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<li  id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Simulation">Simulation</a></li>
<li  id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Simulation">Simulation</a></li>
<li  id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Experiment">Experiment</a></li>
<li  id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Experiment">Experiment</a></li>
<li  id="gn-protocol"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Protocol">Protocol</a></li>
<!--<li  id="gn-protocol"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Protocol">Protocol</a></li>-->
<li  id="gn-dis"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Discussion">Discussion</a></li>
<li  id="gn-dis"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Discussion">Discussion</a></li>
<li  id="gn-team"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Team">Team</a></li>
<li  id="gn-team"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Team">Team</a></li>
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<h1>System Design</h1>
<h1>Design</h1>
<p>To complete our goal, we propose two different types of system. One is DNA molecules system using enzyme, polymerase, nickase, and restriction enzyme. The other is enzyme-free system only using DNA, inspired by seesaw gate (Lulu Qian et.al, 2011). And to demonstrate these systems, we put taste substances into liposomes and effuse them.</p>
<p>To complete our goal, we need to develop next two systems.</p>
1. Programmable Output System<br>
2. Taste Releasing System<br><br>


<h2>1-a.Enzyme System</h2>
<!--
The system using enzymes has three processes
polymerase, nickase, and restriction enzyme.
<ol>
<li>The process in which a DNA polymerase synthesizes supplemental DNA by making a mold of input-DNA sequence and nickaze peel it.</li>
<li>The system which releases DNA as outputs.</li>
<li>The process which changes the end of input-DNA sequence by using restriction enzyme.</li>
</ol>


<h3>1.Reading system</h3>
In addition, to demonstrate these systems, we put taste substances into liposomes and effuse them.</p>
<img src="http://openwetware.org/images/c/c9/Figure-01.png">
This system aims to output signals to each input signals in order. To achieve this goal,
-->


<table>
<h1>1. Programmable Output System </h1>
<tr></tr>
<p> The purpose of this system is to release output DNA in order.
<tr>
We propose two different approaches.<br><br>
<td>
<figure>
<img src="http://openwetware.org/images/b/bf/Figure1-2_figure1-2a.png">
<figcaption>あなたのまちの はたらく にっかーぜ</figcaption>
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<figure>
<img src="http://openwetware.org/images/5/50/Figure1-2_figure1-2b.png">
<figcaption>説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明</figcaption>
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<img src="http://openwetware.org/images/a/a7/Figure1-2_figure1-2c.png">
<figcaption>説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明</figcaption>
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<p>In this system, polymerase and nickase read input-DNA arrangement from one end to another, and effuse output to it.
<h2>1st Approach; Enzyme system</h2>
Information (A, B, and C) is recorded as input-DNA arrangement (A, B and C are able to be permutated voluntarily). When input-DNA is put into this system, template A, B, and C cohere with input A, B, and C correspondingly. Then complementary arrangement to remaining template nearest input’s 3’ end (figure A1) is copied and effused with polymerase and nickase. This DNA arrangement (We will call it A1.) is an input to following 2 and 3 system.
<p>Enzyme System has three processes.</p>
<br>
1st Process:The process in which DNA Polymerase amplifies KEY DNA. (Amplifying process) <br>
&#9312; Domains A, B, and C in the template combine with domains A, B, and C in the input respectively.
2nd Process:The process in which KEY DNA releases the liposome. (Releasing process) <br>
3rd Process:The process in which restriction enzyme renews the 3’ end of the input-DNA sequence to get an output. (Renewing process)<br>
<img src="http://openwetware.org/images/9/9e/Fde1a0-01.png">
 
<h3>1.Amplifying process</h3>
 
<p>
In this process, first, domains A, B, and C in the template combine with domains A, B, and C in the input respectively. Then, polymerase copies 5’ end of the template sequence and extends input sequence. After that, nickase cleaves the end of the copied domain. Then, polymerase works at the gap created by the nickase and push out the domain A. Repeating this process again and again, we amplify the domain A. (Fig.1)
</p>
<p>
This DNA domain, we call it A1, becomes an input to following process 2 and 3.
</p>
 
