A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT
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{"title"=>"A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT", "type"=>"journal", "authors"=>[{"first_name"=>"Pengfei", "last_name"=>"Ding", "scopus_author_id"=>"56404064300"}, {"first_name"=>"Kirsty A.", "last_name"=>"McFarland", "scopus_author_id"=>"24767939500"}, {"first_name"=>"Shujuan", "last_name"=>"Jin", "scopus_author_id"=>"56714413500"}, {"first_name"=>"Grace", "last_name"=>"Tong", "scopus_author_id"=>"56714939200"}, {"first_name"=>"Bo", "last_name"=>"Duan", "scopus_author_id"=>"56715039200"}, {"first_name"=>"Ally", "last_name"=>"Yang", "scopus_author_id"=>"55768777400"}, {"first_name"=>"Timothy R.", "last_name"=>"Hughes", "scopus_author_id"=>"34975073500"}, {"first_name"=>"Jun", "last_name"=>"Liu", "scopus_author_id"=>"54993506700"}, {"first_name"=>"Simon L.", "last_name"=>"Dove", "scopus_author_id"=>"35606731800"}, {"first_name"=>"William Wiley", "last_name"=>"Navarre", "scopus_author_id"=>"6506622718"}, {"first_name"=>"Bin", "last_name"=>"Xia", "scopus_author_id"=>"7102762276"}], "year"=>2015, "source"=>"PLoS Pathogens", "identifiers"=>{"scopus"=>"2-s2.0-84936751537", "sgr"=>"84936751537", "doi"=>"10.1371/journal.ppat.1004967", "pui"=>"605161892", "pmid"=>"26068099", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)", "issn"=>"15537374"}, "id"=>"528b4278-89a0-35c9-82b9-e292b946eec4", "abstract"=>"Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an \"AT-pincer\" motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.", "link"=>"http://www.mendeley.com/research/novel-atrich-dna-recognition-mechanism-bacterial-xenogeneic-silencer-mvat", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>9, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>9, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>17, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Australia"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2108086"], "description"=>"<p>(A) Selected helix parameters of the solution structures of MvaT<sub>ctd</sub>-bound 3AT DNA (blue), a free DNA with ATATAT sequence (PDB 2LWG) (magenta) and an A-tract DNA with AAAAAA sequence (PDB 1FZX [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004967#ppat.1004967.ref052\" target=\"_blank\">52</a>]) (gold). Average minor groove width, roll and inclination angles including standard deviations are shown. Base steps of 3AT are indicated. (B) Mean structures of MvaT<sub>ctd</sub>-bound 3AT (blue), 2LWG (magenta) and 1FZX (gold). Axes are shown by sticks.</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447084, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.g005", "stats"=>{"downloads"=>1, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_MvaT_ctd_bound_DNA_conformation_/1447084", "title"=>"Analysis of MvaT<sub>ctd</sub>-bound DNA conformation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108083"], "description"=>"<p>(A) Superimposition for the ensemble of 20 structures of MvaT<sub>ctd</sub>/DNA complex. Protein backbone is represented by ribbon and the target DNA is shown as lines. (B) Electrostatic potential of MvaT<sub>ctd</sub>, calculated with APBS in the absence of DNA. (C) Close view of the binding interface. Residues of MvaT<sub>ctd</sub> involved in DNA recognition are shown as sticks with one-letter amino acid code and residue number labeled. (D) Schematic representation of the intermolecular contacts. The DNA is drawn as a cylindrical projection viewed from the minor groove side. Hydrogen bonds between MvaT<sub>ctd</sub> and DNA bases are indicated by red arrows. Green lines show the hydrophobic contacts. The interactions between positively charged lysine residues and DNA backbone phosphate groups are indicated by blue arrows.</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447081, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.g004", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_of_MvaT_ctd_and_AT_rich_DNA_complex_/1447081", "title"=>"Structure of MvaT<sub>ctd</sub> and AT-rich DNA complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108100", "https://ndownloader.figshare.com/files/2108101", "https://ndownloader.figshare.com/files/2108102", "https://ndownloader.figshare.com/files/2108103", "https://ndownloader.figshare.com/files/2108104", "https://ndownloader.figshare.com/files/2108105"], "description"=>"<div><p>Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of <i>Pseudomonas</i> sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an “AT-pincer” motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both <i>in vitro</i> and <i>in vivo</i> assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.