title: Structures of mismatch replication errors observed in a DNA polymerase.
abstract: Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.
authors.affiliation: Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
authors.forename: Sean J
authors.initials: SJ
authors.lastname: Johnson
authors.forename: Lorena S
authors.initials: LS
authors.lastname: Beese
mesh_terms: D020137:Base Pair Mismatch / Q000235:genetics*; D001483:Base Sequence / Q000235:genetics; D004247:DNA / Q000096:biosynthesis* / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics*; D004259:DNA-Directed DNA Polymerase / Q000235:genetics* / Q000378:metabolism; D001411:Geobacillus stearothermophilus; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D009711:Nucleotides; D011687:Purines; D011743:Pyrimidines; D004247:DNA; D004259:DNA-Directed DNA Polymerase