Biomod/2012/TeamSendaiA/Project: Difference between revisions

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<!—二段組み本文 -->
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<h1><img src="http://openwetware.org/images/3/35/Formattop2.jpg " alt="Mother Cube2" "width="800" height="141"//></h1>
<h1 align="center";><!--Team Sendai--><img src="http://openwetware.org/images/c/c2/Title-kai.png" ></h1>
<p> </p>
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<!-- パンくずリスト -->
<h1>Abstract</h1>
<p id="Bread">
<p>
<a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Team Sendai</a> &gt;
All the creatures on Earth are made of cells. The exterior and the interior of the cell are compartmentalized by biomembranes.</br>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Top ">Team Sendai A Top</a>&gt;
A nanodevice that is able to actively transport only the specific oligonucleotide through the biomembrane has a great potential to deliver siRNA into the cell or to extract mRNA expressed in the cell.</br>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Project">Project</a>
Here, we decided to create a novel device with such a function. </br>
We have designed <strong>a cylindrical injector/extractor device made of DNA origami</strong> (we named this device: <strong>CELL-GATE</strong>). Inside the cylinder, a cascade of single stranded DNAs is planted. Once the outer-most ssDNA binds to a target oligonucleotide, the target is passed to the inner-ones one by one because of the higher bonding energy assigned to the inner ones.</br>
We also investigate how the cylinder penetrates the biomembrane by using liposome as a model membrane.</br>
</p>
</p>




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<h2>Project</h2>


<div id="pop">
<h2><!--Abstract-->Project Image</h2>
<p>
<p>
&nbsp; In order to create the Mother Cube, we need first to explore the method for parallel bonding DNA origami planes.</br>
<strong>Our PROJECT CELL-GATE is divided into three sub-projects:</strong><br>
&nbsp; We think on three bonding methods:"Using cationic lipid as adhesive", "Using sticky ends growing from origami", and "Using cationic lipid and sticky ends".</br>
<a href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#PORTER">PORTER</a>: Composed of single stranded DNA (ssDNA) sequences. Each ssDNA is called  Porter. Porters are designed to transfer target DNA strands into (or out from) the membrane.</br>
&nbsp; We think "Using cationic lipid as adhesive" is the best method among the three because there is no need of annealing-time.
<a href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#GATE">GATE</a>: Cylindrical DNA nanostructure connecting the inside and outside of membrane like a channel. A cascade of the Porters is planted inside this cylinder. We can use this Gate as an injector or an extractor.</br>
In addition cationic lipid will reduce the force of repulsion of the negatively charged DNA. Cationic lipid will enable us to　make
<a href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#MEMBRANE">MEMBRANE</a>: The exterior and the interior of the cell are compartmentalized by biomembranes. We use liposome as a model membrane.
huge DNA structures　in other words multi-functional mother cubes.  
</p>
</p>


<p><img src="http://openwetware.org/images/5/51/Stage1.jpg" alt="stage1" "width="580" height="23"/></p>
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<area shape="rect" coords="310,8,390,45" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#PORTER" alt="Porter">
<area shape="rect" coords="310,95,370,132" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#GATE" alt="Gate">
<area shape="rect" coords="33,213,165,245" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#MEMBRANE" alt="Membarane">
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Please CLICK ITEMS, GATE, PORTER, AND MEMBRANE in the picture!
</div>


<p>
&nbsp; Studying the interaction between lipid and DNA origami, and creating the following shapes with cadnano.
</p>


