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

Latest revision as of 19:59, 27 October 2012

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<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>

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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>

<div id="outborder" style="background: #FAFAFA url(http://openwetware.org/images/d/d1/TJU2012-BMD-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>

<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 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:

Is the activity of Cu²⁺ DNAzyme influenced by the presence of 8-17?
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?

<html>

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

Latest revision as of 19:59, 27 October 2012

Module 1

Module 2

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+font-family:Cambria,Calibri;
+font-size:140%;
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+}
+</style>
 <!-- Abstract in the page starts here -->
 <div id="tianjin-right-content">
-<ul><li> <strong class="selflink">Abstract</strong>
+<ul><li> <a href="http://openwetware.org/wiki/Biomod/2012/Tianjin/Project/Background" title="Background">Background</a>
-</li><li> <a href="#" title="#">Title 1</a><div class="tianjin-description">1xxx</div>
+</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="#" title="#">Title 2</a><div class="tianjin-description">2xxx</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="#" title="#">Title 3</a><div class="tianjin-description">3xxx</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><li> <a href="#" title="#">Title 4</a><div class="tianjin-description">4xxx</div>
-</li><li> <a href="#" title="#">Title 5</a><div class="tianjin-description">5xxx</div>
 </li></ul>
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+<div id="outborder" style="background: #FAFAFA url(http://openwetware.org/images/d/d1/TJU2012-BMD-Stripe.png) repeat; height:360px; width:640px; padding:10px;">
-<div id="inborder" style="background: #fff;height:420px;width:620px;">
+<div id="inborder" style="background: #fff;height:340px;width:620px;padding:10px;">
-<a href="http://openwetware.org/index.php?title=Biomod/2012/Tianjin/Project/LogicGate&action=edit">this page edit</a>
+<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>
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 ==Module 1==
-Many scientists have devised various logic gates, 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 as 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.
+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 Cu<sup>2+</sup> DNAzyme. The gate will require both Pb<sup>2+</sup> and Cu<sup>2+</sup> to carry its function of cleaving the substrate.
-The first logic gate we design is shown in Figure X. It is made up of a sensor and a reporter. The sensor is responsible for the detection of Pb2+ and Cu2+ ion, while the substrate acts as the reporter to indicate the activity of the sensor.
+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 Pb<sup>2+</sup> and Cu<sup>2+</sup> ion, while the substrate acts as the substrate to indicate the activity of the logic gate.
-[[Image:]]
+<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;">
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+</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 Cu<sup>2+</sup> 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 Cu<sup>2+</sup>, 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 Cu<sup>2+</sup> is added into the system, the Cu<sup>2+</sup> 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 Pb<sup>2+</sup>, the substrate cannot be cleaved by 8-17. Therefore, when we add Pb<sup>2+</sup>, 8-17 is activated and cuts the substrate. In conclusion, when Pb<sup>2+</sup> and Cu<sup>2+</sup> are both present, the substrate can be cut, while there is only Pb<sup>2+</sup> or Cu<sup>2+</sup>, the substrate cannot be cut due to 8-17 inactivity or occupied binding arm.
-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 sensor 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.
+[[Image:TJU2012-BMD-6.png|thumb|350px|center|'''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 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.
+Looking at this design, there are two critical problems regarding our design:
+#Is the activity of Cu<sup>2+</sup> DNAzyme influenced by the presence of 8-17?
+#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 Cu<sup>2+</sup> DNAzyme, while Cu<sup>2+</sup> 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 Cu<sup>2+</sup> DNAzyme, thus preventing Cu<sup>2+</sup> DNAzyme from binding with the substrate. When Pb<sup>2+</sup> is added, 8-17 cuts the right binding arm of Cu<sup>2+</sup> DNAzyme, make it available for substrate to bind. Then we add Cu<sup>2+</sup>, it activates Cu<sup>2+</sup> DNAzyme and cuts the substrate.
-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 activ2ates Cuzyme and cuts the reporter.
-[[Image:]]
+[[Image:TJU2012-BMD-1'.png|thumb|350px|center|'''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-cutting work? Will the structure lock Cuzyme?
+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 Cu<sup>2+</sup> DNAzyme?