Final answer:
In mismatch repair, enzymes identify the new DNA strand by its lack of methylation in E. coli and potential nicks or replication protein associations in eukaryotes, allowing them to remove incorrect bases and insert the correct ones.
Step-by-step explanation:
The question asks about the mechanism by which mismatch repair enzymes identify the newly synthesized DNA strand in order to correct mismatched nucleotides after DNA replication. In E. coli, post-replicative methyl-directed mismatch repair uses methylation status to distinguish between the parent and the new strand. The parental DNA strand is methylated, and the new strand initially lacks these methyl groups. Mismatch repair proteins (MutS, MutL, and MutH) recognize this difference and excise the incorrect nucleotide from the nonmethylated (newly synthesized) strand. The gap is then filled in with the correct base by DNA polymerase III and sealed with DNA ligase.
In eukaryotes, while the mechanism is not fully understood, it is thought to involve the recognition of nicks in the new strand and possibly a temporary association of replication proteins with the new daughter strand which helps signal which strand to repair.