Difference between revisions of "Biomod/2012/Tianjin/Project/LogicGate"

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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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<div id="tianjin-right-content"> <ul><li> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background" title="Background">Background</a> </li><li> <strong class="selflink">The Logic Gate</strong><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> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Origami" title="Origami">The Origami Amplifier</a><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;"> <div id="frametext"><br><br><span style="font-size:300%;">T</span>eam Tianjin this year utilized the great selectivity to screen the input signal to control the DNAzyme. Our logic gate is made up of 8-17, the Cu<sup>2+</sup> dependent DNAzyme, the gate will require both Pb<sup>2+</sup> and Cu<sup>2+</sup> to carry its function of cleaving the substrate.</div> <div id="frameimg"><img src="http://openwetware.org/images/d/d4/TJU2012-frame-DLG.png"></div> </div> </div>

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Module 1

Many scientists have devised various logic gate systems, such as AND, OR, NOR gate etc., using DNAzyme, but the input signal for the logic gate is mostly ssDNA. Team Tianjin this year utilized the great selectivity to screen the input signal to control the DNAzyme. Our logic gates is made up of 8-17, the Cu2+ DNAzyme. The gate will require both Pb2+ and Cu2+ to carry its function of cleaving the substrate.

The first logic gate system we design is shown in Figure 7. It is made up of a logic gate and a substrate. The logic gate is responsible for the detection of Pb2+ and Cu2+ ion, while the substrate acts as the substrate to indicate the activity of the logic gate.

<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/a/a8/TJU2012-BMD-f3.swf"> <param name=quality value=high> <embed src="http://openwetware.org/images/a/a8/TJU2012-BMD-f3.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 7.</b> The design of the logic gate and its principle. (From BIOMOD Team Tianjin 2012).</span> </div> </div> </html>

In Figure 7, orange sequence is the conservative sequence of 8-17, and the purple part is an 8bp binding arm. In addition, the Cu2+ DNAzyme is include the in black box. It binds with the corresponding sequence, thus preventing 8-17 from matching with the substrate, just like a lock. When there is no Cu2+, the 8-bp duplex and 8-bp triplex guarantee the stability of the stem-loop like structure. Even when the substrate matches the purple sequence, the rest sequence cannot bind to 8-17 because of the occupied binding arm. When Cu2+ is added into the system, the Cu2+ DNAzyme cuts the logic gate at A site, weakening the stem-loop structure as to separate. Now, the substrate can easily bind to 8-17. At this time, there is no Pb2+, the substrate cannot be cleaved by 8-17. Therefore, when we add Pb2+, 8-17 is activated and cuts the substrate. In conclusion, when Pb2+ and Cu2+ are both present, the substrate can be cut, while there is only Pb2+ or Cu2+, the substrate cannot be cut due to 8-17 inactivity or occupied binding arm.

Figure 8. Self-cleaved logic gate and its NuPack thermodynamics simulation. (From BIOMOD Team Tianjin 2012.)

Looking at this design, there are two critical problems regarding our design:

  1. Is the activity of Cu2+ DNAzyme influenced by the presence of 8-17?
  2. Can the structure really lock the binding arm of 8-17?

Therefore, we conduct the following experiment to verify our consumption.

Module 2

In the module 2, we switched the role of the two DNAzymes. 8-17 locks Cu2+ DNAzyme, while Cu2+ DNAzyme cuts the substrate. In Design 2-1, 8-17 is shown in the box. The left binding arms of 8-17 base-paired with the right one of Cu2+ DNAzyme, thus preventing Cu2+ DNAzyme from binding with the substrate. When Pb2+ is added, 8-17 cuts the right binding arm of Cu2+ DNAzyme, make it available for substrate to bind. Then we add Cu2+, it activates Cu2+ DNAzyme and cuts the substrate.

Figure 9. The design of logic gate 2-1 (A), logic gate 2-2 (B). (From BIOMOD Team Tianjin 2012.)

The only difference between 2-1 and 2-2 is that the left arm of 8-17 in 2-2 is longer than 2-1, because we think the longer it is, the tighter our system will be. There are the same two questions present pertaining our design: will the 8-17 self-cleavage work? Will the structure lock Cu2+ DNAzyme?


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