</p></div>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447098, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1004967.s001", "https://dx.doi.org/10.1371/journal.ppat.1004967.s002", "https://dx.doi.org/10.1371/journal.ppat.1004967.s003", "https://dx.doi.org/10.1371/journal.ppat.1004967.s004", "https://dx.doi.org/10.1371/journal.ppat.1004967.s005", "https://dx.doi.org/10.1371/journal.ppat.1004967.s006"], "stats"=>{"downloads"=>11, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Novel_AT_Rich_DNA_Recognition_Mechanism_for_Bacterial_Xenogeneic_Silencer_MvaT_/1447098", "title"=>"A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108091"], "description"=>"<p>*Pairwise RMSD was calculated among 20 refined structures over residues A79-G124 (MvaT<sub>ctd</sub>) and/or C1-G24 (DNA).</p><p>Restraints and structural statistics for MvaT<sub>ctd</sub> and its complex with DNA.</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447089, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.t001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Restraints_and_structural_statistics_for_MvaT_ctd_and_its_complex_with_DNA_/1447089", "title"=>"Restraints and structural statistics for MvaT<sub>ctd</sub> and its complex with DNA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108076"], "description"=>"<p>Complexes of MvaT (300 nM) with 1 nM radiolabeled AT-rich <i>cupA1</i> promoter DNA fragment (upper panel) or a radiolabeled GC-rich <i>PA3900</i> DNA fragment (lower panel), were pre-formed prior to the addition of excess unlabeled competitor DNA as indicated.</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447074, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.g001", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_competition_binding_assay_for_MvaT_binding_to_cupA1_promoter_DNA_and_PA3900_fragment_/1447074", "title"=>"DNA competition binding assay for MvaT binding to <i>cupA1</i> promoter DNA and <i>PA3900</i> fragment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108090"], "description"=>"<p>(A) Alignment of <i>Pseudomonas</i> MvaT with members of the H-NS family reveals regions of similarity outside of the canonical H-NS motif. Clustal Omega alignment of C-terminal domains of MvaT and MvaU from <i>P</i>. <i>aeruginosa</i> PAO1 with Bv3F from <i>Burkholderia vietnamiensis</i> G4 (Buv), H-NS from <i>S</i>. <i>typhimurium</i> (Sal), <i>Xanthomonas albilineans</i> (Xan), and <i>X</i>. <i>fastidiosa</i> (Xyl), and Lsr2 from <i>M</i>. <i>tuberculosis</i>. The canonical H-NS motif is boxed. In bold are the residues corresponding to the AT-hook-like motif in Lsr2 and H-NS. (B) Superimposing structures of MvaT<sub>ctd</sub> (cyan) and <i>S</i>. <i>typhimurium</i> H-NS<sub>ctd</sub> (magenta). Side chain conformations of K97 and N100 of MvaT<sub>ctd</sub> are nearly identical to those of T110 and R114 of H-NS<sub>ctd</sub>, respectively. MvaT<sub>ctd</sub> lacks the corresponding residue of Q112, functioning as the first critical residue of the “Q/RGR” AT-hook-like structure in H-NS<sub>ctd</sub>. When MvaT<sub>ctd</sub> is complexed with DNA, side chain of R80 occupies similar position as the side chain of Q112 from H-NS<sub>ctd</sub>. A blue circle is drawn to indicate the gap between the R80 side chain and the backbone of loop2. (C) MvaT<sub>ctd</sub>/DNA complex structure viewed from one end of the double helix. The cavity above A6-T19 base pair is shown by red spheres.</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447088, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.g007", "stats"=>{"downloads"=>7, "page_views"=>193, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_alignments_and_structural_comparisons_of_MvaT_ctd_with_AT_hook_like_motif_containing_DNA_binding_domains_/1447088", "title"=>"Sequence alignments and structural comparisons of MvaT<sub>ctd</sub> with AT-hook-like motif containing DNA-binding domains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108088"], "description"=>"<p>(A) Dissociation constants for WT MvaT<sub>ctd</sub> and its mutants when binding with 3AT as measured using ITC. Error bars represent standard deviation. (B) Phenotypes of <i>cupA lacZ</i> strains containing plasmids directing the expression of WT MvaT or its mutants (upper panel). The phase-variable expression of <i>cupA</i> genes can be repressed by providing the <i>mvaT</i> gene in trans, giving rise to white colonies. Derivative with functionally impaired MvaT gives rise to blue (phase-ON) and white (phase-OFF) colonies. Western blot analysis probed with antibody against VSV-G tag (lower panel). Sample loading control of western blot is probed with antibody against the α subunit of RNA polymerase. (C) Quantification of the <i>cupA lacZ</i> expression in cultures of strains containing WT MvaT or its mutants. Error bars represent standard deviation of the mean (n = 3).