Biomod/2014/Sendai/Design: Difference between revisions

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<h2>2nd Approach; Enzyme-free System</h2>
<h2>2nd Approach; Enzyme-free System</h2>
<img src="http://openwetware.org/images/9/97/Figure_EnzymeFree-01.png">
 
<img src="http://openwetware.org/images/f/f6/Figure_EnzymeFree-03.png">
<img src="http://openwetware.org/images/8/89/Figure_EnzymeFree-04.png">
<p>This approach is inspired by seesaw gate (Lulu Qian et.al, 2011). Our goal is to get different output signals in order of input signals. In this system , we should arrange a input , a trigger ,fuels, the double strand DNA bonding with liposome.</p>
<p>This approach is inspired by seesaw gate (Lulu Qian et.al, 2011). Our goal is to get different output signals in order of input signals. In this system , we should arrange a input , a trigger ,fuels, the double strand DNA bonding with liposome.</p>
<img src="http://openwetware.org/images/7/79/Figure_EnzymeFree-02.png">
<img src="http://openwetware.org/images/7/79/Figure_EnzymeFree-02.png">
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<p> When we perform process3 and 4 repeatedly , the number of DNA2 is increasing. DNA2 is the key  of next process.
<p> When we perform process3 and 4 repeatedly , the number of DNA2 is increasing. DNA2 is the key  of next process.
</p>
</p>
<img src="http://openwetware.org/images/9/97/Figure_EnzymeFree-01.png">
<img src="http://openwetware.org/images/f/f6/Figure_EnzymeFree-03.png">
<img src="http://openwetware.org/images/8/89/Figure_EnzymeFree-04.png">
<img src="http://openwetware.org/images/4/42/Enzyme-free_System_picture2.jpg" width="441px" height="599px">
<img src="http://openwetware.org/images/4/42/Enzyme-free_System_picture2.jpg" width="441px" height="599px">


Revision as of 01:42, 28 August 2014

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<body> <div id="header"> <a href="http://openwetware.org/wiki/Biomod/2014/Sendai/temp/0821"> <img src="http://openwetware.org/images/f/fa/Topbg_1.png" width="96px" height="96px"></a> </div>

<div id="globalnav" class="design"> <ul> <li id="gn-home"><a href="/wiki/Biomod/2014/Sendai">Home</a></li> <li id="gn-intro"><a href="/wiki/Biomod/2014/Sendai/Introduction">Introduction</a></li> <li id="gn-design"><a href="/wiki/Biomod/2014/Sendai/Design">Design</a></li> <li id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/Simulation">Simulation</a></li> <li id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/Experiment">Experiment</a></li> <!--<li id="gn-protocol"><a href="/wiki/Biomod/2014/Sendai/Protocol">Protocol</a></li>--> <li id="gn-dis"><a href="/wiki/Biomod/2014/Sendai/Discussion">Discussion</a></li> <li id="gn-team"><a href="/wiki/Biomod/2014/Sendai/Team">Team</a></li> <li id="gn-end"><a href="#"></a></li> </ul> </div> <div id="main">

<h1>Design</h1> <p>To complete our goal, it is necessary to develop system that releases output DNA in order. Following two different systems are proposed. </p>

<h2>1st Approach: Enzyme system</h2> <p>In this approach, polymerase, nickase, and restriction enzyme can be regarded as hardware while DNA serves as software. This Enzyme system has three processes shown in Fig.1. .</p> 1. Amplifying process: DNA polymerase amplifies Key DNA for releasing liposome. <br> 2. Releasing process: Key DNA releases the liposome encapsulates taste substances. <br> 3. Updating process: Restriction enzyme updates the 3’ end of the input-DNA sequence to continue to next circle. <br>

<img src="http://openwetware.org/images/9/9e/Fde1a0-01.png"><br> Fig.1 Schematic figure of Enzyme system (That shows the case of input “ABC”)<br>

<h3>1. Amplifying process</h3>

<p> In this process, first, domains <span style="text-decoration: overline">A</span><sub>0</sub>, <span style="text-decoration: overline">B</span><sub>0</sub>, and <span style="text-decoration: overline">C</span><sub>0</sub> in the template combine with domains A<sub>0</sub>, B<sub>0</sub>, and C<sub>0</sub> in the input respectively. (①) Then, polymerase extends the input from 3’ end synthesizing the new sequence complementary to the template DNA. (②) After that, the nickase cleaves by recognizing the sequence in A<sub>0</sub>. Then, polymerase works at the gap created by the nickase and push out the domain A.(③) Repeating &#9314, &#9315, the sequence A<sub>1</sub> is amplified.(④) This amplified sequence becomes an input to following process 2 and 3. </p>

