Major DNA repair mechanisms take advantage of the fact that DNA is double-stranded, with the same information on both strands. Consequently, in cases where damage is present in just one strand, the damage can be accurately repaired by excising and replacing it with new DNA, synthesized using the complementary strand as template. All organisms, prokaryotic and eukaryotic, employ at least three excision mechanisms: 1) mismatch repair, 2) base excision repair, and 3) nucleotide excision repair. Mismatch repair functions mainly in concert with replication and recognizes rare mismatches embedded in millions of correctly base-paired nucleotides in the newly replicated DNA. By virtue of the directionality of the replication machinery and the location of Okazaki fragments, repair is directed to the newly synthesized strand (26354434
).Mismatch repair removes a section of nascent DNA, including the misincorporated nucleotide, terminating excision just beyond the mismatch. Finally, mismatch repair fills the excision gap by high fidelity DNA synthesis. Ligation subsequently restores strand continuity.
DNA mismatch repair in eukaryotes is a complex, multistep process. First, the mismatch is bound by MutSα heterodimer MSH2/MSH6 (for base-base mismatches and one or two base loops), or MutSβ heterodimer MSH2/MSH3 for loops of 2-14 bp. The mismatch-bound Msh2/Msh6 undergoes an ATP-dependent conformational change which converts it to a sliding clamp capable of translocating along the DNA backbone. The MSH2/MSH6-ATP-DNA complex is bound by a second heterodimer composed of MLH1 and PMS2 (which compose MutLα) in a second ATP-dependent step. This complex can translocate in either direction in search of a strand discontinuity. MLH1 and PMS2 are endonucleases that create a series of nicks around the mispair to prime that strand for exonuclease digestion, and are stimulated by PCNA.
Mismatch repair must be directed to the newly synthesized strand, which in eukaryotes can be distinguished from the template strand by the presence of gaps between Okazaki fragments on the lagging strand or by the free 3' terminus on the leading strand. The replication-derived strand break that directs correction can be located either 3' or 5' to the mispair, with mismatch provoked excision removing that portion of the incised strand spanning the two DNA sites. Communication appears to be through space, followed by translocation of the PCNA/RFC complex over the intervening DNA to the mismatch complex (17921148
In strand resynthesis the Msh2/Msh6 sliding clamp stimulates the activity of EXO1, a 5'-to-3' exonuclease that degrades a stretch of several hundred nucleotides starting from a nick situated 5' from the mispair and traveling towards the mispair. The resulting single stranded DNA is stabilized by RPA. This makes the gapped substrate refractory to further degradation by EXO1 until RPA is stimulated by further molecules of ATP-bound Msh2/Msh6 heterodimer arriving from the direction of the mispair. MSH2,3,6, MLH1, EXO1, PMS2, RPA, and DNA polymerase-δ support mismatch repair directed by a strand break located either 3' or 5' to the mispair, while RFC and PCNA are additionally required when the break is 3' to the mismatch. Polymerase-δ and its cofactors PCNA and RFC fill in the resulting single-stranded gap, and DNA ligase I seals the remaining nick. (Upgraded 04/2022)