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| {{Biomod/2014/Sendai/temp/0821/Styles}}
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| <html>
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| <head>
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| <title></title>
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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="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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| <h2>1-1.Enzyme system</h2>
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| <h3>Results</h3>
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|
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| <p>
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| The core of our system is that it gives outputs in order with time intervals. Here we examine the functions of the system in simulation to confirm whether it is programmable and scalable.br>
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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/4/44/0823tetsuya-01.png">
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| <figcaption>Fig.1#</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 simulated the behavior when the system had no input. <br>
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| Of course, the system gave no outputs (Fig.1). This system needs some inputs to start the actions.<br>
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| </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/c3/0823tetsuya_gyaku-01.png">
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| <figcaption>Fig.2#</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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|
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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/5/59/0824simulation04-01.png">
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| <figcaption>Fig.4#</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/e/e7/0824simulation03-01.png">
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| <figcaption>Fig.5#</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/9/91/0827simulation08-01.png" width="610px" height="460px">
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| <figcaption>Fig.6#</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">
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| <figcaption>Fig.7#</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">
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| <figcaption>Fig.8#</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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|
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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>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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|
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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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| Input DNA concentration: 10nM<br>
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| Template1 concentration: 10nM<br>
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| Template2 concentration: 10nM<br>
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| Liposome1 concentration: 10nM<br>
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| Liposome2 concentration: 10nM<br>
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| Gate1 concentration: 10nM<br>
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| Gate2 concentration: 10nM<br>
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| Simulation time: 100[sec]<br>
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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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| Hybridization:kh=5.0*10^6<br>
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| Denaturation:kd=1.0*10^3<br>
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| Branch migration:kb=1.0*10^-1<br>
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| Polymerase:kp:=17<br>
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| Nickase:kn=3.0<br>
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| Restriction enzyme:kr=3.0<br>
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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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| </div>
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| </body>
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| </html>
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