Biomod/2012/Tianjin/Result/YDNA

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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 class='has-sub'><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background'><span>Designs</span></a>
  	        <ul>
  	            <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>
               <li><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Origami"><span>The Origami Amplifier</span></a></li>
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  	            <li><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/LogicGate'><span>The Logic Gate</span></a></li>
               <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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           <li class='active'><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Attributions'><span>Attributions</span></a></li>

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<div id="tianjin-right-content"> <ul><li> <a href="#" title="#">Abstract</a> </li><li> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/LogicGate" title="LogicGate">The Logic Gate</a><div class="tianjin-description">Looking at this design, there are two critical problems regarding our design</div> </li><li> <strong class="selflink">Y-DNA</strong><div class="tianjin-description">The Y-DNA was synthesized from three ssDNAs, each of which has partial complementary sequences to the other two ssDNAs.</div> </li><li> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Result/Origami" title="Origami">The Origami Amplifier</a><div class="tianjin-description">In this design, we focus on two essential problems.</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/Result/YDNA&action=edit">this page edit</a> <div id="frametext"><br><br><span style="font-size:300%;">T</span>he Y-DNA was synthesized from three ssDNAs, each of which has partial complementary sequences to the other two ssDNAs. It occurred to us that we can utilize this logic gate to control the formation of Y-DNA by making the sensor one of the ssDNAs.</div> </div> </div>


<!-- text starts here --> <div id="text-content"> </html> Y-DNA formation and EcoRI digestion both needs particular buffers. If we want to accomplish the formation and digestion under one condition, we need to investigate how we can achieve the same results in a simple buffer combination complex interactions.

[[Image:]]

From the PAGE result (Figure X), we can see that the first step cleavage (self-cleavage) of the sensor are equally effective under the EcoRI, original and the mixed buffers. What is better is that the EcoRI buffer alone is enough for the formation and digestion. Furthermore, our optimized new sensor still carried out the same function as we predicted.

[[Image:]]

Next, we use the determined reaction condition to produce Y-DNA and its polymerization. We put the logic gate, two ssDNAs and Cu2+ into the system, denatured and annealed. We can see the band of self-cleaved logic gate, the two-ssDNA. Later, EcoRI and T4 ligase were added to create the sticky ends and link them together. In Figure X, we can see the polymer of Y-DNA, the complex of two ssDNA, the self-cleaved logic gate, compared with the marker. This demonstrated the success of our design. <html>

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