Journal of Aging Research from DNA is crucial due to its ability to pair with adenine, causing GC to AT transition mutations upon replication. Despite UNG was the ﬁrst DNA-glycosylase investigated, it is Ogg1 the one that has been investigated most extensively. Ogg1 is a bifunctional DNA glycosylase that recognizes and cleaves 8-hydroxi-guanine (8-oxoG) from double-strand DNA. For many years, this DNA lesion has been the most broadly used as DNA damage marker, both in nuclear and mitochondrial DNA, mainly because 8-oxoG is relatively easy to detect and measure. However, it does not necessarily mean that 8-oxoG is the most frequent and biologically relevant DNA lesion. Actually, oxidative DNA lesions such as 2,6- diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA) have been detected in genomic DNA at similar or even higher levels than 8-oxoG. Recently a new group of DNA glycosylases, NEIL glycosylases, has been identiﬁed in mammalian tissues primarily excising FapyG and FapyA. These glycosylases are homologous of the Escherichia coli DNA glycosylases Fpg/Nei and three main isoforms, NEIL1, NEL2, and NEIL3, have been described [43, 44], being present both in nucleus and mitochondria [34, 44, 45]. Moreover, some of them have been involved in repair mechanisms of oxidative lesions in transcribed or replicating DNA [46]. The identiﬁcation of this group of DNA glycosylases in mammals was of great interest, particularly when the knock-out (KO) mouse for NEIL1 was developed [47]. Due to the partial redundancy in the activity of DNA glycosylases, KO mice for most of them do not exhibit a signiﬁcant phenotype. However, KO mice for NEIL1 accumulate mtDNA deletions to a higher extent than wild-type mice and develop symptoms associated with the metabolic syndrome [47]. After recognition and cleavage of the modiﬁed or erroneous base by the speciﬁc DNA glycosylase, an abasic site is generated. Repair of these lesions shares common steps with that of ROS-induced DNA single-strand breaks and spontaneously generated AP sites. These DNA lesions are continuously generated and various enzymatic processes have evolved to repair them. Among those processes, AP endonuclease (APE) is the most important and ubiquitous [48]. Although two isoforms of APE, APE1 and APE2, have been described in mammalian tissues, APE1 is the main AP endonuclease in mammalian cells taking part of the BER processes both in nucleus and mitochondria [49]. The absence of signiﬁcant APE-speciﬁc activity of the recombinant APE2 has suggested that it functions in other cellular processes diﬀerent than BER [50]. Together with its activity in DNA repair processes, APE1 also has a redox activity that is involved in signal transduction. APE1 participates in several important cellular mechanisms such as apoptosis, proliferation, and diﬀerentiation functioning as a transcriptional coactivator [51–53]. Unlike most of the known enzymes taking part in the BER process in mitochondria, mitochondrial APE nature remains unclear. It is still discussed whether the mitochondrial APE is an N- terminal truncated product of APE1 [54]. The deletion of the N-terminal residues containing the nuclear localization signal has been described to induce a 3-fold increase in the speciﬁc activity of APE1 [55], and APE activity is higher in 3 mitochondrial fractions than in nuclear fractions. However, the presence of this truncated isoform of APE1 has only been reported in bovine liver mitochondria, while no truncated product has been observed in mitochondrial extracts of diﬀerent human cell lines [55]. The relevance of APE1 in mammalian cells is stressed by the reports showing a signiﬁcant increase in single-strand breaks as well as AP sites when APE1 is inactivated [56, 57]. Moreover, and in contrast to DNA glycosylase KO mice, cellular survival is critically compromised in the absence of APE1, and KO mice for APE1 show embryonic lethality [58]. 3.2. Mitochondrial BER: Final Steps, Short- and Long-Patch BER. Once the AP site has been processed by APE1, the following step in the BER pathway is catalyzed by a DNA polymerase, which inserts the correct nucleotide(s) in the generated gap. There is only one known DNA polymerase in mammalian mitochondria, the DNA polymerase gamma (polγ), which is involved in all replication and repair of mtDNA. Two diﬀerent BER subpathways exist depending on whether polγ inserts one nucleotide or more: short- patch (SP) or long-patch (LP) BER [26]. During the SP- BER, one single nucleotide is incorporated into the gap by polγ, while the LP-BER involves the incorporation of several nucleotides, typically 2 to 7. Long-patch BER processing of a DNA lesion is more complex than SP-BER, since the incorporation of various nucleotides results in the exposure of the original DNA strand as part of a single-strand overhang or ﬂap structure. Additional enzymatic activities are required in order to process such structure [27]. In the nucleus, the ﬂap structure is recognized and cleaved by the ﬂap endonuclease 1 (FEN-1), which is an essential enzyme for LP-BER [59]. Why BER proceeds through the short- or long-patch is not completely understood. It seems to depend, at least in part, on the type of lesion and on the intermediates that are generated during the process. For instance, AP sites can be further oxidized, and this sort of DNA lesion requires to be processed by LP-BER [60]. Until recently it was believed that SP-BER occurred both in nucleus and mitochondria, whereas LP-BER only took place in the nucleus. However, considering the constant exposure of mtDNA to mitochondrial-free radicals, it was likely that certain types of lesions, such as oxidized AP sites, were generated at a signiﬁcant rate in mtDNA [60]. Therefore, SP-BER would be insuﬃcient to cope with all the collection of lesions inﬂicted in mtDNA. Various investigations have recently shown that, likewise nuclear BER, mitochondrial BER can also progress in a long-patch manner [30–32, 61]. Furthermore, and similarly to nuclear long-patch BER, diﬀerent studies support that FEN-1 plays an important role in mitochondrial LP-BER [31, 61]. Besides, during the processing of the 5 ﬂap structure FEN-1 interacts with Dna2, a helicase/nuclease protein, in human HeLa cell mitochondria [35]. The ﬁnal step of the mitochondrial BER pathway, the nick sealing, is catalyzed by a DNA ligase. While two DNA ligases are described in the nucleus (I and III), in mammalian mitochondria only DNA ligase III has been detected, acting both in replication and repair. DNA ligase