*2.1.1 Base excision repair (BER)*

BER pathway corrects DNA damage from oxidation, deamination, alkylation, and other small DNA alterations that do not distort the overall structure of double helix. In general, BER is initiated by a DNA glycosylase that recognizes and

#### **Figure 2.**

*Age-related changes in DNA repair and their consequences. Aging involves deterioration of DNA repair systems allowing the damages to accumulate and eventually cause a malfunction of the cells. In general, all agerelated changes in DNA repair pathways promote genomic instability in different ways. Decline in efficiency and fidelity of BER and NER leads to point mutations, whereas inefficient MMR leads to microsatellite instability and point mutations. Meanwhile, deficiencies in NHEJ and HRR result in deletions and genomic rearrangements.* 

 removes the damaged base, leaving an abasic (apurinic/apyrimidinic; AP) site that is subsequently processed by an AP endonuclease (APE), an exonuclease, a DNA polymerase, a ligase, and many other ancillary factors in a short-patch repair or long-patch repair [26]. Notably, several pieces of evidence indicate that the efficacy of BER may negatively change with age, and it has a significant impact in longevity together with homologous recombination repair (HRR) [27]. Age-related changes in the BER mechanism have been studied mainly in neuronal extracts where it constitutes the main repair pathway. In this way, an overall deficiency in several factors has been observed [28], where DNA polymerase β (pol β) together with DNA ligase [29] and APE1 activities [30, 31] seem to be the most limiting factors. Interestingly, an age-dependent attenuation in the transcriptional activation of pol β and APE1 was observed in response to DNA damage [32] together with APE1 accumulation in the nucleus and mitochondria [33]. Aging has also been shown to have a significant effect on cleavage efficacy of tetrahydrofuran:A, U:G mispair, U:A base pair, thymine glycol:A, and 8-oxo-7,8-dihydroguanine:C [34]. Thus, senescent human fibroblasts as well as leukocytes from old donors showed higher basal level of AP sites than young donors. However, after a challenge with the oxidizing agent H2O2 or the alkylating agent methyl methanesulfonate (MMS), the number of AP sites increased quickly in young cells, whereas in senescent and older cells, they were observed to grow slowly with a concomitant loss of viability, suggesting a decrease in DNA glycosylase activity, mainly in OGG1 8-oxoguanine and 3-methyladenine DNA glycosylases [35], although other reports have also mentioned a decrease in the UDG uracil-DNA glycosylase [28]. Because polyADP-ribosylation (PARylation) levels are linked to downstream mechanisms in DNA repair together with other cellular deficiencies as cell-cycle arrest, cell survival, cell death, and/or cell transformation, a decline in PARP1 activity is important since it has been linked with the age in humans and rats [36]. Further, a decrease in the interaction between the endonuclease VIII-like NEIL1 and PARP1 was observed in old mice when compared to young mice [37], which also could be associated with the decrease in PARP1 activity. Meanwhile, a significant decrease in the expression of SIRT6 has been reported to have a relevant role in BER because it regulates repair activity through a PARP1-dependent pathway [38]. Since sirtuins can function as metabolic sensors, they could also be related with a significative increase in pol β [39] and APE activities [30] under caloric restricted diets. Consequently, BER pathway showed to be deficient when repairing age-downregulated genes in comparison with genes that are not affected by age [40].

On the other hand, the mitochondrial free radical theory of aging states that free radicals generated in mitochondria are strongly related with the intrinsic aging process, mainly due to the accumulation of oxidative damage and derived mutations in mitochondrial DNA (mtDNA) mainly in D-loop region. mtDNA is more susceptible to oxidative damage than the nuclear genome, presumably because of the physical proximity of the source of ROS and lack of histones [41]. BER is the predominant and best understood DNA repair pathway in mitochondria involving at least four components, a DNA glycosylase, an AP endonuclease (or other mechanism for processing abasic sites), DNA polymerase γ (pol γ), and DNA ligase [42]. Recently, pol β was also detected in mitochondrial protein extracts, where it is required to provide enhanced mtDNA BER activity [43]. In a similar way to nuclear BER, in rat brain mitochondria, there is a marked age-dependent decline in mitochondrial BER activity, as indicated by a pol β, pol γ, ligase, APE1 endonuclease, and OGG1 glycosylase activities [44]. Interestingly, activity of mitochondrial OGG1 AE8-oxoguanine DNA glycosylase increases in mouse liver mitochondria according with the age [45]. However, a significant fraction of the OGG1 remains in the outer membrane and intermembrane space in an immature form, presumably because

its import into the mitochondrial matrix is impaired as a consequence of aging. In addition, a nearly identical phenomenon was observed with the mitochondrial uracil-DNA glycosylase [46].