</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447086, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.g006", "stats"=>{"downloads"=>2, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterization_of_MvaT_mutants_/1447086", "title"=>"Characterization of MvaT mutants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108079"], "description"=>"<p>(A) Superimposition of backbone traces for the ensemble of 20 structures of MvaT<sub>ctd</sub>. (B) Ribbon representation of the MvaT<sub>ctd</sub> mean structure. The side chains of residues forming the hydrophobic core are shown in orange. (C) Overlay of 2D <sup>1</sup>H-<sup>15</sup>N HSQC spectra of free (blue) and DNA-bound MvaT<sub>ctd</sub> (red, concentration ratio 1:1). Residues showing significant chemical shift changes are indicated. (D) Combined <sup>1</sup>H and <sup>15</sup>N chemical shift differences (Δδ<sub>comb</sub> = [δ<sub>HN</sub><sup>2</sup> + (δ<sub>N</sub>/6.5)<sup>2</sup>]<sup>1/2</sup>) between free and DNA bound-MavT<sub>ctd</sub> are plotted against residue number (blue bars). (E) Overlay of the finger print region showing intraresidue H1’-H6/H8 NOE peaks of 2D <sup>1</sup>H NOESY spectra of free (blue) and MvaT<sub>ctd</sub>-bound DNA (red; concentration ratio 1:1). The sequence and secondary structure of the DNA dodecamer is shown above, with residues affected by MvaT<sub>ctd</sub> binding indicated in green. (F) <sup>1</sup>H chemical shift differences (Δδ) for H1’ (blue bars) and H6/H8 (yellow bars) chemical shifts between free and MvaT<sub>ctd</sub>-bound DNA are plotted against residue number.</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447077, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Solution_structure_of_MvaT_ctd_and_its_interaction_with_AT_rich_DNA_/1447077", "title"=>"Solution structure of MvaT<sub>ctd</sub> and its interaction with AT-rich DNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-11 03:55:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2108078"], "description"=>"<p>PBM data for H-NS and Lsr2 was previously published [<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004967#ppat.1004967.ref029\" target=\"_blank\">29</a>]. Tukey boxplots show the <i>E</i>-score distributions of the 8-mer oligonucleotide sequences and the whiskers indicate points within the 1.5 inter-quartile range. In all charts the sequence parameters are plotted against the <i>E</i>-score, which reflects relative affinity for a particular sequence. (A) <i>E</i>-score vs. AT-content of 8-mer target sequence. (B) Number of TpA steps for oligos containing only A or T (100% AT). (C) Length of A-tract sequence(s) in 8-mers with %GC ≥ 75. Some sequences contain two A-tracts (e.g. AAAGGAAA) and in those cases the length of each is indicated. (D) <i>E</i>-score vs. maximum length of uninterrupted A or T bases in a 75% AT sequence. Sequences such as GCAATAAT have 6 adjacent A or T bases while the longest stretch of adjacent A or T bases in the 8-mer AAGTTCAA is 2.</p>", "links"=>[], "tags"=>["lysine side chains", "DNA binding mechanism", "Bacterial Xenogeneic Silencer MvaT", "novel DNA binding mode", "DNA sequences", "Lsr 2 family proteins", "protein binding microarrays", "affinity DNA dodecamer", "nmr", "Lsr 2. Comparison", "xenogeneic silencers", "xenogeneic silencer families"], "article_id"=>1447076, "categories"=>["Biological Sciences"], "users"=>["Pengfei Ding", "Kirsty A. McFarland", "Shujuan Jin", "Grace Tong", "Bo Duan", "Ally Yang", "Timothy R. Hughes", "Jun Liu", "Simon L. Dove", "William Wiley Navarre", "Bin Xia"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004967.g002", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_binding_microarray_analysis_of_DNA_binding_preferences_for_MvaT_H_NS_and_Lsr2_/1447076", "title"=>"Protein binding microarray analysis of DNA binding preferences for MvaT, H-NS and Lsr2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-11 03:55:25"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"28", "full-text"=>"33", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
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  • {"unique-ip"=>"12", "full-text"=>"15", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"17", "full-text"=>"42", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"25", "full-text"=>"28", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"15", "full-text"=>"18", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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