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AP site

An apurinic/apyrimidinic (AP) site, also known as an abasic site, is a common form of DNA damage characterized by the loss of a nucleobase from the DNA strand, leaving a deoxyribose sugar-phosphate backbone without an attached purine or pyrimidine base.^[1] This lesion arises primarily from the hydrolysis of the glycosidic bond between the sugar and base, occurring spontaneously at a rate of 10,000 to 50,000 times per day in a typical aerobic human cell.^[1] AP sites are highly mutagenic and cytotoxic because they destabilize the DNA helix and can lead to strand breaks if unrepaired.^[2] AP sites form through both endogenous and exogenous pathways, including spontaneous base loss, enzymatic action by DNA glycosylases during base excision repair (BER) of other lesions, and exposure to environmental agents like ionizing radiation, alkylating chemicals, or oxidative stress.^[3] As key intermediates in BER, they are recognized and processed by AP endonucleases, such as APE1 in humans, which cleave the phosphodiester backbone to initiate repair.^[4] However, persistent AP sites can block DNA replication and transcription, potentially causing mutations, chromosomal aberrations, or cell death, contributing to aging, cancer, and neurodegenerative diseases.^[4] The structural flexibility of AP sites—often existing in equilibrium between closed (intact sugar) and open (deoxyribose ring-opened) forms—poses unique challenges for DNA polymerases and repair enzymes, influencing translesion synthesis and repair fidelity.^[4] Research into AP site detection and repair has advanced through techniques like aldehyde-reactive probes and high-throughput sequencing, enabling single-nucleotide resolution mapping in genomes.^[3] These insights underscore the critical role of AP sites in genomic stability and highlight therapeutic targets for modulating DNA damage responses in disease contexts.^[2]

Formation

Endogenous Mechanisms

Apurinic/apyrimidinic (AP) sites in DNA arise endogenously through several internal cellular processes, primarily involving the spontaneous or enzymatically catalyzed loss of nucleobases. One major mechanism is the spontaneous hydrolysis of the N-glycosidic bond that links a base to the deoxyribose sugar in the DNA backbone, resulting in base loss and formation of an AP site. This process, known as depurination for purine bases (adenine or guanine) or depyrimidination for pyrimidine bases (cytosine or thymine), occurs due to thermal fluctuations under physiological conditions. Depurination predominates, happening at a rate approximately 20- to 100-fold higher than depyrimidination, with an estimated 10,000 AP sites generated per mammalian cell per day through this spontaneous mechanism alone.^[5]^[6] Another significant endogenous source of AP sites is the base excision repair (BER) pathway, where DNA glycosylases initiate repair by recognizing and excising damaged or mismatched bases, thereby creating AP sites as obligatory intermediates. Monofunctional DNA glycosylases, such as those targeting oxidized or alkylated bases, cleave only the N-glycosidic bond, leaving an intact AP site that requires subsequent processing by AP endonucleases. These glycosylase activities are essential for maintaining genomic integrity but transiently increase the pool of AP sites during normal cellular metabolism.^[7]^[8] Endogenous oxidative stress from metabolic processes, such as mitochondrial respiration, also contributes to AP site formation by generating reactive oxygen species (ROS) that damage DNA bases, often leading to their subsequent removal via glycosylases and thus AP site generation. While direct ROS-induced depurination is less common than hydrolysis, the overall oxidative burden from normal cellular activities amplifies the endogenous AP site load, with estimates suggesting that a substantial portion of AP sites originates from ROS-mediated base modifications rather than purely spontaneous events. This interplay underscores the constant challenge of endogenous DNA damage in living cells.^[9]

