Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity

Tjalle P. Hoekstra, Martin Depken, Szu-Ning Lin, Jordi Cabanas-Danes, Peter Gross, Remus T. Dame, Erwin J. G. Peterman, Gijs J. L. Wuite

Research output: Contribution to JournalArticleAcademicpeer-review

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.
Original languageEnglish
Pages (from-to)575-583
JournalBiophysical Journal
Volume112
Issue number4
DOIs
Publication statusPublished - 28 Feb 2017

Cite this

Hoekstra, Tjalle P. ; Depken, Martin ; Lin, Szu-Ning ; Cabanas-Danes, Jordi ; Gross, Peter ; Dame, Remus T. ; Peterman, Erwin J. G. ; Wuite, Gijs J. L. / Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity. In: Biophysical Journal. 2017 ; Vol. 112, No. 4. pp. 575-583.
@article{6fcbf7628ff045af8ee87f25c74a239c,
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.",
author = "Hoekstra, {Tjalle P.} and Martin Depken and Szu-Ning Lin and Jordi Cabanas-Danes and Peter Gross and Dame, {Remus T.} and Peterman, {Erwin J. G.} and Wuite, {Gijs J. L.}",
year = "2017",
month = "2",
day = "28",
doi = "10.1016/j.bpj.2016.12.044",
language = "English",
volume = "112",
pages = "575--583",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "4",

}

Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity. / Hoekstra, Tjalle P.; Depken, Martin; Lin, Szu-Ning; Cabanas-Danes, Jordi; Gross, Peter; Dame, Remus T.; Peterman, Erwin J. G.; Wuite, Gijs J. L.

In: Biophysical Journal, Vol. 112, No. 4, 28.02.2017, p. 575-583.

Research output: Contribution to JournalArticleAcademicpeer-review

TY - JOUR

T1 - Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity

AU - Hoekstra, Tjalle P.

AU - Depken, Martin

AU - Lin, Szu-Ning

AU - Cabanas-Danes, Jordi

AU - Gross, Peter

AU - Dame, Remus T.

AU - Peterman, Erwin J. G.

AU - Wuite, Gijs J. L.

PY - 2017/2/28

Y1 - 2017/2/28

N2 - 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.

AB - 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.

U2 - 10.1016/j.bpj.2016.12.044

DO - 10.1016/j.bpj.2016.12.044

M3 - Article

VL - 112

SP - 575

EP - 583

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 4

ER -