Biomod/2012/Tianjin/Project/Origami: Difference between revisions

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Last year, Harvard BIOMOD team used the DNA origami to design two containers of sphere and cube, and install the containers with special function of loading and releasing cargo. The basic principle behind the design is through the basepairing between the cargo marked with ssDNA and the protruding sequence on the staple strand to load the cargo. When releasing the cargo, another ssDNA that is complementary to the protruding staple strand is added to replace the cargo through strand replacement. However, we noticed that the added ssDNA and released cargo are 1:1 in mole, thus cannot achieve amplification. On the other hand, 8-17 DNAzyme is capable of multiple turnover, its substrate is RNA, and miRNA is an essentially potential drug. Therefore, we’d like to build an origami container capable of loading miRNA, and use our logic gate to control the release of the drug.
Last year, Harvard BIOMOD team used the DNA origami to design two containers of sphere and cube, and install the containers with special function of loading and releasing cargo. The basic principle behind the design is through the basepairing between the cargo marked with ssDNA and the protruding sequence on the staple strand to load the cargo. When releasing the cargo, another ssDNA that is complementary to the protruding staple strand is added to replace the cargo through strand replacement. However, we noticed that the added ssDNA and released cargo are 1:1 in mole, thus cannot achieve amplification. On the other hand, 8-17 DNAzyme is capable of multiple turnover, its substrate is RNA, and miRNA is an essentially potential drug. Therefore, we’d like to build an origami container capable of loading miRNA, and use our logic gate to control the release of the drug.


[[Image:TJU2012-BMD-23.png|thumb|500px|center|'''Figure 23.''' The design of Harvard’s origami container. (From Harvard BIOMOD 2011.)]]
[[Image:TJU2012-BMD-23.png|thumb|500px|center|'''Figure 14.''' The design of Harvard’s origami container. (From Harvard BIOMOD 2011.)]]


==Design==
==Design==

Revision as of 18:18, 27 October 2012

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<div id="header"> <div class="title" style="height: 180px;"> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin"><img src ="http://openwetware.org/images/7/79/TJU2012-Header.png"></a> <div style="float:right;"><img src="http://openwetware.org/images/c/cd/TJU2012-logo.png"></div> <div class="topsearch" style="position:absolute;top:175px;right:90px;"> <form method="GET" action="http://www.google.com/search"> <input type="hidden" name="hl" value="en"> <input type="hidden" name="sitesearch" value="openwetware.org"> <input type="hidden" name="domains" value="openwetware.org"> <input type="hidden" name="as_epq" value="Tianjin"> <input type="text" name="q" class="frm"><input type="submit" class="btn" value="Search"> </form> </div> </div> </div>

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  	    <li class='active '><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin'><span>Home</span></a></li>
  	    <li class='active '><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Team'><span>Team</span></a>
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  	            <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background'><span>Background</span></a></li>
               <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/LogicGate'><span>The Logic Gate</span></a></li>
               <li><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/YDNA"><span>Y-DNA</span></a></li>
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               <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/YDNA'><span>Y-DNA</span></a></li>
               <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/Origami'><span>The Origami Amplifier</span></a></li>

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<div id="tianjin-right-content"> <ul><li> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background" title="Background">Background</a> </li><li> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/LogicGate" title="LogicGate">The Logic Gate</a><div class="tianjin-description">DNAzymes are DNA molecules that have the ability to perform a chemical reaction, such as catalytic action.</div> </li><li> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/YDNA" title="YDNA">Y-DNA</a><div class="tianjin-description">Y-DNA is composed of three ssDNA that is complementary of each other.</div> </li><li> <strong class="selflink">The Origami Amplifier</strong><div class="tianjin-description">DNA origami is the nanoscale folding of DNA to create arbitrary two and three dimensional shapes at the nanoscale.</div> </li></ul> </div>

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<div id="outborder" style="background: #FAFAFA url(http://biomod.net/sites/all/themes/biomod/images/stripe.png) repeat; height:360px; width:640px; padding:10px;"> <div id="inborder" style="background: #fff;height:340px;width:620px;padding:10px;"> <a href="http://openwetware.org/index.php?title=Biomod/2012/Tianjin/Project/Origami&action=edit">this page edit</a> <div id="frametext"><br><br><span style="font-size:300%;">T</span>his year, we used the design from 2012 Harvard BIOMOD team to build the origami. What’s different is that we load ssDNAs on the staple strand. The ssDNAs can serve as the substrate of logic gate of 8-17 and Cu<sup>2+</sup> DNAzyme, thus the release can be controlled by it. This new origami can serve as a miRNA delivery system based on ion detection.</div> <div id="frameimg"><img src="http://openwetware.org/images/6/66/TJU-frame-DOr.png"></div> </div> </div>


<!-- text starts here --> <div id="text-content"> </html>

The Origami Amplifier

Last year, Harvard BIOMOD team used the DNA origami to design two containers of sphere and cube, and install the containers with special function of loading and releasing cargo. The basic principle behind the design is through the basepairing between the cargo marked with ssDNA and the protruding sequence on the staple strand to load the cargo. When releasing the cargo, another ssDNA that is complementary to the protruding staple strand is added to replace the cargo through strand replacement. However, we noticed that the added ssDNA and released cargo are 1:1 in mole, thus cannot achieve amplification. On the other hand, 8-17 DNAzyme is capable of multiple turnover, its substrate is RNA, and miRNA is an essentially potential drug. Therefore, we’d like to build an origami container capable of loading miRNA, and use our logic gate to control the release of the drug.

Figure 14. The design of Harvard’s origami container. (From Harvard BIOMOD 2011.)

Design

First, we took advantage of the staple strands that are capable of loading cargo in last year Harvard’s design, and made it longer. The extended sequence acts as the substrate in the logic gate. (conceptual verification) The extended sequence can be designed as any miRNA sequence we want, and we can easily alter the logic gate design to accommodate different miRNA release requirement.

When Cu2+ and Pb2+ are present, 8-17 in the logic gate is activated and starts its cleavage on the substrate. Because of its multiple turnover, only a few logic gate molecules can serve as a constant input signal for releasing large amount of miRNA, and achieve the amplification of signal.

<html> <div align:"center;" style="height:336px;width:562px;padding:5px;background:#f9f9f9;border:1px solid #cccccc;"> <div style="height:315px;width:560px;background:#fff;border:1px solid #cccccc;"> <object classid="clsid:D27CDB6E－AE6D－11cf－96B8－444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab＃4,0,0,0" width="560px" height=“315px"> <param name="SRC" value=“http://openwetware.org/images/9/9a/TJU2012-BMD-f2.swf"> <param name=quality value=high> <embed src="http://openwetware.org/images/9/9a/TJU2012-BMD-f2.swf" quality=high pluginspage="http://www.macromedia.com/shockwave/download/index.cgi?P1_Prod_Version=ShockwaveFlash" type="application/x-shockwave-flash" width="560" height="315"> </embed> </object> </div> <div style="width:560;"> <span style="font-size:14px;"><b>Figure X.</b> Concept of the drug carrier. (From BIOMOD Team Tianjin 2012).</span> </div> </div> </html>

In this design, we focus on two essential problems:

  1. Is our design able to load cargo?
  2. Is 8-17 DNAzyme still capable of multiple turnover in our new design? We subsequently answered the questions in the experiment.


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