Exogenous Causes

Exogenous causes of apurinic/apyrimidinic (AP) sites in DNA primarily arise from environmental, physical, and chemical agents that induce oxidative damage, base alkylation, or photoproducts, leading to base loss or excision by DNA glycosylases. These factors contrast with intrinsic cellular processes by being preventable through exposure reduction, and they often generate AP sites as intermediates in damage recognition or direct destabilization of the N-glycosylic bond. Ionizing radiation, such as gamma rays from radioactive sources, exemplifies a key physical agent, producing reactive oxygen species (ROS) through water radiolysis in cells. These ROS, particularly hydroxyl radicals, oxidize DNA bases—such as forming 8-oxoguanine or thymine glycol—destabilizing the glycosidic bond and causing spontaneous base loss, thereby generating AP sites. In clustered damage scenarios, high-linear energy transfer (LET) radiation exacerbates this by creating multiple lesions within one or two helical turns, hindering repair and increasing AP site persistence. Experimental evidence from Monte Carlo simulations and biochemical assays confirms that gamma irradiation yields thousands of AP sites per cell, with yields scaling with dose and ROS flux. Chemical agents further contribute to AP site formation by directly modifying DNA bases, prompting glycosylase-mediated excision. Alkylating agents like methyl methanesulfonate (MMS), an SN2-type mutagen used in chemotherapy and found in industrial pollutants, methylate nucleophilic sites on purines (e.g., N7-guanine), leading to apurinic site creation via hydrolytic depurination of the weakened N-glycosylic bond. This process is concentration- and time-dependent, with MMS inducing detectable AP sites in calf thymus DNA at micromolar levels, as quantified by aldehyde-reactive probe assays. Similarly, ultraviolet (UV) light, particularly UVB wavelengths (280–315 nm), generates cyclobutane pyrimidine dimers and 6-4 photoproducts, alongside cytosine hydrates that deaminate to uracil; subsequent action by uracil DNA glycosylase (UDG) excises the damaged base, yielding AP sites as repair intermediates. These UV-induced AP sites occur more readily in single-stranded DNA regions, amplifying mutagenic risk during replication. Environmental toxins, including cigarette smoke and air pollutants, indirectly promote AP sites through chronic ROS generation and adduct formation. Cigarette smoke contains over 70 carcinogens that produce superoxide anions and hydrogen peroxide, oxidizing lung cell DNA to form base lesions like 8-oxoguanine, which DNA glycosylases (e.g., OGG1) remove to create AP sites; studies in human lung fibroblasts show elevated AP site levels post-exposure, correlating with impaired base excision repair. Pollutants such as polycyclic aromatic hydrocarbons (PAHs) from vehicle exhaust or industrial emissions form bulky adducts on guanine via metabolic activation to epoxides, destabilizing the base and triggering glycosylase activity for AP site generation. These toxin-induced AP sites accumulate in exposed tissues, contributing to chronic inflammation and carcinogenesis, with ROS-mediated mechanisms predominant in both smoke and pollutant exposures.

Chemical Properties

Molecular Structure

An apurinic/apyrimidinic (AP) site in DNA represents a form of damage where the purine or pyrimidine base is absent, leaving a deoxyribose sugar residue covalently linked to the intact phosphodiester backbone on both the 3' and 5' sides. This abasic site arises from the hydrolytic cleavage of the N-glycosidic bond between the base and the C1' carbon of the deoxyribose, resulting in an electrophilic site that disrupts normal base pairing and helical integrity. The structure maintains the overall B-form DNA scaffold but introduces flexibility at the lesion, with the sugar-phosphate unit serving as a non-instructional placeholder in the genome. The canonical AP site consists of an intact 2'-deoxy-D-erythro-pentofuranose sugar in dynamic equilibrium, predominantly in ring-closed hemiacetal forms (approximately 99%), including α- and β-anomers where the C1' hydroxyl group participates in the furanose ring. A minor fraction (about 1%) exists in the ring-opened aldehyde form, exposing the C1' carbonyl as a reactive aldehyde group. In structural models, such as those derived from NMR spectroscopy, the abasic deoxyribose often adopts an extrahelical conformation, with the opposing strand's base often forming hydrogen bonds to water molecules rather than the lesion. This can be diagrammatically represented as a DNA duplex segment where one nucleotide's base is replaced by an "X" or tetrahydrofuran analog, highlighting the sugar ring's C1'-OH or C1'=O, flanked by phosphate groups (e.g., as shown in equilibrium depictions between furanose and open-chain forms). AP sites also encompass variants beyond the canonical form, including oxidized derivatives like 2-deoxyribonolactone or cleaved products from β-elimination, such as the 3'-terminal α,β-unsaturated aldehyde (often termed 3'-phosphoaldehyde end) generated when the 3' phosphodiester bond breaks, leaving a strand nick with a 5'-phosphate. These cleaved variants alter the sugar remnant, transforming the intact deoxyribose into a unsaturated aldehyde chain that terminates the 3' end, increasing reactivity and complicating repair. Chemically, the core AP sugar is formulaically denoted as C₅H₁₀O₄ (deoxyribose minus base) integrated into the oligonucleotide, with the C1' position key to its representation: in the open form, it is -CH=O, rendering the site prone to nucleophilic attack, while the closed form features a five-membered ring with -CH(OH)-O- bridging C1' to C4'.