<div id="pop">
<h2>Movie</h2>
<p>
<p>
<a href="http://openwetware.org/wiki/BIOMOD/2012/Team_Sendai_A/CADNANO " target="_blank">
</br>
<img src="http://openwetware.org/images/f/f1/Planeshape.jpg" alt="plane shape"  border="0" "width="580" height="185"/></a>
<iframe width="420" height="315" src="http://www.youtube.com/embed/8OB8ytltxwY" frameborder="0" allowfullscreen></iframe>
</p>
</p>
<p>
&nbsp; <em>If you click this image, you get the DNA sequences.</em>
</p>
<p><img src="http://openwetware.org/images/0/0f/Stage2.jpg" alt="stage2"  "width="580" height="27"/></p>
<p>
&nbsp; We have three ideas about what method to follow in order to bond a plane to other DNA origami plane. We are looking for the best method. </p>
<p><img src="http://openwetware.org/images/2/20/Method.jpg " alt="bond method"  "width="580" height="517"/></p>
<p><img src="http://openwetware.org/images/b/b9/Stage3.jpg " alt="stage3"  "width="580" height="27"/></p>
<p>
&nbsp; Creating the cubes. Loading function and bonding them.
<p><img src="http://openwetware.org/images/c/cb/Hako_drug.jpg" alt="stage2"  "width="580" height="320"/></p>
<p>
</p>
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<li><a href="http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Top">Top</a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Project">Project</a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/caDNAnoWorks">caDNAno Works</a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Results_%26_Discussion" >Results & Discussion</a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Methods">Methods</a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Movie">Movie</a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Member">Member</a></li>
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<!-- フッター -->
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<address>Copyright (C) Team Sendai A, All rights reserved.</address>
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</div>

Latest revision as of 18:34, 27 October 2012

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<body> <div id="Container"> <!-- Menu --> <ul id="menu"> <li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Home</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea ">Project</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design">Design</a> </li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation">Simulation</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment ">Experiment</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Future Application">Future Application</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Diary">Diary</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Team ">Team</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/Tohoku/Team Sendai/header"></a> </li>

</ul>

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</body> </div> </html> <html> <div id="Container"> <!—二段組み本文 --> <div id="Header"> <h1 align="center";><!--Team Sendai--><img src="http://openwetware.org/images/c/c2/Title-kai.png" ></h1> </div>

<h1>Abstract</h1> <p> All the creatures on Earth are made of cells. The exterior and the interior of the cell are compartmentalized by biomembranes.</br> A nanodevice that is able to actively transport only the specific oligonucleotide through the biomembrane has a great potential to deliver siRNA into the cell or to extract mRNA expressed in the cell.</br> Here, we decided to create a novel device with such a function. </br> We have designed <strong>a cylindrical injector/extractor device made of DNA origami</strong> (we named this device: <strong>CELL-GATE</strong>). Inside the cylinder, a cascade of single stranded DNAs is planted. Once the outer-most ssDNA binds to a target oligonucleotide, the target is passed to the inner-ones one by one because of the higher bonding energy assigned to the inner ones.</br> We also investigate how the cylinder penetrates the biomembrane by using liposome as a model membrane.</br> </p>


<div id="pop"> <h2><!--Abstract-->Project Image</h2> <p> <strong>Our PROJECT CELL-GATE is divided into three sub-projects:</strong><br> <a href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#PORTER">PORTER</a>: Composed of single stranded DNA (ssDNA) sequences. Each ssDNA is called Porter. Porters are designed to transfer target DNA strands into (or out from) the membrane.</br> <a href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#GATE">GATE</a>: Cylindrical DNA nanostructure connecting the inside and outside of membrane like a channel. A cascade of the Porters is planted inside this cylinder. We can use this Gate as an injector or an extractor.</br> <a href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#MEMBRANE">MEMBRANE</a>: The exterior and the interior of the cell are compartmentalized by biomembranes. We use liposome as a model membrane. </p>

<img src="http://openwetware.org/images/c/c5/Projectcellgate.png" alt="D-Heart" width="440px" usemap="#D-Heart"> <map name="D-Heart"> <area shape="rect" coords="310,8,390,45" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#PORTER" alt="Porter"> <area shape="rect" coords="310,95,370,132" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#GATE" alt="Gate"> <area shape="rect" coords="33,213,165,245" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#MEMBRANE" alt="Membarane"> </map> Please CLICK ITEMS, GATE, PORTER, AND MEMBRANE in the picture! </div>


<div id="pop"> <h2>Movie</h2> <p> </br> <iframe width="420" height="315" src="http://www.youtube.com/embed/8OB8ytltxwY" frameborder="0" allowfullscreen></iframe> </p> </div> <br clear = "left">


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