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<h1>Team Sendai</h1>
<h1 align="center";><!--Team Sendai--><img src="http://openwetware.org/images/c/c2/Title-kai.png" ></h1>
<p>Tohoku University</p>
</div>
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<!—トップメニュー -->
<h1>Abstract</h1>
<ul id="Topmenu">
<p>
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Top">Top</a></li>
All the creatures on Earth are made of cells. The exterior and the interior of the cell are compartmentalized by biomembranes.</br>
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Project">Project</a></li>
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>
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Results_%26_Discussion">Experiment</a></li>
Here, we decided to create a novel device with such a function. </br>
<li><a href=" http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/diary">Diary</a></li>
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>
<li><a href=" http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/member">Team</a></li>
We also investigate how the cylinder penetrates the biomembrane by using liposome as a model membrane.</br>
</ul>
</p>


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<h2>Contents</h2>
<ol>
<li><a href="#Motivation">Motivation</a></li>
<li><a href="#ProjectPlan">Project plan</a></li>
<li><a href="#Selector">Selector</a></li>
<li><a href="#Gate">Gate</a></li>
<li><a href="#Membrane">Membrane</a></li>
<li><a href="#Future">Future</a></li>
</ol>
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<h2><!--Abstract-->Project Image</h2>
<!--
<a name="Motivation"></a><h2>Motivation</h2>
<p>
<p>
現在チャネルの研究は進められているが、それらは単純な穴であり、選択性を持って物質交換を行うものは少ない。そこで我々は選択性をもったチャネルの開発に着手した。</br>
<strong>Our PROJECT CELL-GATE is divided into three sub-projects:</strong><br>
我々が設計したチャネルはこうである。まず、穴としてDNAオリガミで作った六角柱を用意（Gate）。その内側に一本鎖DNAを数本並べておく。この一本鎖DNAをSelectorと名付けた。DNAはその相補性により、DNAはもとよりRNAやタンパク質などの様々な生体分子と相互作用を持ち、また簡単に配列を変更することが可能であるため、六角柱内に一本鎖DNAが並ぶ構造によって、汎用性を持った選択的なチャネルを作成することが可能である。Selectorの配列はチャネルの奥に行くほどターゲット分子との結合を強いように設計する。こうすることでターゲット分子は選別されながら、チャネルの出口へ向かって行くことができる。</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>
また、我々はチャネルの取り付く細胞膜のモデルとしてリポソームを使う。
<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>
</p>
-->
<a name="ProjectPlan"></a><h2>Project plan</h2>
<p>
Our project is divided large three parts, Selector, Gate and Liposome.</br>
So we'll do each experiments abreast and finally we'll mix. </br>


我々のプロジェクトは大きく三つに分けることができる。セレクター、チャネル、リポソームである。そこで我々はこの三つの実験を並行して行う。それぞれの実験がうまくいったところで組み合わせる。（D-Hertを分解した画像をこの下に欲しい）
<img src="http://openwetware.org/images/c/c5/Projectcellgate.png" alt="D-Heart" width="440px" usemap="#D-Heart">
</p>
<map name="D-Heart">
 
<area shape="rect" coords="310,8,390,45" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#PORTER" alt="Porter">
<a name="Selector"></a><h2>Selector</h2>
<area shape="rect" coords="310,95,370,132" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#GATE" alt="Gate">
<p>
<area shape="rect" coords="33,213,165,245" href="http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea#MEMBRANE" alt="Membarane">
セレクターの作動動画希望</br>
</map>
<div align="center">
Please CLICK ITEMS, GATE, PORTER, AND MEMBRANE in the picture!
<img src="http://openwetware.org/images/4/45/Suceed.gif" width="420px" height="300px"><br>
</div>
</div>
  Inside the gate, a cascade of three single stranded DNAs is planted. We named the DNAs Selector1, Selector2, and Selector3 from the outside of the gate. In addition, another Selector, which is called Selector4, is in the vesicle.<br>
[In the gate]  Selector1and 2 have complementary sequences to a target oligonucleotide here and there and consecutive adenine sequences in other portion. We made an attempt to capture a target distant from the gate with high specificity. So we lay out a long Selector1. By catching a target and making loops, it can shrink and go in the gate.<br>
  Selector3 is complementary to the target, but it is shorter than the target. When it binds to the target, the upper end of the target makes a toehold.<br>
  We designed the inner Selector has higher bonding energy. So once the outer-most ssDNA binds to a target, the target is passed to the inner-ones one by one.<br>
[In liposome]  Selector4 is perfectly complementary to the target. After the target reaches Selector3, Selector4 conveys the target into liposome.<br>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Results_%26_Discussion#Selector">Experiment page</a>


