Biomod/2011/Aarhus/DanishNanoArtists/Overview: Difference between revisions
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==Summary== | |||
==Overview== | |||
===Summary=== | |||
We designed an octahedron shaped RNA structure, each side of the structure consists of a 27 base pair long double stranded region and a 4 nucleotide single stranded loop at the corners. In five corners a staple strand was nicked and to nucleotides removed in order to create the 2 nt 3' overhangs recognized be the Dicer enzyme. The idea was that the octahedron should be able to contain a high molecular weight drug as well as being degraded by Dicer into siRNA. Polyacrylamide gel electrophoresis (PAGE) confirms that a complex is formed when the staple strands are added to the scaffold. Furthermore florescence resonance energy transfer (FRET) and small angle x-ray scattering (SAXS) together confirm that the structure does indeed form as predicted. | We designed an octahedron shaped RNA structure, each side of the structure consists of a 27 base pair long double stranded region and a 4 nucleotide single stranded loop at the corners. In five corners a staple strand was nicked and to nucleotides removed in order to create the 2 nt 3' overhangs recognized be the Dicer enzyme. The idea was that the octahedron should be able to contain a high molecular weight drug as well as being degraded by Dicer into siRNA. Polyacrylamide gel electrophoresis (PAGE) confirms that a complex is formed when the staple strands are added to the scaffold. Furthermore florescence resonance energy transfer (FRET) and small angle x-ray scattering (SAXS) together confirm that the structure does indeed form as predicted. | ||
In Vitro Dicer experiments show that a structure designed with 3' overhangs has way higher affinity for the Dicer enzyme than a structure with no overhangs, leading us to conclude that the structure interacts with Dicer as intended. Furthermore the dual-luciferase assay confirms that the structure will indeed cause statistically significant gene knock down in human cancer cells expressing renilla luciferase. | In Vitro Dicer experiments show that a structure designed with 3' overhangs has way higher affinity for the Dicer enzyme than a structure with no overhangs, leading us to conclude that the structure interacts with Dicer as intended. Furthermore the dual-luciferase assay confirms that the structure will indeed cause statistically significant gene knock down in human cancer cells expressing renilla luciferase. | ||
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Revision as of 15:28, 1 November 2011
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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 ></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>
</body> </html>
Overview
Summary
We designed an octahedron shaped RNA structure, each side of the structure consists of a 27 base pair long double stranded region and a 4 nucleotide single stranded loop at the corners. In five corners a staple strand was nicked and to nucleotides removed in order to create the 2 nt 3' overhangs recognized be the Dicer enzyme. The idea was that the octahedron should be able to contain a high molecular weight drug as well as being degraded by Dicer into siRNA. Polyacrylamide gel electrophoresis (PAGE) confirms that a complex is formed when the staple strands are added to the scaffold. Furthermore florescence resonance energy transfer (FRET) and small angle x-ray scattering (SAXS) together confirm that the structure does indeed form as predicted.
In Vitro Dicer experiments show that a structure designed with 3' overhangs has way higher affinity for the Dicer enzyme than a structure with no overhangs, leading us to conclude that the structure interacts with Dicer as intended. Furthermore the dual-luciferase assay confirms that the structure will indeed cause statistically significant gene knock down in human cancer cells expressing renilla luciferase.
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