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| {{Biomod/2014/Sendai/temp/0821/Styles}}
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| <title></title>
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| <style type="text/css">
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| .overline {
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| text-decoration: overline;
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| </style>
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| </head>
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| <body>
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| <div id="header">
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| <div id="left_header">
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| <a href="http://openwetware.org/wiki/Biomod/2014/Sendai">
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| <img src="http://openwetware.org/images/f/fa/Topbg_1.png" width="96px" height="96px"></a>
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| </div>
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| <div id="globalnav" class="design">
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| <ul>
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| <li id="gn-home"><a href="/wiki/Biomod/2014/Sendai">Home</a></li>
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| <li id="gn-intro"><a href="/wiki/Biomod/2014/Sendai/Introduction">Introduction</a></li>
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| <li id="gn-design"><a href="/wiki/Biomod/2014/Sendai/Design">Design</a></li>
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| <li id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/Simulation">Simulation</a></li>
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| <li id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/Experiment">Experiment</a></li>
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| <!--<li id="gn-protocol"><a href="/wiki/Biomod/2014/Sendai/Protocol">Protocol</a></li>-->
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| <li id="gn-dis"><a href="/wiki/Biomod/2014/Sendai/Discussion">Discussion</a></li>
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| <li id="gn-team"><a href="/wiki/Biomod/2014/Sendai/Team">Team</a></li>
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| <li id="gn-end"><a href="#"></a></li>
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| </ul>
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| </div>
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| </div>
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| <div id="main">
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| <h1>Design</h1>
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| <p>To complete our goal, it is necessary to develop a system that releases output DNA in order. Following two different systems are proposed. <br />
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| <a href="#approach1">1st Approach</a> /
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| <a href="#approach2">2nd Approach</a>
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| </p>
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|
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| <h2 id="approach1">1st Approach: Enzyme system</h2>
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| <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.
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| .</p>
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| 1. Amplifying process: DNA polymerase amplifies Key-DNA to release liposome. <br>
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| 2. Releasing process: Key-DNA releases the liposome encapsulates taste substances. <br>
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| 3. Updating process: Restriction enzyme updates the 3’ end of the input-DNA sequence to repeat next circle. <br>
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|
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| <img src="http://openwetware.org/images/9/9e/Fde1a0-01.png"><br>
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| Fig.1 Schematic figure of Enzyme system (in the case that input DNA is “ABC”)<br>
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|
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| <h3>1. Amplifying process</h3>
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| <p>
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| 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 templates combine with domains A<sub>0</sub>, B<sub>0</sub>, and C<sub>0</sub> in the inputs respectively. (①)<br>Then, polymerase extends the input from 3’ end synthesizing the new sequence complementary to the template DNA. (②)<br> After that, the nickase cleaves between A<sub>0</sub> and A<sub>1</sub> by recognizing the sequence in A<sub>0</sub>. Then, polymerase works at the gap created by the nickase thereby DNA pushes out the domain A.(③)<br> Repeating ②,③, the sequence A<sub>1</sub> is amplified.(④)<br>This amplified sequence will become an input of following process 2 and 3.
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| </p>
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|
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| <img src="http://openwetware.org/images/c/c9/Figure-01.png"><br><br>
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|
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| <h3>2. Releasing process</h3>
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|
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| <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 existing hybridization. (⑥)
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| </p>
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| <p>
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| Eventually, output-A is released.
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| </p>
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|
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|
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| <img src="http://openwetware.org/images/a/a2/Figure2_fusen-04.png">
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|
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| <h3>3. Updating process</h3>
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|
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| <img src="http://openwetware.org/images/7/7f/Figure3-01.png"><br>
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|
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| <p> After A<sub>1</sub> hybridize to Gate-A(⑦), polymerase extends A<sub>1</sub> and displace a signal DNA.(⑧) When the signal DNA hybridizes to input complex, a recognition site for the restriction enzyme is formed(⑨), then restriction enzyme cleaves the sequence.(⑩) The process is repeated from Amplifying process with the domain changed to B→C. Regardless of the numbers and kinds of domains, the order of outputs only depend on encoded information in the input.
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| </p>
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|
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| <h2 id="approach2">2nd Approach; Enzyme-free System</h2>
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| <img src="http://openwetware.org/images/8/82/Enzyme-free.png">
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| <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>
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| <img src="http://openwetware.org/images/7/79/Figure_EnzymeFree-02.png">
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| <p>（用意するもの）
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| fuel,gate、Liposomeが結合した二本鎖DNA (Fa,b,c Ga,b,c La,b,c)
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| input(I1),trigger(T1)それぞれ一種類
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| </p>
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|
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| <p>Reactions as follows : </p>
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| <h3>1.</h3>
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| <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
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| the single strand DNA (DNA1)which makes input are released. </p>
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|
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| <h3>2.</h3>
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| <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.
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| This reaction causes earlier so that toehold is longer than that of gate.
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| </p>
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|
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| <h3>3.</h3>
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| <p> Other DNA1 combine with gate(Ga).
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| the single strand DNA (DNA2)which makes gate(Ga) are released so that the length of the double strand is difference.
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| In addition , DNA1 combines with gate.
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| </p>
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|
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| <h3>4.</h3>
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| <p> DNA1 is released again so that DNA3 react with fuel(Fa) ,
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| due to the difference in length of DNA.
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| </p>
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|
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| <h3>5.</h3>
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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.
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| </p>
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| <img src="http://openwetware.org/images/9/97/Figure_EnzymeFree-01.png">
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| <img src="http://openwetware.org/images/f/f6/Figure_EnzymeFree-03.png">
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| <img src="http://openwetware.org/images/8/89/Figure_EnzymeFree-04.png">
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| <img src="http://openwetware.org/images/4/42/Enzyme-free_System_picture2.jpg" width="441px" height="599px">
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|
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| <h3>6.</h3>
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| <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 .
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| </p>
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| <img src="http://openwetware.org/images/2/20/Enzyme-free_System_picture3.jpg" width="426px" height="600px">
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|
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| <h3>7.</h3>
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| <p> DNA4 combines with input as trigger , so the reaction said above caused.
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| </p>
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| <img src="http://openwetware.org/images/d/d4/Enzyme-free_System_picture4.jpg" width=395px height="599px">
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|
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| <p> We can get output signals in order by using this reaction.
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| </p>
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|
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| </div>
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| </body>
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| </html>
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