High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
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gky296.pdf
Description
Published version
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1.02 MB
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Unknown
Checksum (MD5)
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Author(s)
de Paz, Alexandra M
Cybulski, Thaddeus R
Marblestone, Adam H
Zamft, Bradley M
Church, George M
Boyden, Edward
Kording, Konrad P
Tyo, Keith EJ
Date Issued
2018
Journal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Version
Final published version
Abstract
DNA polymerase fidelity is affected by both intrinsic properties and environmental conditions. Current strategies for measuring DNA polymerase error rate in vitro are constrained by low error subtype sensitivity, poor scalability, and lack of flexibility in types of sequence contexts that can be tested. We have developed the Magnification via Nucleotide Imbalance Fidelity (MagNIFi) assay, a scalable next-generation sequencing assay that uses a biased deoxynucleotide pool to quantitatively shift error rates into a range where errors are frequent and hence measurement is robust, while still allowing for accurate mapping to error rates under typical conditions. This assay is compatible with a wide range of fidelity-modulating conditions, and enables high-throughput analysis of sequence context effects on base substitution and single nucleotide deletion fidelity using a built-in template library. We validate this assay by comparing to previously established fidelity metrics, and use it to investigate neighboring sequence-mediated effects on fidelity for several DNA polymerases. Through these demonstrations, we establish the MagNIFi assay for robust, high-throughput analysis of DNA polymerase fidelity.
MIT Department
Massachusetts Institute of Technology. Media Laboratory
Massachusetts Institute of Technology. Department of Biological Engineering
McGovern Institute for Brain Research at MIT
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1093/NAR/GKY296
