**4. Single Base Variations and Mismatched Base Pairs Are Repaired by Specific Pathways Linked to Cancer**

BER is a pathway involved in repair of small base lesions such as oxidation, alkylation, and deamination (Figure 3A). The steps of the mechanism are: DNA damage recognition, excision of the base by a DNA glycosylase to generate an abasic (AP) site, and cleavage of the AP site by the AP endonuclease APE1 to form a DNA single strand break (SSB) [67]. When the SSB is formed, one of the first proteins activated is PARP1, which, acting as a SSB sensor, promotes recruitment of other enzymes involved in the repair process, such as XRCC1 [68,69]. Finally, the gap is filled by DNA polymerase β and the complex XRCC1 and LIG3 seals the nick, or as an alternative, two to 10 nucleotides are removed, a new nucleotide chain is synthetized by DNA polymerase and the final ligation step is performed by LIG1 (Figure 3A). *Int. J. Mol. Sci.* **2020**, *21*, x FOR PEER REVIEW 8 of 30

**Figure 3.** Small base lesions are repaired by base excision repair; mismatched base pairs and insertion/deletion loops are corrected by mismatch repair pathway. (**A**) DNA lesion is recognized by PARP1 which recruits a DNA glycosylase that removes the damaged base; then, APE1 digests the abasic site determining a SSB that is repaired by the combined action of LIG1/3, XRCC1 and Pol-β. (**B**) The mismatched base is recognized by the complexes MutS and MutL that, in turn, recruit the DNA helicases II to unwind the DNA strands; thereafter, the complex formed by MLH1/PMS1 digests DNA several bases from the mismatch, forming a nick. The EXO1 nuclease digests the DNA from the nick towards the mismatch; finally, the removed strand is re-synthetized by Pol-δ and ligated by LIG1. **Figure 3.** Small base lesions are repaired by base excision repair; mismatched base pairs and insertion/deletion loops are corrected by mismatch repair pathway. (**A**) DNA lesion is recognized by PARP1 which recruits a DNA glycosylase that removes the damaged base; then, APE1 digests the abasic site determining a SSB that is repaired by the combined action of LIG1/3, XRCC1 and Pol-β. (**B**) The mismatched base is recognized by the complexes MutS and MutL that, in turn, recruit the DNA helicases II to unwind the DNA strands; thereafter, the complex formed by MLH1/PMS1 digests DNA several bases from the mismatch, forming a nick. The EXO1 nuclease digests the DNA from the nick towards the mismatch; finally, the removed strand is re-synthetized by Pol-δ and ligated by LIG1.

MMR is a pathway responsible for correcting mismatched base pairs and insertion/deletion loops (IDLs) that may occur during DNA replication [70] (Figure 3B). The central players are MutS proteins that form two heterodimers, MutSα (MSH2-MSH6) and MutSβ (MSH2-MSH3), and MutL

endonuclease activity of MLH1-PMS1, activated by the PCNA clamp produces a nick of the DNA strand [71]. Subsequently, the nicked DNA strand with the mismatch is excised by EXO1. Finally,

POL δ synthesizes a new fragment and DNA ligase I (LIG1) catalyzes strand ligation [72].

MMR is a pathway responsible for correcting mismatched base pairs and insertion/deletion loops (IDLs) that may occur during DNA replication [70] (Figure 3B). The central players are MutS proteins that form two heterodimers, MutSα (MSH2-MSH6) and MutSβ (MSH2-MSH3), and MutL proteins that form three heterodimers, MutLα (MLH1-PMS2), MutLβ (MLH1-MLH3), and MutLγ (MLH1-PMS1). MutS dimer recognizes the mismatched base on the daughter strand and binds the damaged DNA; MutL recruits the DNA Helicase II to separate the two strands. Then, the entire complex slides along the DNA, unwinding the strand that must be excised. Thereafter, the endonuclease activity of MLH1-PMS1, activated by the PCNA clamp produces a nick of the DNA strand [71]. Subsequently, the nicked DNA strand with the mismatch is excised by EXO1. Finally, POL δ synthesizes a new fragment and DNA ligase I (LIG1) catalyzes strand ligation [72].

There are few relations between BER and cancer; alterations in this pathway have been associated with colon and breast cancer [73,74]. Particularly, Pol-β expression seems to have a protective role against breast and lung carcinomas by impairing cancer cell metastasis due to an increased DNA de-methylation [75]; accordingly, Pol-β deficiency is associated with aggressive breast cancer [76]. Moreover, variants of this protein affecting its fidelity are associated to prostate and colon cancer [77,78] and could drive cellular transformation leading to cancer onset [79]. Instead, germline mutations in MMR genes are associated with hereditary non-polyposis colorectal cancer (HNPCC), also known as Lynch Syndrome, an autosomal dominant disease. Moreover, mutations in all the MMR genes, *MLH1* and *MSH2, PMS2* and *MSH6* have been found related to breast cancer susceptibility [50,80–84].
