High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing

Alexandra M. de Paz, Thaddeus R. Cybulski, Adam H. Marblestone, Bradley M. Zamft, George M. Church, Edward S. Boyden, Konrad P. Kording, Keith E.J. Tyo

Research output: Contribution to journalArticle

3 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)e78
JournalNucleic acids research
Volume46
Issue number13
DOIs
StatePublished - Jul 27 2018

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing'. Together they form a unique fingerprint.

  • Cite this

    de Paz, A. M., Cybulski, T. R., Marblestone, A. H., Zamft, B. M., Church, G. M., Boyden, E. S., Kording, K. P., & Tyo, K. E. J. (2018). High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. Nucleic acids research, 46(13), e78. https://doi.org/10.1093/nar/gky296