Stability and Reactivity

AP sites in DNA are inherently unstable due to their susceptibility to β-elimination, a chemical process that cleaves the phosphodiester backbone at the 3' side of the lesion, resulting in single-strand breaks. This instability arises from the open-chain aldehydic tautomer of the deoxyribose sugar, which facilitates elimination of the 3'-phosphate group. Under physiological conditions (pH 7.4, 37°C), the half-life of an AP site in duplex DNA is on the order of weeks (approximately 1000 hours), but it shortens dramatically when embedded in nucleosomes, where histones can catalyze the reaction up to 100-fold faster.^[1]^[10] The rate of β-elimination is strongly dependent on environmental factors, particularly pH and temperature. At neutral pH, the process is slow, but it accelerates significantly under mildly alkaline conditions (e.g., pH > 8), leading to complete strand cleavage within minutes to hours. Elevated temperatures further enhance this reactivity, with thermal degradation promoting the elimination even at neutral pH. These dependencies highlight the lesion's vulnerability in cellular environments where local pH fluctuations or heat stress could exacerbate DNA damage.^[1]^[11] AP sites are highly reactive toward nucleophiles owing to the electrophilic nature of the C1' aldehyde in their ring-opened form, enabling the formation of Schiff bases with primary amines. This reactivity allows AP sites to covalently cross-link with nearby nucleobases, such as deoxyguanosine in a 5'-C-AP-G sequence (yielding up to 20% interstrand cross-links within 12 hours), or with protein residues like lysine in repair enzymes, trapping them as DNA-protein cross-links (DPCs). These cross-links can be reversible imines but may stabilize into more persistent structures, impeding enzymatic processing.^[1]^[12] The persistence of AP sites is modulated by the local DNA sequence context, with greater stability observed in GC-rich regions compared to AT-rich ones. In AT-rich sequences, AP sites exhibit increased propensity for interstrand cross-link formation (e.g., with opposing adenine), accelerating their conversion to more complex lesions and reducing their standalone half-life under physiological conditions. Conversely, GC-rich contexts hinder such reactions, allowing AP sites to persist longer before undergoing β-elimination or other transformations.^[13]^[14]

