ...
[10]
Instability and decay of the primary structure of DNA - Nature
Apr 22, 1993 · The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments ...
[11]
Endogenous DNA Damage as a Source of Genomic Instability ... - NIH
The majority of lesions (75%) are single-strand DNA (ssDNA) breaks, which can arise from oxidative damage during metabolism or base hydrolysis. ssDNA breaks can ...Endogenous Dna Damage As A... · Figure 2. Dna Repair... · Base Substitution And...
[12]
None
Nothing is retrieved...<|control11|><|separator|>
[13]
https://www.pnas.org/doi/10.1073/pnas.0508499103
[14]
Nonenzymatic release of N7-methylguanine channels repair ... - PNAS
Jan 16, 2018 · It has been estimated that 2,000–10,000 AP sites arise spontaneously per mammalian cell per generation (2). ... AP sites generated by spontaneous ...Results · The Dna Phosphatase Zdp... · Fpg Incises Ap Sites...
[15]
Self-catalyzed site-specific depurination of guanine residues ... - PNAS
Mar 21, 2006 · We have shown that the self-catalytic depurination rate correlates with the ability of a single-stranded DNA fragment to form a stable hairpin ...Missing: double- | Show results with:double-
[16]
Complex genomic patterns of abasic sites in mammalian DNA ...
Oct 5, 2022 · those caused by spontaneous depurination, considering that in mammalian cells, AP sites can be generated by 11 DNA glycosylases that are ...
[17]
A method for detecting abasic sites in living cells - NIH
The high number of AP sites in old cells may reflect (i) an increase in endogenous oxidative insult with age that increases the damage to DNA (28, 29), repair ...
[18]
Effect of aging on intracellular distribution of abasic (AP ...
AP sites are also produced due to spontaneous depurination, and after ... increased DNA damage after chronic oxidative stress associated with aging.
[19]
Histone tails decrease N7-methyl-2′-deoxyguanosine depurination ...
Nov 14, 2018 · Monofunctional alkylating agents preferentially react at the N7 position of 2′-deoxyguanosine in duplex DNA. Methylated DNA, such as that ...
[20]
Complex genomic patterns of abasic sites in mammalian DNA ...
Oct 5, 2022 · Second, we treated HeLa and K562 cells in vivo with the alkylating agent methyl methanesulfonate (MMS) which is well known to induce AP site ...
[21]
Nuclear DNA damages generated by reactive oxygen molecules ...
DNA damages induced by ionizing radiation. Ionizing radiation induces base damages, DNA strand breaks from deoxyribose destruction, as well as DNA-protein ...
[22]
Ionizing radiation-induced metabolic oxidative stress and prolonged ...
Reactive oxygen and nitrogen species can attack DNA resulting in several alterations, including DNA ... Ionizing radiation-induced micronucleus formation ...
[23]
Hyperthermia - an overview | ScienceDirect Topics
Hyperthermic temperatures below 45°C do not produce single or double strand DNA breaks, do not cause depurination, or do not affect nucleosome structure. At ...
[24]
Aflatoxin B1-induced DNA damage and its repair - PubMed
AFB(1)-N(7)-guanine can convert to the ring-opened formamidopyrimidine, or the adducted strand can undergo depurination. AFB(1)-N(7)-guanine and AFB(1)- ...
[25]
Interaction of bisphenol A 3,4-quinone metabolite with glutathione ...
Feb 5, 2017 · BPAQ react with DNA at the N7 position of guanine (Gua) and the N7 position of adenine (Ade) to form depurinating adducts in most cases [13].
[26]
Abasic and Oxidized Abasic Site Reactivity in DNA - NIH
Abasic lesions are a family of DNA modifications that lack Watson-Crick bases. The parent member of this family, the apurinic/apyrimidinic lesion (AP), occurs ...
[27]
Abasic sites in DNA: repair and biological consequences ... - PubMed
Jan 5, 2004 · AP sites can stall DNA replication forks, as well as they block in vitro DNA synthesis by DNA polymerase delta. Restart of stalled forks can ...
[28]
The chemical stability of abasic RNA compared to abasic DNA - PMC
Thus abasic RNA is significantly more stable than abasic DNA. The higher stability of abasic RNA is discussed in the context of its potential biological role.
[29]
Rapid DNA–protein cross-linking and strand scission by an abasic ...
Dec 13, 2010 · We find that independently generated AP sites within nucleosome core particles are highly destabilized, with strand scission occurring ∼60-fold more rapidly ...
[30]
Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites ...
Here, we investigate APE1 cleavage of abasic substrates that mimic APE1 interactions at stalled replication forks or gaps.