<img src="http://openwetware.org/images/c/c9/Figure-01.png"><br><br>
 
<!--
 
&#9312; Domains A0, B0, and C0 in the template combine with domains A0-, B0-, and C0- in the input respectively. Input-Template complex is created.<br>
&#9313; Polymerase recognizes 3’ end of input. (Identified with dashed circle) <br>
&#9314; Extending input sequence. The sequence A1 is newly formed. <br>
&#9315; Polymerase runs away from Input-Template complex. <br>
&#9316; Nickase combines with its recognition cite. <br>
&#9317; Cleaving the end of the copied domain./ Making nick between A0 and A1. <br>
&#9318; Polymerase works from the gap (Identified with dashed circle) created by the nickase. <br>
&#9319; Running on DNA with making nucleotides and pushing out the A1. <br>
&#9320; Repeating this process again and again amplifies the number of domain A1. <br><br>
 
-->
 
<h3>2.Releasing process</h3>
<p> A1 combines with the 3’ end of the DNA which is combined with the DNA modified with liposome (output-A). Polymerase recognizes the 3’ end of the A1 and then extend the chain.
</p>
<p>
At the same time, output-A is denatured and released.
</p>
</p>
<h3>2.Releasing system</h3>
<table>
<tr></tr>
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<td>
<figure>
<img src="http://openwetware.org/images/7/72/Figure2_fusen_figure1-2a.png">
<figcaption>説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明</figcaption>
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<img src="http://openwetware.org/images/f/fd/Figure2_fusen_figure1-2b.png">
<figcaption>説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明</figcaption>
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<td>
<figure>
<img src="http://openwetware.org/images/e/e8/Figure2_fusen_figure1-2c.png">
<figcaption>説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明説明</figcaption>
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<img src="http://openwetware.org/images/1/1f/IMG_3657-02.jpg" width="735px" height="600px">
<img src="http://openwetware.org/images/1/1f/IMG_3657-02.jpg" width="735px" height="600px">
<p>A1 combines with the end of the DNA which fixes the liposome-modifying DNA (output-A).
<p>A1 combines with the end of the DNA which fixes the liposome-modifying DNA (output-A).
Polymerases recognize the 3’end of the A1 and extend the chain.
Polymerases recognize the 3’end of the A1 and extend the chain.
At the same time, output-A is denatured and released.</p>
At the same time, output-A is denatured and released.</p>
<h3>3.Cutting system</h3>
<img src="http://openwetware.org/images/7/7f/Figure3-01.png">
<p>When A1 combines with the gate-A, thanks to polymerases, the DNA which has the recognition sequence corresponding to the restriction enzyme releases. (thanks to polymerases → by polymerases)
When this DNA combines with the input, restriction enzyme is activated, and cuts the chain between A and B.
To do so, A is replaced by B in the area near the 3’ end of the input and back to the system-1 .</p>
<p>In this way, output-A, output-B, and output-C are released in order.</p>




<h3>3.Renewing process</h3>
<img src="http://openwetware.org/images/7/7f/Figure3-01.png">
<p> When A1 combines with the gate-A, the DNA which has the recognition sequence corresponding to the restriction enzyme is released by polymerase. When this DNA combines with the structure made of input and template, a restriction enzyme activates, and cleaves the chain between A and B. By doing this, the domain near the 3’ end of the input becomes domain B. Then, the process goes back to the system-1.
</p>
<p> In this way, output-A, output-B, and output-C are released in order.</p>


