title: Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity.
abstract: DNA polymerase catalyzes the accurate transfer of genetic information from one generation to the next, and thus it is vitally important for replication to be faithful. DNA polymerase fulfills the strict requirements for fidelity by a combination of mechanisms: 1) high selectivity for correct nucleotide incorporation, 2) a slowing down of the replication rate after misincorporation, and 3) proofreading by excision of misincorporated bases. To elucidate the kinetic interplay between replication and proofreading, we used high-resolution optical tweezers to probe how DNA-duplex stability affects replication by bacteriophage T7 DNA polymerase. Our data show highly irregular replication dynamics, with frequent pauses and direction reversals as the polymerase cycles through the states that govern the mechanochemistry behind high-fidelity T7 DNA replication. We constructed a kinetic model that incorporates both existing biochemical data and the, to our knowledge, novel states we observed. We fit the model directly to the acquired pause-time and run-time distributions. Our findings indicate that the main pathway for error correction is DNA polymerase dissociation-mediated DNA transfer, followed by biased binding into the exonuclease active site. The number of bases removed by this proofreading mechanism is much larger than the number of erroneous bases that would be expected to be incorporated, ensuring a high-fidelity replication of the bacteriophage T7 genome.
authors.affiliation: Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, the Netherlands; LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands.
authors.forename: Tjalle P
authors.initials: TP
authors.lastname: Hoekstra
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
authors.forename: Martin
authors.initials: M
authors.lastname: Depken
authors.affiliation: Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, the Netherlands; LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands; Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
authors.forename: Szu-Ning
authors.initials: SN
authors.lastname: Lin
authors.affiliation: Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, the Netherlands; LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands.
authors.forename: Jordi
authors.initials: J
authors.lastname: Cabanas-Danés
authors.affiliation: Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, the Netherlands; LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands.
authors.forename: Peter
authors.initials: P
authors.lastname: Gross
authors.affiliation: Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
authors.forename: Remus T
authors.initials: RT
authors.lastname: Dame
authors.affiliation: Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, the Netherlands; LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands.
authors.forename: Erwin J G
authors.initials: EJG
authors.lastname: Peterman
authors.affiliation: Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, the Netherlands; LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands. Electronic address: g.j.l.wuite@vu.nl.
authors.forename: Gijs J L
authors.initials: GJL
authors.lastname: Wuite
mesh_terms: D017123:Bacteriophage T7 / Q000201:enzymology* / Q000235:genetics*; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism*; D016679:Genome, Viral / Q000235:genetics; D007700:Kinetics; D008954:Models, Biological; D058105:Polymerization; D013696:Temperature
chemical_list: D004259:DNA-Directed DNA Polymerase