Biomod/2011/Aarhus/DanishNanoArtists/Supplementary/Sequences

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</style> <body> <a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists"> <IMG class="displogo" src="http://openwetware.org/images/6/67/DNALogo.png" alt=""/> </a> <script type='text/javascript' src='https://ajax.googleapis.com/ajax/libs/jquery/1.6.4/jquery.min.js'></script> <script> function mainmenu(){ $(" #nav li").hover(function(){ $(this).find('ul:first').css({visibility: "visible",display: "none"}).show(400); },function(){ $(this).find('ul:first').css({visibility: "hidden"}); }); } 

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<ul id="nav">
   <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team">Team</a>
       <ul>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team/Mie">Mie</a></li>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team/Irene">Irene</a></li>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team/Jens">Jens</a></li>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team/HansChristian">Hans Christian</a></li>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team/Steffen">Steffen</a></li>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team/OompaLoompas">Oompa-Loompas</a></li>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Team/Acknowledgements">Acknowledgements</a></li>
       </ul>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Idea">Idea</a>
       <ul>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Idea#Idea">Video</a></li>
           <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Idea#Goals">Goals</a></li>
       </ul>
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project">Project</a>
       <ul>
         <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project#Self-assembly_and_characterization_of_the_structure">Self-assembly of the structure</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project#Gene_knockdown_using_the_RNAi_pathway">Gen knock-down using the RNAi pathway</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project#Controlled_opening_of_the_structure">Controlled opening of the structure</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project/Methods">Methods&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;></a>
           <ul>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project/Methods#Gel_electrophoresis">Gels electrophoresis</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project/Methods#SAXS">SAXS</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project/Methods#FRET">FRET</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project/Methods#Dicer">Dicer</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project/Methods#Dual_Luciferace_assay">Dual Luciferase assay</a></li>
           </ul>
         </li>
         <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Project/Abbreviations">Abbreviations</a></li>
       </ul>
   </li>
  <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Overview">Overview</a>
      <ul>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Overview/Goals">Goals</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Overview/Achievements">Achievements</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Overview/FutureWork">Future work</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Overview/Perspectives">Perspectives</a></li>
           </ul>
  </li>
  <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Supplementary">Supplementary</a>
     <ul>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Supplementary/Protocols">Protocols</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Supplementary/Sequences">Sequences</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Supplementary/SAXS">SAXS</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Supplementary/FRET">FRET</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Supplementary/Luciferase">Luciferase</a></li>
             <li><a href="http://openwetware.org/wiki/Biomod/2011/Aarhus/DanishNanoArtists/Supplementary/Literature">Literature</a></li>
           </ul>
  </li>
</ul>

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Sequences

Figure 1: The sequencing data of the scaffold.
Figure 2: The expected secondary structure of the RNA scaffold predicted with CLC Main Worckbench. The colors indicate base pair probabilities of the different parts of the structure going from 100% to 0% in the order purple, blue, cyan, green, yellow and red.
Figure 3: 2D blueprint of the structures used for the FRET experiments. The edges are consecutively numbered from 5’ to 3’ of the scaffold. Z and V staples are colored blue and green, respectively. The T-linkers are not shown. The purple sequences are the modified staples with Cy3 (green) and Cy5 (orange). The staples forming the lock are colored grey, but the lock and toehold are not shown.


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