Detecting DNA Depurination with Solid-State Nanopores
Publication Date
July 02, 2014
Journal
PLOS ONE
Authors
Michael M. Marshall, Jan A. Ruzicka, Ethan W. Taylor & Adam R. Hall
Volume
9
Issue
7
Pages
e101632
DOI
https://dx.plos.org/10.1371/journal.pone.0101632
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0101632
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24988437
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079296
Europe PMC
http://europepmc.org/abstract/MED/24988437
Web of Science
000341354100122
Scopus
84903790895
Mendeley
http://www.mendeley.com/research/detecting-dna-depurination-solidstate-nanopores
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1578685"], "description"=>"<p>Mean conductance change measured for 61-10. No significant variation is observed. Error bars represent the width of a Gaussian fit to the data and the dashed line represents the average value from all data sets.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA damage", "biophysics", "Bionanotechnology", "biotechnology", "Small molecules", "nanotechnology", "blockade", "ph"], "article_id"=>1092277, "categories"=>["Biological Sciences"], "users"=>["Michael M. Marshall", "Jan A. Ruzicka", "Ethan W. Taylor", "Adam R. Hall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101632.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conductance_blockade_depth_across_the_pH_range_/1092277", "title"=>"Conductance blockade depth across the pH range.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-02 03:13:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1578705"], "description"=>"<p>Dwell time histograms for two different SS-nanopore measurements of dsDNA incubated at pH 4. (a) Incubation and measurement in 1 M KCl at pH 4 (same data as pH 4 histogram in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101632#pone-0101632-g003\" target=\"_blank\">Fig. 3</a>) and (b) incubation in 1 M KCl at pH 4 and measurement in 1 M KCl at pH 8 (n = 408).</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA damage", "biophysics", "Bionanotechnology", "biotechnology", "Small molecules", "nanotechnology", "solvent"], "article_id"=>1092290, "categories"=>["Biological Sciences"], "users"=>["Michael M. Marshall", "Jan A. Ruzicka", "Ethan W. Taylor", "Adam R. Hall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101632.g004", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Isolating_structural_factors_from_solvent_effects_/1092290", "title"=>"Isolating structural factors from solvent effects.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-02 03:13:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1578684"], "description"=>"<p>(a) Schematic of the measurement system. A voltage applied across a membrane containing a single nanopore drives dsDNA from the cis- side to the trans- side. Inset: typical conductance blockade event shape with depth (<i>ΔG</i>) and duration (<i>Δt</i>) indicated. (b) Cartoon representation of pH-induced DNA depurination. Acidic conditions preferentially remove purine bases (G and A), which cause progressive loss of structure.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA damage", "biophysics", "Bionanotechnology", "biotechnology", "Small molecules", "nanotechnology", "detection"], "article_id"=>1092276, "categories"=>["Biological Sciences"], "users"=>["Michael M. Marshall", "Jan A. Ruzicka", "Ethan W. Taylor", "Adam R. Hall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101632.g001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SS_nanopore_detection_of_DNA_depurination_/1092276", "title"=>"SS-nanopore detection of DNA depurination.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-02 03:13:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1578708"], "description"=>"<div><p>Among the different types of DNA damage that occur endogenously in the cell, depurination is especially prevalent. These lesions can initiate mutagenesis and have been implicated in a variety of diseases, including cancer. Here, we demonstrate a new approach for the detection of depurination at the single-molecule scale using solid-state nanopores. We induce depurination in short duplex DNA using acidic conditions and observe that the presence of apurinic sites results in significantly slower dynamics during electrokinetic translocation. This procedure may be valuable as a diagnostic for <i>in situ</i> quantification of DNA depurination.</p></div>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA damage", "biophysics", "Bionanotechnology", "biotechnology", "Small molecules", "nanotechnology", "depurination", "solid-state"], "article_id"=>1092293, "categories"=>["Biological Sciences"], "users"=>["Michael M. Marshall", "Jan A. Ruzicka", "Ethan W. Taylor", "Adam R. Hall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101632", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detecting_DNA_Depurination_with_Solid_State_Nanopores_/1092293", "title"=>"Detecting DNA Depurination with Solid-State Nanopores", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-02 03:13:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1578690"], "description"=>"<p>(a) Event duration histograms for 61 bp DNA translocation events from pH 10 (top) to pH 2 (bottom). Total numbers of events considered are n = 714 (pH 10), 662 (pH 8), 552 (pH 6), 423 (pH 4) and 1852 (pH 2). The black lines represent Gaussian fits to the data (pH 10 & 8: single peak; pH 6 & 4: two peaks; pH 2: three peaks). (b) Example traces of typical events measured at the adjacent pH level. Black traces represent undamaged (low <i>Δt</i>) events. For pH 6, 4 and 2, the blue traces are typical events derived from the long duration (i.e. depurinated) population, indicated by a blue arrow on the histograms. For each event trace shown, the label indicates a coarse approximation of the relative amount of depurination. Note that the final event at pH 2 (marked with *) may be indicative of DNA fragmentation (see text). (c) Fraction of translocation events in the undamaged population and (d) intensity of the DNA band on a gel (see also Supplementary Information), each measured over the entire range of pH investigated. Dashed lines are logarithmic fits to the data.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA damage", "biophysics", "Bionanotechnology", "biotechnology", "Small molecules", "nanotechnology", "durations", "ph"], "article_id"=>1092282, "categories"=>["Biological Sciences"], "users"=>["Michael M. Marshall", "Jan A. Ruzicka", "Ethan W. Taylor", "Adam R. Hall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101632.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Event_durations_across_the_pH_range_/1092282", "title"=>"Event durations across the pH range.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-02 03:13:47"}

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