<h2>1-b.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/9/97/Figure_EnzymeFree-01.png">
<img src="http://openwetware.org/images/f/f6/Figure_EnzymeFree-03.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/8/89/Figure_EnzymeFree-04.png">
<p>This system aims to output signals to each input signals in order. To achieve this goal, we prepared an Input-DNA sequence, a trigger-DNA sequence, three kinds of DNA sequence (fuel, input, gate), and three kinds of double strand DNA with liposome (figure 1). We assembled a circuit with seesaw gate mechanism and those DNA sequences.</p>
<p>This approach is inspired by seesaw gate (Lulu Qian et.al, 2011).We prepared an Input-DNA sequence, a trigger-DNA sequence, three kinds of DNA sequence (fuel, input, gate), and three kinds of double strand DNA with liposome (figure 1). We assembled a circuit with seesaw gate mechanism and those DNA sequences.</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">
<p>Reactions as follows : </p>
<p>Reactions as follows : </p>
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<p>Taking advantage of such reactions, we are convinced of outputting the targeting output in order. (taking advantage of such reactions → by these reactions)</p>
<p>Taking advantage of such reactions, we are convinced of outputting the targeting output in order. (taking advantage of such reactions → by these reactions)</p>


<h2>2.Demonstration</h2>
<h2>2. Taste releasing system </h2>
<p>
<p>
We contained a taste substances in a liposome. The liposome was modified with a DNA (outputA etc.) The DNA attached to the liposome and the DNA which had the complementary arrangement (agaDNA) were sprouted on agarose gel, and were hybridized each other.
The purpose of this system is to encapsulate taste substances in liposome and to release liposome attached to substrate.
The template reacted with the input, polymerase, and nickase. Then the DNA (A1 etc.) is generated. With this DNA, we caused to denature output and agaDNA, then the liposome was released from agarose gel, and taste substances were effused.</p>


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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Latest revision as of 08:31, 27 August 2014

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<body> <div id="globalnav" class="design"> <ul> <li id="gn-home"><a href="/wiki/Biomod/2014/Sendai/temp/0821">Home</a></li> <li id="gn-intro"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Introduction">Introduction</a></li> <li id="gn-design"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Design">Design</a></li> <li id="gn-simu"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Simulation">Simulation</a></li> <li id="gn-xp"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Experiment">Experiment</a></li> <!--<li id="gn-protocol"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Protocol">Protocol</a></li>--> <li id="gn-dis"><a href="/wiki/Biomod/2014/Sendai/temp/0821/Discussion">Discussion</a></li> <li id="gn-team"><a href="/wiki/Biomod/2014/Sendai/temp/0821/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, we need to develop next two systems.</p> 1. Programmable Output System<br> 2. Taste Releasing System<br><br>

<!-- polymerase, nickase, and restriction enzyme.

In addition, to demonstrate these systems, we put taste substances into liposomes and effuse them.</p> This system aims to output signals to each input signals in order. To achieve this goal, -->

<h1>1. Programmable Output System </h1> <p> The purpose of this system is to release output DNA in order. We propose two different approaches.<br><br>

<h2>1st Approach; Enzyme system</h2> <p>Enzyme System has three processes.</p> 1st Process:The process in which DNA Polymerase amplifies KEY DNA. (Amplifying process) <br> 2nd Process:The process in which KEY DNA releases the liposome. (Releasing process) <br> 3rd Process:The process in which restriction enzyme renews the 3’ end of the input-DNA sequence to get an output. (Renewing process)<br> <img src="http://openwetware.org/images/9/9e/Fde1a0-01.png">

<h3>1.Amplifying process</h3>

<p> In this process, first, domains A, B, and C in the template combine with domains A, B, and C in the input respectively. Then, polymerase copies 5’ end of the template sequence and extends input sequence. After that, nickase cleaves the end of the copied domain. Then, polymerase works at the gap created by the nickase and push out the domain A. Repeating this process again and again, we amplify the domain A. (Fig.1) </p> <p> This DNA domain, we call it A1, becomes an input to following process 2 and 3. </p>

