Wortmannin DNA repair is essential for cell survival and for
DNA repair is essential for cell survival and for tissue homeostasis given that cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that generate DNA damage: structural and chemical modifications of a primary DNA sequence. Various organisms have evolved multiple DNA repair systems to deal with these insults. Nonbulky Wortmannin damage is specifically recognized among the vast majority of regular bases by DNA glycosylases and apurinic/apyrimidinic (AP) endonucleases in the base excision repair (BER) and nucleotide incision repair (NIR) pathways, respectively [, , , ]. In the BER pathway, a DNA glycosylase hydrolyses the N-glycosidic bond between the damaged base and sugar, leaving either an apurinic/apyrimidinic (AP) site or a single-stranded DNA break. Based on the mechanism of action, DNA glycosylases are classified into mono- and bifunctional. Monofunctional DNA glycosylases such as human mismatch-specific thymine-DNA glycosylase (TDG), methyl-CpG-binding domain 4 (MBD4, a.k.a. MED1), and alkyl-N-purine-DNA glycosylase (ANPG, a.k.a. Aag or MPG) cleave the N-glycosidic bond, releasing the modified base and generating an AP site [, , ]. Bifunctional DNA glycosylases such as human 8-oxoguanine-DNA glycosylase 1 (OGG1) and endonuclease VIII-like glycosylases (NEIL1-3) not only cleave the N-glycosidic bond but also exert an associated AP lyase activity that eliminates the 3′ phosphate (β-elimination) or 3′ and 5′ phosphates (β,δ-elimination) of the resulting AP site either in a concerted or in a nonconcerted manner [, ]. It should be noted that mammalian bifunctional DNA glycosylases such as NEIL1 and NEIL2 excise the modified base and cleave the resulting AP site in DNA via β/δ-elimination in a highly concerted manner [, ]. In contrast, other bifunctional DNA glycosylases such as OGG1 and NEIL3 manifest nonconcerted action, with base excision being more efficient than AP site cleavage activity [, ]. β-Elimination produces a nick flanked by a 3′-terminal α,β-unsaturated aldehyde and a 5′-terminal phosphate, whereas β,δ-elimination yields a single-nucleoside gap flanked by two phosphates [, ]. At a subsequent step, the 3′-terminal phosphoaldehyde and phosphate are removed by an AP endonuclease and polynucleotide kinase (PNK), respectively, allowing DNA polymerase to fill the gap before DNA ligase seals the resulting DNA nick [, ]. BER, initiated by multiple DNA glycosylases, is the main pathway for removal of the majority of nonbulky DNA lesions [, ]; however, a certain type of lesions – such as the α-anomers of 2′-deoxynucleosides (αdN) – is repaired by AP endonucleases in the NIR pathway, not by DNA glycosylases [, , ]. Human major apurinic/apyrimidinic (AP) endonuclease 1 (APE1, a.k.a. APEX1, HAP-1, or Ref-1) plays essential roles in both pathways. In BER, it acts downstream of DNA glycosylases by incising a DNA duplex at AP sites and removing 3′-blocking sugar phosphate moieties. Alternatively, in NIR, APE1 makes an incision 5′ to a damaged base and generates a single-strand break with a 5′-dangling modified nucleotide and a 3′-hydroxyl group [, ]. Human APE1 is a ubiquitous 36-kDa multifunctional protein that performs essential functions in DNA repair, transcription, RNA biogenesis, and cell proliferation [, ]. Moreover, DNA substrate specificity of APE1 is modulated by concentrations of divalent cations, pH, and ionic strength in an apparently allosteric manner . At low concentrations of Mg2+ (≤1 mM) and acidic or neutral pH (≤7), APE1 binds strongly to both the DNA substrate and the reaction product and exerts NIR endonuclease activity. By contrast, at high concentrations of Mg2+ (≤5 mM) and neutral or alkaline pH (≤8), APE1 shows high AP site cleavage activity mainly due to a dramatic increase in the enzyme turnover rate. Changes in intracellular Mg2+ concentration can induce conformational changes in the APE1 protein [, ]. Due to dynamic conformational changes, APE1 can recognize diverse types of DNA base lesions including αdN, oxidized pyrimidines [, ], formamidopyrimidines , exocyclic DNA bases, thymine glycol, uracil [, ], and bulky lesions such as benzene-derived DNA adducts  and a UV-induced 6–4 photoproduct . Furthermore, the chemical structures of these DNA lesions have very little in common, implying that contrary to DNA glycosylases, APE1 tends to recognize damage-induced structural distortions of the DNA helix and not a modified base itself.