Biological Effects

Cellular Consequences

AP sites in DNA pose significant threats to cellular processes by acting as non-instructive lesions that disrupt normal enzymatic activities. During DNA replication, these sites strongly impede the progression of DNA polymerases, such as polymerases ε and δ, leading to stalling of replication forks.^[15] This blockage occurs because the absence of a base creates a structural barrier in the template strand, preventing accurate nucleotide incorporation and causing the replisome to pause, which can result in single-stranded DNA gaps if not promptly addressed.^[16] In mammalian cells, where 10,000–30,000 AP sites form daily from endogenous damage, such stalling increases the risk of fork collapse and double-strand breaks, contributing to genomic instability.^[15] Unresolved replication fork stalling at AP sites can trigger cell death pathways, including apoptosis, particularly when repair mechanisms are overwhelmed or deficient. For instance, suppression of AP endonuclease 1 (APE1), which processes AP sites, leads to accumulation of these lesions and subsequent cytotoxicity via blocked replication, ultimately inducing apoptosis in mammalian cells.^[17] This highlights the lethal potential of persistent AP sites, as they convert benign replication pauses into irreversible cellular damage. In transcription, AP sites interfere with RNA polymerase II (RNAPII) elongation by serving as physical obstacles in the template strand, causing polymerase arrest and production of truncated RNA transcripts.^[18] Studies using in vitro assays have shown that RNAPII halts specifically at abasic lesions, leading to backtracking and potential cleavage of the nascent RNA, which disrupts gene expression and cellular homeostasis.^[19] Such interference is particularly detrimental in actively transcribed regions, where unresolved blockages can amplify stress signals and contribute to broader transcriptional dysregulation. The presence of AP sites also activates DNA damage response checkpoints to mitigate immediate threats. Processing of AP sites during base excision repair generates single-strand breaks that recruit ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia and Rad3-related (ATR) kinases, initiating the ATM-Chk2 and ATR-Chk1 pathways, respectively.^[20]^[21] For ATR activation, incision of AP sites by APE2 produces single-stranded DNA coated with replication protein A, which facilitates ATR recruitment and phosphorylation of Chk1, enforcing cell cycle arrest in S phase to allow time for resolution.^[21] Similarly, ATM responds to BER intermediates from AP sites, promoting Chk2 activation and halting progression through G2/M to prevent propagation of damage.^[20] These checkpoints collectively pause the cell cycle, enabling coordination of repair efforts and averting catastrophic outcomes like widespread genomic alterations.

Mutagenic Potential

AP sites pose a significant mutagenic threat during DNA replication, as they lack a base for accurate template-directed synthesis, leading to error-prone translesion synthesis (TLS) by specialized DNA polymerases. In humans, Y-family polymerases such as DNA polymerase η (pol η) and ι (pol ι), along with B-family polymerases like pol δ in complex with PCNA, facilitate bypass of AP sites, but with low fidelity; for instance, pol δ/PCNA inserts adenine (A) opposite the lesion in approximately 58% of cases, while pol α prefers A in 85% of insertions, adhering to the "A-rule" observed across species.^[22] This preferential insertion of A can result in base substitutions, particularly G:C to A:T transitions if the original base was guanine, thereby introducing point mutations that alter the genetic code.^[22] The error-prone nature of TLS across AP sites extends to other polymerases, such as REV1, which favors cytosine insertion, further diversifying potential mismatches and contributing to a spectrum of mutations including transversions and, less commonly, frameshifts if bypass occurs in repetitive regions.^[22] In model organisms, unrepaired AP sites induce mutations through TLS mediated by polymerases, often following the A-rule, which underscores the lesion's high mutagenic potential.^[23] These mutations can propagate heritably, driving genetic instability that may confer evolutionary advantages through increased variation, though at the cost of potential deleterious effects in populations.^[23] AP sites play a central role in mutagenesis assays, such as site-specific lesion studies in yeast and bacteria, where they are introduced to quantify TLS fidelity and mutation spectra, revealing dependencies on polymerases like pol ζ for extension beyond the lesion.^[23] In humans, deficiencies in base excision repair components like APE1 or MUTYH predispose individuals to cancer; for example, biallelic MUTYH mutations cause MUTYH-associated polyposis, leading to colorectal cancer with elevated G:C to T:A transversions due to unrepaired oxidative DNA damage.^[24] Similarly, polymorphisms in OGG1 (e.g., Ser326Cys) increase lung cancer risk by reducing the efficiency of removing oxidized bases, leading to persistent DNA damage and increased mutagenesis, highlighting the lesion's contribution to tumorigenesis when repair is compromised.^[24]