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

<!--

&#9312; Domains A0, B0, and C0 in the template combine with domains A0-, B0-, and C0- in the input respectively. Input-Template complex is created.<br> &#9313; Polymerase recognizes 3’ end of input. (Identified with dashed circle) <br> &#9314; Extending input sequence. The sequence A1 is newly formed. <br> &#9315; Polymerase runs away from Input-Template complex. <br> &#9316; Nickase combines with its recognition cite. <br> &#9317; Cleaving the end of the copied domain./ Making nick between A0 and A1. <br> &#9318; Polymerase works from the gap (Identified with dashed circle) created by the nickase. <br> &#9319; Running on DNA with making nucleotides and pushing out the A1. <br> &#9320; Repeating this process again and again amplifies the number of domain A1. <br><br>

-->

<h3>2.Releasing process</h3> <p> A1 combines with the 3’ end of the DNA which is combined with the DNA modified with liposome (output-A). Polymerase recognizes the 3’ end of the A1 and then extend the chain. </p> <p> At the same time, output-A is denatured and released. </p> <img src="http://openwetware.org/images/1/1f/IMG_3657-02.jpg" width="735px" height="600px"> <p>A1 combines with the end of the DNA which fixes the liposome-modifying DNA (output-A). Polymerases recognize the 3’end of the A1 and extend the chain. At the same time, output-A is denatured and released.</p>


<h3>3.Renewing process</h3> <img src="http://openwetware.org/images/7/7f/Figure3-01.png"> <p> When A1 combines with the gate-A, the DNA which has the recognition sequence corresponding to the restriction enzyme is released by polymerase. When this DNA combines with the structure made of input and template, a restriction enzyme activates, and cleaves the chain between A and B. By doing this, the domain near the 3’ end of the input becomes domain B. Then, the process goes back to the system-1. </p> <p> In this way, output-A, output-B, and output-C are released in order.</p>

<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).We prepared an Input-DNA sequence, a trigger-DNA sequence, three kinds of DNA sequence (fuel, input, gate), and three kinds of double strand DNA with liposome (figure 1). We assembled a circuit with seesaw gate mechanism and those DNA sequences.</p> <img src="http://openwetware.org/images/7/79/Figure_EnzymeFree-02.png"> <p>Reactions as follows : </p> <h3>1.</h3> <p>First, add input to trigger-, fuel-, gate-DNA sequence, and three kinds of double strand DNA with a liposome solution. Then, input reacts with trigger, and DNA (1) peels off.</p> <h3>2.</h3> <p>DNA (1) which peeled off at process 1 reacts with double strand DNA with a liposome, and effuse a single strand DNA with a liposome. This reaction takes place before process 3 because toe hold is longer than gate toe hold as seesaw gate’s threshold reaction.</p> <h3>3.</h3> <p>On the other hand, remaining DNA(1) reacts with the gate, and DNA(2) is released from the gate. Then, the gate free from DNA(2) and the part of DNA(1) couples complementarily . As a result, we get double-strand DNA(3) from them.</p> <h3>4.</h3> <p>Double-strand DNA and fuel react, and DNA(2) is made.</p> <h3>5.</h3> <p>Repeating the method3 and method4 again and again, the amount of DNA(2) increases. (If you want to know about method1~5, refer Figure2.)

</p> <img src="http://openwetware.org/images/4/42/Enzyme-free_System_picture2.jpg" width="441px" height="599px"> <h3>6.</h3> <p>DNA(2) plays the role as a trigger, reacts with the input, induces the same reaction as the one previously described. At this point, we get DNA(4) in the same manner as DNA(2).

</p> <img src="http://openwetware.org/images/2/20/Enzyme-free_System_picture3.jpg" width="426px" height="600px"> <h3>7.</h3> <p>DNA(4) plays the role as a trigger, reacts with the input, induces the same reaction as the one previously described.(Figure4)</p> <img src="http://openwetware.org/images/d/d4/Enzyme-free_System_picture4.jpg" width=395px height="599px"> <p>Taking advantage of such reactions, we are convinced of outputting the targeting output in order. (taking advantage of such reactions → by these reactions)</p>

<h2>2. Taste releasing system </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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