Biomod/2014/Sendai/temp/0821/Design

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<body> <div id="globalnav"> <ul> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821">Home</a></li> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Introduction">Introduction</a></li> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Design">Design</a></li> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Simulation">Simulation</a></li> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Experiment">Experiment</a></li> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Protocol">Protocol</a></li> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Discussion">Discussion</a></li> <li><a href="/wiki/Biomod/2014/Sendai/temp/0821/Team">Team</a></li> </ul> </div> <div id="main"> <h1>System Design</h1> <p>To complete our goal, we propose two different types of system. One is DNA molecules system using enzyme, polymerase, nickase, and restricted enzyme. The other is enzyme-free system only using DNA, inspired by seesaw gate. (Lulu Qian et.al, 2011)</p>

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

<h3>1(reading system)</h3> <img src="http://openwetware.org/images/9/90/IMG_3657-01.jpg" width="800px" height="327px"> <p>In this system, polymerase and nickase read input-DNA arrangement from one end to another, and effuse output to it. 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> <h3>2(releasing system)</h3> <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 fix 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(cutting system)</h3> <p>When A1 combines with the gate-A, thanks to polymerases, the DNA which has the recognition sequence corresponding to the restriction enzyme releases. When this DNA combines with the input, restriction enzyme activated, cut 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 release in order.</p>


<h2>2.Enzyme-free System</h2> <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>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) increase. (If you want to know about method1~5, refer Figure2.) </p> <h3>6.</h3> <p>DNA(2) plays the role as a trigger, react with the input, induce the same reaction as the one previously descrived. At this point, we get DNA(4) in the same manner as DNA(2). </p>

<img src="http://openwetware.org/images/f/f8/Enzyme-free_System_picture1.jpg" width="635px" height="599px"> <img src="http://openwetware.org/images/4/42/Enzyme-free_System_picture2.jpg" width="441px" height="599px"> <img src="http://openwetware.org/images/2/20/Enzyme-free_System_picture3.jpg" width="426px" height="600px"> </div> </body> </html>

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