</p>


<a name="Gate"></a><h2>Gate</h2>
<div id="pop">
<h2>Movie</h2>
<p>
<p>
Gate should be able to transport the target with selector inside gate and go through cell membrane.</br>
</br>
To transport the target with selector, we decided to make hexagonal tube as gate.</br>
<iframe width="420" height="315" src="http://www.youtube.com/embed/8OB8ytltxwY" frameborder="0" allowfullscreen></iframe>
The reasons we adopted hexagonal tube as gate are that surfaces of hexagonal tube are suitable for being attached selector, </br>
high strength of honeycomb structure are easy to be observed. To go through cell membrane, we placed the staple attached lipid on center of gate.</br>
We expect gate is introduced liposome simultaneously with creation of liposome.</br>
In addition, we attached edge of the gate to adenine staple like a "mustache" to make easy watching by AFM and interrupt other DNA approaching. </br>
We think because of our selector 1 is enough long, only target is transported into the gate. </br>
 
（とりあえずこれでkakutei）</br>
ゲートの目的として内部にセレクターを生やして膜内外に物質を移動させることが出来、なおかつ脂質に刺すことのできるような構造である必要がある。</br>
物質を移動させるために私たちは筒状の構造体を作ればよいと考えた。更にその中でも六角柱となる構造を選択した。</br>
この構造を選択した理由は面の存在からセレクター等の構造物を生やすのに適している事、ハニカム構造は強度が高いので観察がしやすいことである。</br>
　脂質に刺すことのできる構造にするため、私たちは筒の側面に脂質修飾をしているステイプルを配置した。</br>
これによりリポソームの作成時に一緒になって膜に取り込んでもらえることを期待している。</br>
　またそれ以外にもAFMで観察しやすくかつ、他の物質を寄せ付けないような構造となるよう筒の片側からアデニンの行列からなるひげ状のものを取り付けている。</br>
これにより不要な物質は入りにくいが目的物は十分長いポーターによりひげがある状態でも中に運ばれていくのではないかと考えている。</br>
 
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Results_%26_Discussion#Gate">Experiment page</a>
 
</p>
</p>
<a name="Membrane"></a><h2>Membrane</h2>
<p>
細胞膜モデルとしてリポソームを用いる。どのようにベシクルを形成して、D-Napperをくみあわせるのか。</br>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Results_%26_Discussion#Membrane">Experiment page</a>
</p>
<a name="Future"></a><h2>Future</h2>
<p>
In the future, we expect to make the molecular robot which can transport the object to inside the cell and collect the object from the cell using Cell-gate.</br>
And now we use liposome as a model of the cell.</br>
We think that by using liposome not only as a model of the cell but a bag to put something into,</br>
we can make organelles to collect unnecessary object and release medicine.</br>
将来的にはこのセルゲートを使うことで細胞内への物質の運搬、細胞内からの物質の回収ができるロボットの作製を目指している。</br>
また、実験を行うにあたって細胞のモデルとしてリポソームを現在用いているが、単にモデルとしてリポソームを用いるだけでなくこのリポソームでできた袋を蓄積場として、</br>
不要な物質の回収や、優良物質の散布ができる小器官のようなものを作製し細胞内で働かせるといった応用も考えられる。</br>
</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/Results_%26_Discussion">Experiment</a></li>
<li><a href=" http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/diary">Diary</a></li>
<li><a href=" http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/member">Team</a></li>
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<!-- フッター -->
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<address>Copyright (C) Team Sendai, All rights reserved.</address>
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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>

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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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