[31]
Leading and lagging strand abasic sites differentially affect ...
We show that abasic sites robustly stall DNA synthesis but exert strand-specific effects. Leading strand abasic sites stall leading strands at the lesion, while ...
[32]
RNA polymerase pausing, stalling and bypass during transcription ...
... AP site causes two consecutive transcriptional pauses (106). Being the most abundant type of spontaneous DNA lesions, AP sites do not completely block ...Rna Polymerase Pausing... · Molecular Basis Of Rna... · Abasic Sites
[33]
Molecular Basis of Transcriptional Pausing, Stalling, and ...
Previous studies showed that the presence of AP sites significantly slows down DNA replication and transcription and leads to non-template addition of AMP (A- ...
[34]
Clustered Damages and Total Lesions Induced in DNA by Ionizing ...
Double strand breaks comprise only ∼20% of complex multilesion damages, while the other clustered damages constitute at least 80% of the total of such complex ...Missing: depurination | Show results with:depurination
[35]
Oxidative stress at low levels can induce clustered DNA lesions ...
Although it is well reported that high energy ionizing radiation is a strong inducer of OCDLs, the formation of OCDLs as a result of low levels of oxidative ...
[36]
Clustered DNA Double-Strand Breaks: Biological Effects and ... - MDPI
DSBs are among the most dangerous DNA lesions, in part because unlike single-strand lesions that have an undamaged complementary strand for use as a repair ...Missing: apurinic | Show results with:apurinic
[37]
https://www.sciencedirect.com/science/article/abs/pii/002228369290513J
[38]
Translesion Synthesis Across Abasic Lesions by Human B-family ...
Abasic (AP) sites are the most common DNA lesions formed in cells, induce severe blocks to DNA replication, and are highly mutagenic.
[39]
Mutational specificity and genetic control of replicative bypass of an ...
Jan 29, 2008 · Abasic (AP) sites arise in DNA as a result of spontaneous depurination and from the action of base excision-repair processes, where the ...
[40]
Repair of chromosomal abasic sites in vivo involves ... - EMBO Press
Abasic sites (AP sites) in DNA may arise spontaneously by hydrolytic loss of normal or alkylated bases, or by removal of damaged or inappropriate bases by N‐gly ...Results · Mutation Spectra Of The... · Mutation Frequency Measured...<|control11|><|separator|>
[41]
Mutagenicity of a unique apurinic/apyrimidinic site in mammalian cells
A mutation frequency ranging from 1% to 3% was found, depending on the base ... Since adenine is the most common base inserted opposite AP sites in the SOS ...
[42]
Base excision repair intermediates are mutagenic in mammalian cells
Aug 1, 2005 · Mutation frequency was very high and comparable with that of AP sites (∼3–4%). When the replication machinery encounters these termini, it is ...
[43]
Hypoxia provokes base excision repair changes and a ... - PubMed
Using conditions of chronic hypoxia, decreased expression of BER proteins was observed because of a mechanism involving suppressed BER protein synthesis in ...Missing: apurinic | Show results with:apurinic
[44]
Tumor Hypoxia Drives Genomic Instability - Frontiers
Mar 15, 2021 · Specifically, hypoxic exposure downregulates genes involved in DNA replication and repair pathways, thus increasing genomic instability (Hassan ...Missing: depurination | Show results with:depurination
[45]
DNA repair mechanisms in cancer development and therapy - PMC
When erroneous DNA repair leads to mutations or chromosomal aberrations affecting oncogenes and tumor suppressor genes, cells undergo malignant transformation ...
[46]
Emerging roles of oxidative stress in brain aging and Alzheimer's ...
A key marker of oxidative stress is DNA damage, which leads to apurinic and apyrimidinic DNA sites, oxidized purines and pyrimidines, and DNA breaks.
[47]
Apurinic/apyrimidinic endonuclease 1 is a key modulator of ...
Mar 11, 2013 · Aluminum exacerbates oxidative stress, amyloid beta (Aβ) deposition, and plaque formation in the brain of transgenic mice that overexpress ...
[48]
The multifunctional DNA repair/redox enzyme Ape1/Ref-1 promotes ...
Furthermore, AP sites occur through oxidative damage and cytotoxic chemicals and are found in abundance in the brain [16]. Once AP sites are formed either ...
[49]
Changes in DNA repair during aging - PMC - NIH
DNA repair becomes less efficient and more error-prone leading to cascading accumulation of DNA damage and mutations, which further exacerbate age-related ...
[50]
A method for detecting abasic sites in living cells: Age-dependent ...
Aug 6, 2025 · AP sites result from spontaneous depurination and depyrimidination, ionizing radiation and oxidative damage, and enzymatic removal of damaged ...
