Biomod/2014/Sendai/temp/0821/Simulation

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</style> </head> </html> <html> <head> <title></title> </head>

<body> <div id="globalnav" class="simu"> <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>Simulation</h1> <h2>1-a.Enzyme system</h2> <h3>Results</h3>

<p> Our system gave outputs with time intervals in order.<br><br> </p>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/4/44/0823tetsuya-01.png"> <figcaption>Fig.1#</figcaption> </figure> </div> <div class="blockright"> <span>Our system gave, first, A-outputs, second, B-output with about 10sec interval when we code A-B in the input DNA.</span> </div>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png"> <figcaption>Fig.2#</figcaption> </figure> </div> <div class="blockright"> <span>Our system gave first, B-outputs second, A-output with about 10sec interval when we code B-A in the input DNA.</span> </div>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png"> <figcaption>Fig.3#</figcaption> </figure> </div> <div class="blockright"> <span>Our system gave no outputs when the system accepted no inputs. We need the inputs DNA to start the system.</span> </div>

<p>Our system can change the time intervals by changing concentration’s of components (input, templates). </p>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png"> <figcaption>Fig.4#</figcaption> </figure> </div> <div class="blockright"> <span>Time intervals changed by changing templates. Time interval increased when the concentration of template-A(Fig.4) or template-B(Fig.5) decreased. </span> </div>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png"> <figcaption>Fig.5#</figcaption> </figure> </div> <div class="blockright"> <span>#</span> </div>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png"> <figcaption>Fig.6#</figcaption> </figure> </div> <div class="blockright"> <span>Time interval changed by changing the concentration of gate. (Fig6)</span> </div>

<div class="blockleft"> <figure> <img src="http://openwetware.org/images/c/c3/0823tetsuya_gyaku-01.png"> <figcaption>Fig.7#</figcaption> </figure> </div> <div class="blockright"> <span>Time interval changed when the concentration of input DNA decreased. (Fig.7)</span> <br> <p> Note that outputs DNA didn’t decrease if input DNA did </p> </div>

<br> <h3>Method</h3> <p> Our system behaved properly in scilico, that is , following can be said.<br><br>

・Our system gives outputs as coded in the input DNA. <br> ・Our system gives outputs with time intervals and the interval can be tuned by changing concentrations of the components of the system.<br> </p>

<h3>Condition</h3> <p> Condition of simulating is as follows.<br><br>

Input DNA concentration: 10nM<br> Template1 concentration: 10nM<br> Template2 concentration: 10nM<br> Liposome1 concentration: 10nM<br> Liposome2 concentration: 10nM<br> Gate1 concentration: 10nM<br> Gate2 concentration: 10nM<br> Simulation time: 100[sec]<br> </p>

<p> Values of chemical parameters are as follows.<br><br>

Hybridization:kh=5.0*10^6<br> Denaturation:kd=1.0*10^3<br> Branch migration:kb=1.0*10^-1<br> Polymerase:kp:=17<br> Nickase:kn=3.0<br> Restriction enzyme:kr=3.0<br> </p>

<p> Only Parameter of Reaction of gate and keyDNA is 1.0×10^6 because the toehold is short. </p>

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