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

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<div id="navDiv">

<ul>

  	    <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>
       </li>
  	    <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>
 	        </ul>

</li>

<li class='has-sub'><a href='#'><span>Experiments and Results</span></a>

  	        <ul>
  	            <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>

</ul>

       </li>   	
  	    <li class='active'><a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Protocol"><span>Protocol</span></a>

</li>

           <li class='active'><a href='http://openwetware.org/wiki/Biomod/2012/Tianjin/Attributions'><span>Attributions</span></a></li>

</ul> </div>

</html>

<html>

<div id="tianjin-right-content"> <ul><li> <a href="#" title="#">Background</a> </li><li> <strong class="selflink">The Logic Gate</strong><div class="tianjin-description">1xxx</div> </li><li> <a href="#" title="#">Y-DNA</a><div class="tianjin-description">2xxx</div> </li><li> <a href="#" title="#">The Origami Amplifier</a><div class="tianjin-description">3xxx</div> </li></ul> </div>

<div id="text-content"> </html>

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 Cuzyme. 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 X. It is made up of a logic gate and a reporter. The logic gate is responsible for the detection of Pb²⁺ and Cu²⁺ ion, while the substrate acts as the reporter to indicate the activity of the logic gate.

[[Image:]]

In Figure X, orange sequence is the conservative sequence of 8-17, and the purple part is an 8bp binding arm. In addition, the Cuzyme is include the in black box. It binds with the corresponding sequence, thus preventing 8-17 from matching with the reporter, 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 reporter 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 Cuzyme cuts the logic gate at A site, weakening the stem-loop structure as to separate. Now, the reporter can easily bind to 8-17. At this time, there is no Pb²⁺, the reporter cannot be cleaved by 8-17. Therefore, when we add Pb²⁺, 8-17 is activated and cuts the reporter. In conclusion, when Pb²⁺ and Cu²⁺ are both present, the reporter can be cut, while there is only Pb²⁺ or Cu²⁺, the substrate cannot be cut due to 8-17 inactivity or occupied binding arm.

Looking at this design, there are two critical problems regarding our design: 1. Is the activity of Cuzyme 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

[[Image:]]

In the module 2, we switched the role of the two DNAzymes. 8-17 locks Cuzyme, while Cuzyme cuts the reporter. 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 Cuzyme, thus preventing Cuzyme from binding with the reporter. When Pb²⁺ is added, 8-17 cuts the right binding arm of Cuzyme, make it available for reporter to bind. Then we add Cu²⁺, it activates Cuzyme and cuts the reporter.

[[Image:]]

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 Cuzyme?

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@@ Line 42: / Line 42: @@
 [[Image:]]
-In the module 2, we switched the role of the two DNAzymes. 8-17 locks Cuzyme, while Cuzyme cuts the reporter. 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 Cuzyme, thus preventing Cuzyme from binding with the reporter. When Pb<sup>2+</sup> is added, 8-17 cuts the right binding arm of Cuzyme, make it available for reporter to bind. Then we add Cu<sup>2+</sup>, it activ2ates Cuzyme and cuts the reporter.
+In the module 2, we switched the role of the two DNAzymes. 8-17 locks Cuzyme, while Cuzyme cuts the reporter. 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 Cuzyme, thus preventing Cuzyme from binding with the reporter. When Pb<sup>2+</sup> is added, 8-17 cuts the right binding arm of Cuzyme, make it available for reporter to bind. Then we add Cu<sup>2+</sup>, it activates Cuzyme and cuts the reporter.
 [[Image:]]

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

Revision as of 10:32, 27 October 2012

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