[51]
DNA abasic sites act as rational therapeutic targets to synergize ...
Temozolomide induces the accumulation of DNA abasic sites in both MMR-proficient and deficient cancer cells. To investigate the underlying mechanism for the ...
[52]
Combined Treatment with Temozolomide and Methoxyamine ...
This indicates that AP sites formed by temozolomide also induce topo II–mediated DNA double-strand breaks, but with less potency compared with MX-AP sites.
[53]
Human base excision repair enzymes apurinic/apyrimidinic ... - NIH
We focused here on the interplay of three BER enzymes, pol β, APE1 and PARP-1 in LP-BER DNA synthesis and on the exonuclease function of APE1. Enzyme ...Missing: key | Show results with:key
[54]
Oxidative DNA damage is concurrently repaired by base excision ...
Our results indicate that APE1 can engage the NHEJ mechanism in the repair of oxidative DNA damage in neurons. These findings provide insights into the ...
[55]
A Vital Role for Ape1/Ref1 Protein in Repairing Spontaneous DNA ...
Two independent efforts showed that “knockout” of APE1 in mice causes postimplantation embryonic lethality not associated with any specific developmental ...Missing: lethal | Show results with:lethal
[56]
Roles of base excision repair subpathways in correcting oxidized ...
Mar 31, 2006 · AP sites can also arise spontaneously at a substantial rate and are ... single-strand breaks induced by reactive oxygen species.
[57]
Base Excision Repair - PMC - NIH
Recent evidence has indicated that DNA ligase I, rather than DNA ligase 3, may be the major nuclear DNA ligase both in short-patch BER and long-patch BER, ...
[58]
XRCC1 coordinates the initial and late stages of DNA abasic site ...
(1) APE1, associated with the XRCC1–LIGIII complex, binds to an AP site present in double‐stranded DNA, creating a bend in the DNA. APE1 incises the strand ...<|separator|>
[59]
Proliferating Cell Nuclear Antigen Facilitates Excision in Long-patch ...
These results indicate that PCNA facilitates excision during long-patch BER through its interaction with FEN-1. Damage to DNA bases can occur spontaneously ...Bacterial Expression... · Flap Endonuclease Assay · Results
[60]
Long Patch Base Excision Repair Proceeds via Coordinated ...
Assuming pol β binds the primer terminus and FEN1 binds the flap, a progressively larger gap would be anticipated to strain or break interactions producing the ...
[61]
DNA polymerase β-dependent long patch base excision repair in ...
In SN BER, it is considered well established that DNA polymerase β (Pol β) fills the SN gap and removes the 5′-dRP group, creating a substrate for DNA ligase ...
[62]
Mammalian Base Excision Repair: the Forgotten Archangel
The repair of acute DNA damage requires several rounds of BER and can take several hours, as the amount of BER enzymes is limited. BASE EXCISION REPAIR: ...
[63]
Knockdown of the DNA repair and redox signaling protein Ape1/Ref ...
The importance of Ape1 to cell viability is demonstrated by the lethality of Ape1 mouse knockouts at E3. 5 to E9. 5 and the lack of viable cell lines ...<|separator|>
[64]
Nucleotide excision repair of abasic DNA lesions - PMC - NIH
Jun 21, 2019 · Apurinic/apyrimidinic (AP) sites are a class of highly mutagenic and toxic DNA lesions arising in the genome from a number of exogenous and ...
[65]
A Versatile New Tool to Quantify Abasic Sites in DNA and Inhibit ...
If unrepaired, AP sites cause mutations, strand breaks and cell death. Aldehyde-reactive agent methoxyamine reacts with AP sites and blocks their repair.
[66]
Roles of yeast DNA polymerases δ and ζ and of Rev1 in the bypass ...
Here we show efficient bypass of an AP site by the combined action of yeast DNA polymerases δ and ζ. In this reaction, Polδ inserts an A nucleotide opposite the ...Missing: zeta | Show results with:zeta
[67]
Self-catalyzed Site-specific Depurination of G Residues Mediated by ...
Aug 25, 2011 · Background: Self-catalyzed depurination of G residues occurs readily in single-stranded stem-loops of appropriate sequence.
[68]
The landscape and driver potential of site-specific hotspots across ...
May 13, 2021 · Here we detect, categorize, and characterize site-specific hotspots using 2279 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes project.
[69]
Click-code-seq reveals strand biases of DNA oxidation and ... - Nature
Oct 31, 2025 · 5: Endogenous guanine oxidation and adenosine depurination are more frequent in the − (heavy) strand of mtDNA, while endogenous guanosine ...