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Title: Mapping DNA polymerase errors by single-molecule sequencing

Abstract

Genomic integrity is compromised by DNA polymerase replication errors, which occur in a sequence-dependent manner across the genome. Accurate and complete quantification of a DNA polymerase's error spectrum is challenging because errors are rare and difficult to detect. We report a high-throughput sequencing assay to map in vitro DNA replication errors at the single-molecule level. Unlike previous methods, our assay is able to rapidly detect a large number of polymerase errors at base resolution over any template substrate without quantification bias. To overcome the high error rate of high-throughput sequencing, our assay uses a barcoding strategy in which each replication product is tagged with a unique nucleotide sequence before amplification. Here, this allows multiple sequencing reads of the same product to be compared so that sequencing errors can be found and removed. We demonstrate the ability of our assay to characterize the average error rate, error hotspots and lesion bypass fidelity of several DNA polymerases.

Authors:
ORCiD logo [1];  [1];  [2];  [2];  [1]
  1. Harvard Univ., Cambridge, MA (United States)
  2. Harvard Medical School, Boston, MA (United States)
Publication Date:
Research Org.:
Harvard Univ., Cambridge, MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1360141
Grant/Contract Number:  
SC0012411
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 44; Journal Issue: 13; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; dna; dna-directed dna polymerase; amplification; bar codes; molecule

Citation Formats

Lee, David F., Lu, Jenny, Chang, Seungwoo, Loparo, Joseph J., and Xie, Xiaoliang S. Mapping DNA polymerase errors by single-molecule sequencing. United States: N. p., 2016. Web. doi:10.1093/nar/gkw436.
Lee, David F., Lu, Jenny, Chang, Seungwoo, Loparo, Joseph J., & Xie, Xiaoliang S. Mapping DNA polymerase errors by single-molecule sequencing. United States. doi:10.1093/nar/gkw436.
Lee, David F., Lu, Jenny, Chang, Seungwoo, Loparo, Joseph J., and Xie, Xiaoliang S. Mon . "Mapping DNA polymerase errors by single-molecule sequencing". United States. doi:10.1093/nar/gkw436. https://www.osti.gov/servlets/purl/1360141.
@article{osti_1360141,
title = {Mapping DNA polymerase errors by single-molecule sequencing},
author = {Lee, David F. and Lu, Jenny and Chang, Seungwoo and Loparo, Joseph J. and Xie, Xiaoliang S.},
abstractNote = {Genomic integrity is compromised by DNA polymerase replication errors, which occur in a sequence-dependent manner across the genome. Accurate and complete quantification of a DNA polymerase's error spectrum is challenging because errors are rare and difficult to detect. We report a high-throughput sequencing assay to map in vitro DNA replication errors at the single-molecule level. Unlike previous methods, our assay is able to rapidly detect a large number of polymerase errors at base resolution over any template substrate without quantification bias. To overcome the high error rate of high-throughput sequencing, our assay uses a barcoding strategy in which each replication product is tagged with a unique nucleotide sequence before amplification. Here, this allows multiple sequencing reads of the same product to be compared so that sequencing errors can be found and removed. We demonstrate the ability of our assay to characterize the average error rate, error hotspots and lesion bypass fidelity of several DNA polymerases.},
doi = {10.1093/nar/gkw436},
journal = {Nucleic Acids Research},
number = 13,
volume = 44,
place = {United States},
year = {2016},
month = {5}
}

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