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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots</title><author><name sortKey="Hajdin, Christine E" sort="Hajdin, Christine E" uniqKey="Hajdin C" first="Christine E." last="Hajdin">Christine E. Hajdin</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Bellaousov, Stanislav" sort="Bellaousov, Stanislav" uniqKey="Bellaousov S" first="Stanislav" last="Bellaousov">Stanislav Bellaousov</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Huggins, Wayne" sort="Huggins, Wayne" uniqKey="Huggins W" first="Wayne" last="Huggins">Wayne Huggins</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Leonard, Christopher W" sort="Leonard, Christopher W" uniqKey="Leonard C" first="Christopher W." last="Leonard">Christopher W. Leonard</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Mathews, David H" sort="Mathews, David H" uniqKey="Mathews D" first="David H." last="Mathews">David H. Mathews</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M." last="Weeks">Kevin M. Weeks</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23503844</idno><idno type="pmc">3619282</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619282</idno><idno type="RBID">PMC:3619282</idno><idno type="doi">10.1073/pnas.1219988110</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000734</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000734</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots</title><author><name sortKey="Hajdin, Christine E" sort="Hajdin, Christine E" uniqKey="Hajdin C" first="Christine E." last="Hajdin">Christine E. Hajdin</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Bellaousov, Stanislav" sort="Bellaousov, Stanislav" uniqKey="Bellaousov S" first="Stanislav" last="Bellaousov">Stanislav Bellaousov</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Huggins, Wayne" sort="Huggins, Wayne" uniqKey="Huggins W" first="Wayne" last="Huggins">Wayne Huggins</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Leonard, Christopher W" sort="Leonard, Christopher W" uniqKey="Leonard C" first="Christopher W." last="Leonard">Christopher W. Leonard</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author><author><name sortKey="Mathews, David H" sort="Mathews, David H" uniqKey="Mathews D" first="David H." last="Mathews">David H. Mathews</name><affiliation><nlm:aff id="aff2">Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</nlm:aff></affiliation></author><author><name sortKey="Weeks, Kevin M" sort="Weeks, Kevin M" uniqKey="Weeks K" first="Kevin M." last="Weeks">Kevin M. Weeks</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23503844</article-id><article-id pub-id-type="pmc">3619282</article-id><article-id pub-id-type="publisher-id">201219988</article-id><article-id pub-id-type="doi">10.1073/pnas.1219988110</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Biophysics and Computational Biology</subject></subj-group></subj-group></article-categories><title-group><article-title>Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots</article-title><alt-title alt-title-type="short">SHAPE-directed RNA structure modeling</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hajdin</surname><given-names>Christine E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bellaousov</surname><given-names>Stanislav</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Huggins</surname><given-names>Wayne</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Leonard</surname><given-names>Christopher W.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mathews</surname><given-names>David H.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="corresp" rid="cor1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Weeks</surname><given-names>Kevin M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="corresp" rid="cor1"><sup>2</sup></xref></contrib><aff id="aff1"><sup>a</sup>Department of Chemistry,<institution>University of North Carolina</institution>, Chapel Hill,<addr-line>NC</addr-line> 27599-3290; and</aff><aff id="aff2"><sup>b</sup>Department of Biochemistry and Biophysics, and Center for RNA Biology,<institution>University of Rochester Medical Center</institution>, Rochester,<addr-line>NY</addr-line> 14642</aff></contrib-group><author-notes><corresp id="cor1"><sup>2</sup>To whom correspondence may be addressed. E-mail: <email>weeks@unc.edu</email> or <email>David_Mathews@urmc.rochester.edu</email>.</corresp><fn fn-type="edited-by"><p>Edited by Ignacio Tinoco, University of California, Berkeley, CA, and approved February 5, 2013 (received for review November 15, 2012)</p></fn><fn fn-type="con"><p>Author contributions: C.E.H., S.B., W.H., D.H.M., and K.M.W. designed research; C.E.H., S.B., W.H., and C.W.L. performed research; C.E.H., S.B., W.H., C.W.L., D.H.M., and K.M.W. analyzed data; and C.E.H., S.B., D.H.M., and K.M.W. wrote the paper.</p></fn><fn id="fn1" fn-type="equal"><p><sup>1</sup>C.E.H. and S.B. contributed equally to this work.</p></fn><fn fn-type="conflict"><p>The authors declare no conflict of interest.</p></fn></author-notes><pub-date pub-type="ppub"><day>2</day><month>4</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>15</day><month>3</month><year>2013</year></pub-date><volume>110</volume><issue>14</issue><fpage>5498</fpage><lpage>5503</lpage><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201219988.pdf"></self-uri><abstract><p>A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.</p></abstract><kwd-group><kwd>thermodynamics</kwd><kwd>nearest neighbor parameters</kwd><kwd>circle plot</kwd><kwd>polymer model</kwd><kwd>1M7</kwd></kwd-group><counts><page-count count="6"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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