Alkyltransferases are enzymes that reverse lesions caused by alkylating agents. The excised gap is 12 or 13 nucleotides in prokaryotes, 27-29 nucleotides in eukaryotes. This strand is resynthesized using DNA polymerase I and the strand is sealed using a ligase. DNA glycosylases recognize altered bases and cleave the base from its sugar thereby creating an AP site. AP sites are recognized by AP endonucleases which then excise the AP site and replace it with an appropriate nucleotide using DNA polymerase I and a ligase.
Mismatch repair occurs soon after the DNA is replicated.
Incorrectly matched base pairs are recognized and the incorrect nucleotide is excised and replaced by a correct nucleotide. The difficulty in this system is identifying which strand contains the incorrect nucleotide. This is done in prokaryotes by taking advantage of the fact that when a DNA sequence 5 GATC3 occurs, the adenine will be methylated in prokaryotes. However, this methylation occurs post-replication. Therefore, there is a short period of time during which only one of the two DNA strands is methylated and this represents the older strand and the one with the correct sequence.