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Tertiary architecture of the Oceanobacillus iheyensis group II intron
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id="content-block"> <div class="article abstract-view" itemprop="articleBody"><span class="highwire-journal-article-marker-start"></span><h1 id="article-title-1" itemprop="headline">Tertiary architecture of the <em>Oceanobacillus iheyensis</em> group II intron </h1> <div class="contributors"> <ol class="contributor-list" id="contrib-group-1"> <li id="contrib-1"><span class="name"><a class="name-search" href="/search?author1=Navtej+Toor&sortspec=date&submit=Submit">Navtej Toor</a></span><a id="xref-aff-1-1" class="xref-aff" href="#aff-1">1</a><span class="xref-sep">,</span><a id="xref-fn-1-1" class="xref-fn" href="#fn-1">5</a>, </li> <li id="contrib-2"><span class="name"><a class="name-search" href="/search?author1=Kevin+S.+Keating&sortspec=date&submit=Submit">Kevin S. Keating</a></span><a id="xref-aff-2-1" class="xref-aff" href="#aff-2">2</a>, </li> <li id="contrib-3"><span class="name"><a class="name-search" href="/search?author1=Olga+Fedorova&sortspec=date&submit=Submit">Olga Fedorova</a></span><a id="xref-aff-1-2" class="xref-aff" href="#aff-1">1</a>, </li> <li id="contrib-4"><span class="name"><a class="name-search" href="/search?author1=Kanagalaghatta+Rajashankar&sortspec=date&submit=Submit">Kanagalaghatta Rajashankar</a></span><a id="xref-aff-3-1" class="xref-aff" href="#aff-3">3</a>, </li> <li id="contrib-5"><span class="name"><a class="name-search" href="/search?author1=Jimin+Wang&sortspec=date&submit=Submit">Jimin Wang</a></span><a id="xref-aff-1-3" class="xref-aff" href="#aff-1">1</a> and </li> <li id="contrib-6"><span class="name"><a class="name-search" href="/search?author1=Anna+Marie+Pyle&sortspec=date&submit=Submit">Anna Marie Pyle</a></span><a id="xref-aff-1-4" class="xref-aff" href="#aff-1">1</a><span class="xref-sep">,</span><a id="xref-aff-4-1" class="xref-aff" href="#aff-4">4</a></li> </ol> <ol class="affiliation-list"> <li class="aff"><a id="aff-1" name="aff-1"></a><address> <sup>1</sup>Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA </address> </li> <li class="aff"><a id="aff-2" name="aff-2"></a><address> <sup>2</sup>Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA </address> </li> <li class="aff"><a id="aff-3" name="aff-3"></a><address> <sup>3</sup>The Northeastern Collaborative Access Team (NE-CAT) at the Advanced Photon Source at Argonne National Laboratory, Argonne, Illinois 60439, USA </address> </li> <li class="aff"><a id="aff-4" name="aff-4"></a><address> <sup>4</sup>Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA </address> </li> </ol> <ul class="author-notes"> <li class="fn-present-address" id="fn-1"> <p id="p-1"><a class="rev-xref" href="#xref-fn-1-1">↵</a><span class="fn-label">5</span> <strong>Present address:</strong> Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA. </p> </li> </ul> </div> <div class="section abstract" id="abstract-1" itemprop="description"> <h2>Abstract</h2> <p id="p-4">Group II introns are large ribozymes that act as self-splicing and retrotransposable RNA molecules. They are of great interest because of their potential evolutionary relationship to the eukaryotic spliceosome, their continued influence on the organization of many genomes in bacteria and eukaryotes, and their potential utility as tools for gene therapy and biotechnology. One of the most interesting features of group II introns is their relative lack of nucleobase conservation and covariation, which has long suggested that group II intron structures are stabilized by numerous unusual tertiary interactions and backbone-mediated contacts. Here, we provide a detailed description of the tertiary interaction networks within the <em>Oceanobacillus iheyensis</em> group IIC intron, for which a crystal structure was recently solved to 3.1 Å resolution. The structure can be described as a set of several intricately constructed tertiary interaction nodes, each of which contains a core of extended stacking networks and elaborate motifs. Many of these nodes are surrounded by a web of ribose zippers, which appear to further stabilize local structure. As predicted from biochemical and genetic studies, the group II intron provides a wealth of new information on strategies for RNA folding and tertiary structural organization. </p> </div><span class="kwd-group-title">Keywords:</span><h3 class="kwd-header">Keywords</h3> <ul class="kwd-group"> <li class="kwd"><span><a class="kwd-search" href="/search?fulltext=group%20II%20intron&sortspec=date&submit=Submit&andorexactfulltext=phrase">group II intron</a></span></li> <li class="kwd"><span><a class="kwd-search" href="/search?fulltext=RNA%20tertiary%20structure&sortspec=date&submit=Submit&andorexactfulltext=phrase">RNA tertiary structure</a></span></li> <li class="kwd"><span><a class="kwd-search" href="/search?fulltext=ribozyme&sortspec=date&submit=Submit&andorexactfulltext=phrase">ribozyme</a></span></li> <li class="kwd"><span><a class="kwd-search" href="/search?fulltext=X-ray%20crystallography&sortspec=date&submit=Submit&andorexactfulltext=phrase">X-ray crystallography</a></span></li> </ul> <div class="section fn-group" id="fn-group-1"> <h2>Footnotes</h2> <ul> <li class="fn" id="fn-2"> <p id="p-2"><strong>Reprint requests to:</strong> Anna Marie Pyle, Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Room 334A, Bass Building, New Haven, CT 06511, USA; e-mail: <span class="em-link"><span class="em-addr">anna.pyle{at}yale.edu</span></span>; fax: (203) 432-5316; or Jimin Wang, Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Room 418, Bass Building, New Haven, CT 06511, USA; e-mail: <span class="em-link"><span class="em-addr">jimin.wang{at}yale.edu</span></span>; fax: (203) 432-3282. </p> </li> <li class="fn" id="fn-3"> <p id="p-59">Article published online ahead of print. Article and publication date are at <a href="http://www.rnajournal.org/cgi/doi/10.1261/rna.1844010">http://www.rnajournal.org/cgi/doi/10.1261/rna.1844010</a>. </p> </li> <li class="history" id="history-1"> <ul class="history-list"> <li xmlns:hwp="http://schema.highwire.org/Journal" class="received" hwp:start="2009-07-27"><span class="received-label">Received </span>July 27, 2009. </li> <li xmlns:hwp="http://schema.highwire.org/Journal" class="accepted" hwp:start="2009-10-20"><span class="accepted-label">Accepted </span>October 20, 2009. </li> </ul> </li> </ul> </div><span class="highwire-journal-article-marker-end"></span></div> <div class="social-bookmarking"> <ul class="social-bookmark-links"> <li class="social-bookmarking-item social-bookmarking-item-citeulike"><a 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