Sequence Specificity of BAL 31 Nuclease for ssDNA Revealed by Synthetic Oligomer Substrates Containing Homopolymeric Guanine Tracts
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Mendeley | Further Information

{"title"=>"Sequence specificity of BAL 31 nuclease for ssDNA revealed by synthetic oligomer substrates containing homopolymeric guanine tracts", "type"=>"journal", "authors"=>[{"first_name"=>"April", "last_name"=>"Marrone", "scopus_author_id"=>"25650276300"}, {"first_name"=>"Jack", "last_name"=>"Ballantyne", "scopus_author_id"=>"7103216781"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-56349121315", "pui"=>"352694718", "pmid"=>"18974878", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0003595", "sgr"=>"56349121315"}, "id"=>"f9e12917-26b3-3cbe-bf64-c95200962134", "abstract"=>"BACKGROUND: The extracellular nuclease from Alteromonas espejiana, BAL 31 catalyzes the degradation of single-stranded and linear duplex DNA to 5'-mononucleotides, cleaves negatively supercoiled DNA to the linear duplex form, and cleaves duplex DNA in response to the presence of apurinic sites. PRINCIPAL FINDINGS: In this work we demonstrate that BAL 31 activity is affected by the presence of guanine in single-stranded DNA oligomers. Specifically, nuclease activity is shown to be affected by guanine's presence in minimal homopolymeric tracts in the middle of short oligomer substrates and also by its presence at the 3' end of ten and twenty base oligomers. G*C rich regions in dsDNA are known to cause a decrease in the enzyme's nuclease activity which has been attributed to the increased thermal stability of these regions, thus making it more difficult to unwind the strands required for enzyme access. Our results indicate that an additional phenomenon could be wholly or partly responsible for the loss of activity in these G*C rich regions. Thus the presence of a guanine tract per se impairs the enzyme's functionality, possibly due to the tract's bulky nature and preventing efficient progression through the active site. CONCLUSIONS: This study has revealed that the general purpose BAL 31 nuclease commonly used in molecular genetics exhibits a hithertofore non-characterized degree of substrate specificity with respect to single-stranded DNA (ssDNA) oligomers. Specifically, BAL 31 nuclease activity was found to be affected by the presence of guanine in ssDNA oligomers.", "link"=>"http://www.mendeley.com/research/sequence-specificity-bal-31-nuclease-ssdna-revealed-synthetic-oligomer-substrates-containing-homopol", "reader_count"=>3, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Agricultural and Biological Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"India"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/917446"], "description"=>"<p>C<sub>10</sub>, A<sub>10</sub>, T<sub>10</sub>, and G<sub>10</sub> were incubated at 37°C with 1 U, 0.5 U, and 0 U of BAL 31. The relative hydrolysis efficacy of each homopolymeric oligomer is indicated by the percentage recovery of their constituent 5′dNMPs over time (3–72 h). Incubation at 30°C gave similar results.</p>", "links"=>[], "tags"=>["homodecameric"], "article_id"=>587905, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry"], "users"=>["April Marrone", "Jack Ballantyne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003595.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrolysis_of_homodecameric_oligomers_/587905", "title"=>"Hydrolysis of homodecameric oligomers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:44:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/917704"], "description"=>"<p>Recovery of dNMPs after BAL 31 hydrolysis.</p>", "links"=>[], "tags"=>["dnmps", "bal", "31"], "article_id"=>588164, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry"], "users"=>["April Marrone", "Jack Ballantyne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003595.t001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recovery_of_dNMPs_after_BAL_31_hydrolysis_/588164", "title"=>"Recovery of dNMPs after BAL 31 hydrolysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:46:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/917533"], "description"=>"<p>G<sub>10</sub> and T<sub>10</sub> were hydrolyzed by BAL 31 at 45°C, 50°C, and 55°C for a twenty-four hour period. The relative hydrolysis efficacy of each homopolymeric oligomer is indicated by the percentage recovery of their constituent 5′dNMPs.</p>", "links"=>[], "tags"=>["homodecamers", "refractory", "hydrolysis", "elevated"], "article_id"=>587988, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry"], "users"=>["April Marrone", "Jack Ballantyne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003595.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_G_10_homodecamers_continue_to_be_refractory_to_hydrolysis_at_elevated_temperatures_/587988", "title"=>"G<sub>10</sub> homodecamers continue to be refractory to hydrolysis at elevated temperatures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:45:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/917587"], "description"=>"<p>The relative hydrolysis efficacy of each oligomer is indicated by the percentage recovery of their constituent 5′dNMPs. (A) 300 µM oligomer substrates containing either no guanine (G-NO) or guanine tracts at the ends (G<sub>2</sub>-CAP ) or in the middle (G<sub>4</sub>-MID) of the polynucleotide chain were incubated at 37°C for twenty-four hours with 0.5 U BAL 31 enzyme. (B) The same experiment as in (A) except using 30 µM oligomers and an incubation temperature of 55°C.</p>", "links"=>[], "tags"=>["oligonucleotide", "substrates", "affected", "guanine"], "article_id"=>588049, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry"], "users"=>["April Marrone", "Jack Ballantyne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003595.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrolysis_efficiency_of_oligonucleotide_substrates_is_affected_by_the_location_of_the_guanine_tract_/588049", "title"=>"Hydrolysis efficiency of oligonucleotide substrates is affected by the location of the guanine tract.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:45:39"}

PMC Usage Stats | Further Information

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Relative Metric

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