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| <body>
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| <div id="header">
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| <div id="homebutton">
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| <li id="stamp"><a href="http://openwetware.org/wiki/Biomod/2014/Sendai">Home</a></li>
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| </div>
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| <div id="globalnav" class="simu">
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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>Simulation</h1>
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|
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| <a href="#approach1">1st Approach: Enzyme system</a><br>
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| <a href="#approach2">2nd Approach; Enzyme-free System</a>
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| <h2>1st Approach: Enzyme system</h2>
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| <h3>Results</h3>
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| <p>
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| In our system, as the number of combinations among DNAs is so large, there are a lot of intermediates that are not the major product. We have to confirm that the effects of the products are negligible in our system. Searching for an optimum condition to realize the system is not a simple task because the combination of intermediates and reactions among them is too large to take into considerations. To solve these problems, we check the behaviors by simulation. The optimum condition can be applied to experimental conditions.
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| We wrote out all the reaction formulas in the system, and then made ordinary differential equations. Simulations were implemented by solving the equations by numerical computation software. Details are shown in a <a href="#method">Method section</a>
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| </p>
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| <br>
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| <div class="block">
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| <div class="blockleft">
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| <figure>
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| <img src="http://openwetware.org/images/4/44/0823tetsuya-01.png">
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| <figcaption>Fig.1 Result of simulation when the system accepted A-B input.</figcaption>
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| </figure>
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| </div>
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| <div class="blockright">
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| <span>First, we give an A-B input to the system. Here A-B means the input has commands that give A-output and then B-output.
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| </span>
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| </div>
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| </div>
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| <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
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| <p>The result of simulation is shown in Fig.1. The horizontal axis is time [sec], and the vertical axis is concentration [nM].In Fig.1, the input is mixed at 0[sec]. As a result, the concentration of output-A increases until about 20[sec]. After that, the output-B is released until about 50[sec].</p>
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| <p>These results above show that the system works properly in the mathematical model. We further check the programmability of our system. The programmability is whether the system works accurately, whatever information is coded in the input DNA. We simulate how the system works when it accepts B-A input. If our design is appropriate, the system will give B-output then A-output.</p>
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| <br>
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| <div class="block">
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| <div class="blockleft">
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| <figure>
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| <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png">
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| <figcaption>Fig.2 Result of simulation when the system accepted B-A input.</figcaption>
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| </figure>
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| </div>
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| <div class="blockright">
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| <span>Second, we gave A-B input to the system. Here A-B means the input has commands as the system gives A-output then B-output.<br><br>
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| If our design is correct, the system will give A-output, at first, then B-output.<br><br>
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| In the simulation, we got the result as we expected (Fig.2).<br>
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| </span>
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| </div>
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| </div>
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| <p class="textbox">
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| These results above show that the system seems to work properly, but we need to check the programmability of the system, that is, whether the system works accurately no matter how information is coded in input DNA. Then, thirdly, we simulated how the system works when system accepts B-A input.
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| </p>
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| <div class="block">
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| <div class="blockleft">
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| <figure>
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| <img src="http://openwetware.org/images/3/3e/Ab%28インプットなし%29-01.png">
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| <figcaption>Fig.3#</figcaption>
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| </figure>
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| </div>
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| <div class="blockright">
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| <span>
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| When we coded B-A to the input DNA, the behavior was shown in Fig.3.<br>
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| As we designed, the system gave output B then output A in order. This prove our system can recognize input DNA and change its outputs we coded.<br>
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| <span>
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| </div>
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| </div>
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| <p class="textbox">
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| Moreover, we wanted to know the relations of time intervals between concentration of input, templates, and gates to control the system more precisely.<br>
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| Each concentration related to the system, thus we checked the behavior of time intervals when the concentrations of each component are changed.<br>
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| </p>
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|
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| <p class="textbox">
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| When concentration of input, templates, gates were changed (Fig.4,5,6,7), the results came out as follows.