Repair Mechanisms

Base Excision Repair Pathway

The base excision repair (BER) pathway serves as the principal cellular mechanism for addressing apurinic/apyrimidinic (AP) sites, which arise as intermediates following the removal of damaged bases by DNA glycosylases.^[7] This high-fidelity process prevents mutagenesis and maintains genomic integrity by precisely excising and replacing the lesion without distorting the DNA helix.^[25] In humans, the pathway is initiated at the AP site by apurinic/apyrimidinic endonuclease 1 (APE1), the major AP endonuclease, which hydrolytically cleaves the phosphodiester backbone immediately 5' to the AP site.^[26] This incision generates a single-strand break featuring a 3'-hydroxyl (3'-OH) terminus suitable for polymerase extension and a 5'-deoxyribose phosphate (5'-dRP) blocking group at the 5' end.^[26] APE1's activity accounts for over 95% of cellular AP endonuclease function and is essential for viability, as its deficiency leads to embryonic lethality in mice.^[27] Following APE1-mediated incision, the repair gap is filled through one of two subpathways: short-patch or long-patch BER. In the predominant short-patch variant, DNA polymerase β (Pol β), the primary BER polymerase, utilizes its dRP lyase activity to remove the 5'-dRP moiety via β-elimination, simultaneously incorporating a single correct nucleotide using the 3'-OH primer.^[28] The resulting nick is then sealed by DNA ligase IIIα, often in complex with XRCC1, ensuring efficient closure in non-replicating cells.^[29] This subpathway predominates for simple AP sites and is highly efficient, with Pol β mutations implicated in approximately 30% of human epithelial cancers due to impaired repair.^[30] In contrast, long-patch BER engages replicative polymerases such as DNA polymerase δ/ε, which synthesize 2–10 nucleotides and create a displaced flap on the downstream strand; this flap is subsequently removed by flap endonuclease 1 (FEN1), and the nick is ligated by DNA ligase I.^[31] The long-patch mode is favored in proliferating cells or when 5'-dRP removal is inefficient, involving additional coordination with proliferating cell nuclear antigen (PCNA).^[31] Upstream of APE1, DNA glycosylases exhibit specificity for particular base lesions to generate the AP site, tailoring the pathway to damage type. For instance, 8-oxoguanine DNA glycosylase 1 (OGG1), a bifunctional enzyme, specifically recognizes and excises oxidized purines such as 8-oxoguanine paired with cytosine, employing both glycosylase and β-lyase activities to create the AP site and initiate strand cleavage.^[32] OGG1's high affinity for 8-oxoG (with dissociation constants in the nanomolar range) ensures selective repair of oxidative damage, preventing G-to-T transversions.^[32] Other glycosylases, like uracil-DNA glycosylase (UNG), handle deaminated bases, but the core post-AP site steps remain conserved across BER variants.^[7]

Alternative Repair Processes

While base excision repair serves as the primary pathway for addressing most AP sites in DNA, alternative processes activate when these lesions persist, cluster, or complicate replication. Nucleotide excision repair (NER) provides a secondary mechanism for removing AP sites, especially clustered ones or those associated with bulky lesions that evade or overwhelm base excision repair. In human cells, NER efficiently processes BER-resistant AP lesions, enhancing overall repair efficiency through both global genome NER and transcription-coupled NER subpathways, with essential roles for proteins like XPA and XPF. For example, AP sites arising from UV-induced damage—such as those formed after glycosylase removal of oxidized pyrimidines—are handled by NER, particularly when they distort the DNA helix or block transcription.^[33]^[33]^[34] Unrepaired AP sites can generate single-strand breaks that, during replication or in clustered configurations, convert into double-strand breaks (DSBs). These DSBs are primarily repaired via homologous recombination (HR), which uses an undamaged sister chromatid as a template for error-free restoration, or non-homologous end joining (NHEJ), a faster but error-prone pathway that directly ligates break ends and predominates outside S/G2 phases. In yeast models lacking AP endonucleases, alkylation-induced AP sites lead to DSBs in G2-arrested cells through lyase-generated nicks, with HR—dependent on RAD51, RAD52, and cohesin—being the dominant repair mode, while NHEJ contributes minimally.^[35]^[35]^[35] When replication forks encounter unrepaired AP sites, translesion synthesis (TLS) enables bypass using specialized, low-fidelity polymerases to avoid fork collapse. In yeast, DNA polymerase zeta (Pol ζ), often acting with polymerase delta (Pol δ) for insertion and Rev1 for deoxycytidine transfer, extends from nucleotides opposite the lesion, promoting tolerance at the cost of accuracy. This bypass is mutagenic, with adenine inserted opposite AP sites in approximately 64% of events, followed by cytosine (14%), guanine (11%), and thymine (11%), yielding an error rate far higher than replicative polymerases and contributing to base substitutions if uncorrected.^[36]^[36]^[36]

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