Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing
Publication Date
August 22, 2012
Journal
PLOS ONE
Authors
Bradley Michael Zamft, Adam H. Marblestone, Konrad Kording, Daniel Schmidt, et al
Volume
7
Issue
8
Pages
e43876
DOI
http://doi.org/10.1371/journal.pone.0043876
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0043876
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22928047
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3425509
Europe PMC
http://europepmc.org/abstract/MED/22928047
Web of Science
000308286300097
Scopus
84865175009
Mendeley
http://www.mendeley.com/research/measuring-cation-dependent-dna-polymerase-fidelity-landscapes-deep-sequencing
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/308289", "https://ndownloader.figshare.com/files/308327", "https://ndownloader.figshare.com/files/308365", "https://ndownloader.figshare.com/files/308401", "https://ndownloader.figshare.com/files/308461", "https://ndownloader.figshare.com/files/308479", "https://ndownloader.figshare.com/files/308501"], "description"=>"<div><p>High-throughput recording of signals embedded within inaccessible micro-environments is a technological challenge. The ideal recording device would be a nanoscale machine capable of quantitatively transducing a wide range of variables into a molecular recording medium suitable for long-term storage and facile readout in the form of digital data. We have recently proposed such a device, in which cation concentrations modulate the misincorporation rate of a DNA polymerase (DNAP) on a known template, allowing DNA sequences to encode information about the local cation concentration. In this work we quantify the cation sensitivity of DNAP misincorporation rates, making possible the indirect readout of cation concentration by DNA sequencing. Using multiplexed deep sequencing, we quantify the misincorporation properties of two DNA polymerases – Dpo4 and Klenow exo<sup>−</sup> – obtaining the probability and base selectivity of misincorporation at all positions within the template. We find that Dpo4 acts as a DNA recording device for Mn<sup>2+</sup> with a misincorporation rate gain of ∼2%/mM. This modulation of misincorporation rate is selective to the template base: the probability of misincorporation on template T by Dpo4 increases >50-fold over the range tested, while the other template bases are affected less strongly. Furthermore, cation concentrations act as scaling factors for misincorporation: on a given template base, Mn<sup>2+</sup> and Mg<sup>2+</sup> change the overall misincorporation rate but do not alter the relative frequencies of incoming misincorporated nucleotides. Characterization of the ion dependence of DNAP misincorporation serves as the first step towards repurposing it as a molecular recording device.</p> </div>", "links"=>[], "tags"=>["measuring", "cation", "dna", "polymerase", "fidelity", "landscapes", "sequencing"], "article_id"=>120828, "categories"=>["Information And Computing Sciences", "Molecular Biology", "Biological Sciences", "Biochemistry", "Biotechnology"], "users"=>["Bradley Michael Zamft", "Adam H. Marblestone", "Konrad Kording", "Daniel Schmidt", "Daniel Martin-Alarcon", "Keith Tyo", "Edward S. Boyden", "George Church"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043876.s001", "https://dx.doi.org/10.1371/journal.pone.0043876.s002", "https://dx.doi.org/10.1371/journal.pone.0043876.s003", "https://dx.doi.org/10.1371/journal.pone.0043876.s004", "https://dx.doi.org/10.1371/journal.pone.0043876.s005", "https://dx.doi.org/10.1371/journal.pone.0043876.s006", "https://dx.doi.org/10.1371/journal.pone.0043876.s007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Measuring_Cation_Dependent_DNA_Polymerase_Fidelity_Landscapes_by_Deep_Sequencing/120828", "title"=>"Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-22 00:13:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/588318"], "description"=>"<p>(A) Overview of a strategy for using DNA polymerases as signal recording devices. Signals (top) are coupled to intracellular or extracellular cation concentration through direct or indirect modulation of an ion channel activity. Cation concentration is in turn coupled to DNA polymerase fidelity on a known template according to a known transfer function (orange curve), generating a DNA recording, in which data is represented by the density of misincorporated bases, and which can be read by DNA sequencing (bottom). (B) Modulation of Taq polymerase by Ca<sup>2+</sup> concentration, measured by a traditional blue-white colony counting assay <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876-Bebenek1\" target=\"_blank\">[25]</a>. (C) Biochemical steps of the multiplex deep sequencing assay for measuring the transfer functions of error-prone DNAPs.</p>", "links"=>[], "tags"=>["polymerase", "molecular"], "article_id"=>258810, "categories"=>["Information And Computing Sciences", "Molecular Biology", "Biological Sciences", "Biochemistry", "Biotechnology"], "users"=>["Bradley Michael Zamft", "Adam H. Marblestone", "Konrad Kording", "Daniel Schmidt", "Daniel Martin-Alarcon", "Keith Tyo", "Edward S. Boyden", "George Church"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043876.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_polymerase_DNAP_as_a_molecular_signal_recorder_/258810", "title"=>"DNA polymerase (DNAP) as a molecular signal recorder.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-22 02:26:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/588416"], "description"=>"<p>(A, B, C, D) Mean (top) and template-base-specific (bottom) misincorporation rates as a function of Mn<sup>2+</sup> (A, C) and Mg<sup>2+</sup> (B, D) concentrations. (E, F, G, H) Normalized distributions of misincorporated dNTPs for each template base. (I, J, K, L) Mean (top) and template-base-specific (bottom) misincorporation rates as a function of Ca<sup>2+</sup> concentration at 200 µM background Mn<sup>2+</sup> (I, K) and 7000 µM background Mg<sup>2+</sup> (J, L) concentrations. Errors are given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876.s005\" target=\"_blank\">Tables S1</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876.s006\" target=\"_blank\">2</a>, and are shown as error bars in the line graphs when they are larger than the data symbol.