<img src="http://openwetware.org/images/c/c9/Figure-01.png"><br><br>

<h3>2. Releasing process</h3>

<p>First of all, the liposome (Output-A) is immobilized on substrate by hybridization between 2 DNA sequences: 5’-end cholesterol DNA modified to liposome and DNA fixed on substrate. Then, A<sub>1</sub> sequence from the Amplifying process hybridizes to fixed DNA on substrate.(⑤) Polymerase synthesizes new DNA from the 3’-end of A<sub>1</sub> separating described hybridization. </p> <p> Eventually, output-A is released. </p>


<img src="http://openwetware.org/images/a/a2/Figure2_fusen-04.png">

<h3>3. Updating process</h3>

<img src="http://openwetware.org/images/7/7f/Figure3-01.png"><br>

<p> After A<sub>1</sub> hybridize to Gate-A(&#9317), polymerase extends A<sub>1</sub> and displace a signal DNA.(&#9318) When the signal DNA hybridizes to input complex, a recognition site for the restriction enzyme is formed, then restriction enzyme cleaves the sequence. The process is repeated from Amplifying process with the domain changed to B→C→…etc. depends on the order encoded by the input . </p>

<h2>2nd Approach; Enzyme-free System</h2>

<p>This approach is inspired by seesaw gate (Lulu Qian et.al, 2011). Our goal is to get different output signals in order of input signals. In this system , we should arrange a input , a trigger ,fuels, the double strand DNA bonding with liposome.</p> <img src="http://openwetware.org/images/7/79/Figure_EnzymeFree-02.png"> <p>（用意するもの） fuel,gate、Liposomeが結合した二本鎖DNA (Fa,b,c Ga,b,c La,b,c) input(I1),trigger(T1)それぞれ一種類 </p>

<p>Reactions as follows : </p> <h3>1.</h3> <p> Input-DNA sequence are dissolved in the solution including trigger , fuels , gates , and the double strand DNA bonding with liposome. Then, 　trigger combines with input and the single strand DNA (DNA1)which makes input are released. </p>

<h3>2.</h3> <p> DNA1 combines with the double strand DNA bonding with liposome . In this reaction , the single strand DNA bonding with liposome are released due to the difference in length of DNA sequence which makes the double strand DNA. This reaction causes earlier so that toehold is longer than that of gate. 

</p>

<h3>3.</h3> <p> Other DNA1 combine with gate(Ga). the single strand DNA (DNA2)which makes gate(Ga) are released so that the length of the double strand is difference. In addition , DNA1 combines with gate. </p>

<h3>4.</h3> <p> DNA1 is released again so that DNA3 react with fuel(Fa) , due to the difference in length of DNA. 

</p>

<h3>5.</h3> <p> When we perform process3 and 4 repeatedly , the number of DNA2 is increasing. DNA2 is the key of next process. </p> <img src="http://openwetware.org/images/9/97/Figure_EnzymeFree-01.png"> <img src="http://openwetware.org/images/f/f6/Figure_EnzymeFree-03.png"> <img src="http://openwetware.org/images/8/89/Figure_EnzymeFree-04.png"> <img src="http://openwetware.org/images/4/42/Enzyme-free_System_picture2.jpg" width="441px" height="599px">

<h3>6.</h3> <p> DNA2 combines with input as trigger , so the reaction said above caused.In this reaction , DNA is released as DNA2 in the reaction　said above . </p> <img src="http://openwetware.org/images/2/20/Enzyme-free_System_picture3.jpg" width="426px" height="600px">

<h3>7.</h3> <p> DNA4 combines with input as trigger , so the reaction said above caused. </p> <img src="http://openwetware.org/images/d/d4/Enzyme-free_System_picture4.jpg" width=395px height="599px">

<p> We can get output signals in order by using this reaction. </p>

<h2>2. Taste Encapsulating and Releasing </h2> <p> The purpose of this system is to encapsulate taste substances in liposome and to release liposome attached to substrate.

The DNA which has the complementary sequence (comp DNA) to the Output is sprouted on agarose gel. They are hybridized each other. When A1 reacts with comp DNA, the output is separated from comp DNA, then the liposome is released from the agarose gel, and taste substances are diffused. </p>

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