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| Each result shows that time interval can be adjusted by concentration of components. <br>
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| Decrease of inputs or templates delays releasing outputs because the reactions of input and templates produce Key DNA which produce outputs.<br>
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| Decrease GateA delays releasing B-output because GateA and Key DNA-A start “renewing process”.<br>
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| </p>
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| <div class="block">
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| <div class="blockleft2">
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| <figure>
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| <img src="http://openwetware.org/images/5/59/0824simulation04-01.png" width="480px" height="362px">
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| <figcaption>Fig.4 Result of simulation when concentration of template-A is changed.</figcaption>
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| </figure>
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| </div>
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| <div class="blockright2">
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| <figure>
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| <img src="http://openwetware.org/images/e/e7/0824simulation03-01.png" width="480px" height="362px">
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| <figcaption>Fig.5 Result of simulation when concentration of template-B is changed.</figcaption>
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| </figure>
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| </div>
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| </div>
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| <div class="block">
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| <div class="blockleft">
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| <figure>
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| <img src="http://openwetware.org/images/9/91/0827simulation08-01.png" width="480px" height="362px">
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| <figcaption>Fig.6 Result of simulation when concentration of gate-A is changed.</figcaption>
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| </figure>
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| </div>
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| <div class="blockright">
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| <span>#</span>
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| </div>
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| </div>
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| <div class="block">
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| <div class="blockleft">
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| <figure>
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| <img src="http://openwetware.org/images/c/cf/0827simulation09-01.png" width="480px" height="362px">
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| <figcaption>Fig.7 Result of simulation when concentration of gate-B is changed.</figcaption>
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| </figure>
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| </div>
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| <div class="blockright">
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| <span>#</span>
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| <br>
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| <p>
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| #
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| </p>
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| </div>
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| </div>
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| <div class="block">
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| <div class="blockleft">
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| <figure>
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| <img src="http://openwetware.org/images/6/6e/0824simulation05-01.png" width="480px" height="362px">
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| <figcaption>Fig.8 Result of simulation when concentration of input is changed.</figcaption>
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| </figure>
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| </div>
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| <div class="blockright">
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| <span>#</span>
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| <br>
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| <p>
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| #
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| </p>
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| </div>
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| </div>
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| <p class="textbox">
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| In these simulations, the system can be controlled from perspective of order and time intervals. We concluded followings.<br>
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| ・Our system gives outputs as coded in the input DNA in order.<br>
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| ・Our system gives outputs with time intervals and the interval can be arranged by changing concentrations of the components of the system.<br>
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| </p>
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|
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| <h3 id="method">Method</h3>
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| <p>
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| Our system is described by differential equations obtained from chemical reaction formulas. We solved them by using numerical software (Scilab).
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| </p>
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| <img src="http://openwetware.org/images/b/b8/Dx-01.png">
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| <h3>Condition</h3>
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| <p>
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| Condition of simulating is as follows.<br><br>
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|
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| <table class="table">
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| <tr><td>Input DNA concentration:</td><td>10nM</td></tr>
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| <tr><td>Template1 concentration:</td><td>10nM</td></tr>
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| <tr><td>Template2 concentration:</td><td>10nM</td></tr>
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| <tr><td>Liposome1 concentration:</td><td>10nM</td></tr>
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| <tr><td>Liposome2 concentration:</td><td>10nM</td></tr>
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| <tr><td>Gate1 concentration:</td><td>10nM</td></tr>
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| <tr><td>Gate2 concentration:</td><td>10nM</td></tr>
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| <tr><td>Simulation time:</td><td>100[sec]</td></tr>
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| </table>
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| </p>
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|
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| <p>
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| Values of chemical parameters are as follows.<br><br>
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|
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| <table class="table">
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| <tr><td>Hybridization:</td><td>kh=5.0*10^6</td></tr>
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| <tr><td>Denaturation:</td><td>kd=1.0*10^3</td></tr>
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| <tr><td>Branch migration:</td><td>kb=1.0*10^-1</td></tr>
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| <tr><td>Polymerase:kp:</td><td>=17</td></tr>
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| <tr><td>Nickase:</td><td>kn=3.0</td></tr>
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| <tr><td>Restriction enzyme:</td><td>kr=3.0</td></tr>
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| </table>
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| </p>
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|
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| <p>
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| Only Parameter of Reaction of gate and keyDNA is 1.0×10^6 because the toehold is short.
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| </p>
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|
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| <h2>2nd Approach; Enzyme-free System</h2>
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|
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| </div>
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|
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| <div id="footer1">
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| <div class="lefttext">
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| (C)Copyright Biomod 2014 Team Sendai<br />
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| E-MAIL:
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| <a href="mailto:teamsendai2014@gmail.com"><span style="color:white">teamsendai2014@gmail.com</span></a>
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