</p>", "links"=>[], "tags"=>["misincorporation", "rates", "dpo4", "klenow"], "article_id"=>258906, "categories"=>["Information And Computing Sciences", "Molecular Biology", "Biological Sciences", "Biochemistry", "Biotechnology"], "users"=>["Bradley Michael Zamft", "Adam H. Marblestone", "Konrad Kording", "Daniel Schmidt", "Daniel Martin-Alarcon", "Keith Tyo", "Edward S. Boyden", "George Church"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043876.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ion_dependent_misincorporation_rates_of_Dpo4_and_Klenow_exo_8722_polymerases_/258906", "title"=>"Ion-dependent misincorporation rates of Dpo4 and Klenow exo<sup>−</sup> polymerases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-22 02:28:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/588547"], "description"=>"<p>(A) Template position dependence of Dpo4 misincorporation rates on the original template at varying Mn<sup>2+</sup> (left) and Mg<sup>2+</sup> concentration (right). (B) Template position dependence of Dpo4 misincorporation rates on the swapped template at varying Mn<sup>2+</sup> (left) and Mg<sup>2+</sup> concentration (right). (C) Template position dependence of Klenow exo<sup>−</sup> misincorporation rates on the original template at varying Mn<sup>2+</sup> (left) and Mg<sup>2+</sup> concentration (right). Letters above each data point denote the identity of the template base at that position. Grey shaded areas indicate the noise floor, defined as the maximum over positions of the misincorporation rate (plus SEM) observed in an identical experiment with Pfusion HF DNA polymerase (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043876#pone.0043876.s001\" target=\"_blank\">Figure S1</a>). Red (blue) shaded areas in (A) and (B) correspond to shared sub-sequences between the original and the swapped template.</p>", "links"=>[], "tags"=>["dependence", "misincorporation"], "article_id"=>259039, "categories"=>["Information And Computing Sciences", "Molecular Biology", "Biological Sciences", "Biochemistry", "Biotechnology"], "users"=>["Bradley Michael Zamft", "Adam H. Marblestone", "Konrad Kording", "Daniel Schmidt", "Daniel Martin-Alarcon", "Keith Tyo", "Edward S. Boyden", "George Church"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043876.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Template_position_dependence_of_misincorporation_rates_/259039", "title"=>"Template position dependence of misincorporation rates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-22 02:30:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/588648"], "description"=>"<p>(A) Spatial dependence (un-normalized) of Dpo4 error rate at 800 µM Mn<sup>2+</sup> on the original template (blue curve), and generalized linear model fits of this data set with respect to itself (green curve), and with respect to the swapped template data set (red curve). (B) Spatial dependence (un-normalized) of Dpo4 error rate at 800 µM Mn<sup>2+</sup> on the swapped template (blue curve), and generalized linear model fits of this data set with respect to itself (green curve), and with respect to the original template data set (red curve). (C) Feature weights for generalized linear model fit to Dpo4 original template data. (D) Feature weights for generalized linear model fit to Dpo4 swapped template data. (E) Information gain per base as a function of template position, for discrimination between high (800 µM) and low (75 µM) Mn<sup>2+</sup> by Dpo4. (F) Information gain per base as a function of template position, for discrimination between high (7000 µM) and low (1000 µM) Mg<sup>2+</sup> by Dpo4.</p>", "links"=>[], "tags"=>["misincorporation"], "article_id"=>259143, "categories"=>["Information And Computing Sciences", "Molecular Biology", "Biological Sciences", "Biochemistry", "Biotechnology"], "users"=>["Bradley Michael Zamft", "Adam H. Marblestone", "Konrad Kording", "Daniel Schmidt", "Daniel Martin-Alarcon", "Keith Tyo", "Edward S. Boyden", "George Church"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043876.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_analysis_of_misincorporation_by_Dpo4_/259143", "title"=>"Statistical analysis of misincorporation by Dpo4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-22 02:32:23"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"5"}
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  • {"unique-ip"=>"11", "full-text"=>"17", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"39", "full-text"=>"53", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"26", "supp-data"=>"7", "cited-by"=>"3", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"18", "full-text"=>"22", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
  • {"unique-ip"=>"11", "full-text"=>"15", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"12", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"8", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"13", "full-text"=>"9", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"7", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"6", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
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  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
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  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[316, 541, 663, 766, 856, 950, 1041, 1128, 1218, 1302, 1382, 1456, 1526, 1593, 1657, 1729, 1796, 1862, 1930, 1999, 2065, 2132, 2202, 2261, 2319]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[304, 506, 616, 712, 799, 879, 968, 1052, 1134, 1212, 1284, 1357, 1427, 1494, 1557, 1621, 1689, 1756, 1823, 1883, 1944, 1997, 2056, 2118, 2171]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[302, 508, 622, 720, 804, 888, 973, 1054, 1141, 1219, 1299, 1370, 1442, 1511, 1574, 1644, 1711, 1782, 1846, 1911, 1971, 2030, 2097, 2155, 2217]}]}
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