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[[Image:スクリーンショット 2012-10-28 8.27.26.png|center|600px]]
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We decided to divide our project into several subprojects to do experiments in parallel. The sub-projects are GATE, PORTER, and MEMBRANE projects. We also have SIMULATION project to evaluate design of each sub-project.
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<html><h1><a name="GATE">Sub-project GATE</a></h1></html>
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GATE is the gatekeeper that allows only the target to enter the cell. Actually, is cylindrical DNA nanostructure connecting the inside and outside of membrane like a channel. Because GATE is made of DNA origami, electric repulsions caused by the negative charge of the DNA backbone prevent not desired DNA from entering GATE.
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In order to work as an injector (or extractor) a PORTER system is planted inside this cylinder (see next section).
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[[Image:イラストその１.png|center|700px|thumb|GATE is the gatekeeper that allows only the target to enter the cell.]]
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The goal of this sub-project is to prove this structure is self-assembled by electrophoresis and AFM
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PORTER is in charge of the active transporting of the target into GATE. It is composed of single stranded DNA (ssDNA) sequences. Each ssDNA sequence is called Porter. These Porters are designed to transfer target DNA strands into (or out from) the membrane. <html></br></html>
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[[Image:イラストporter.png|center|700px|thumb|PORTER is in charge of the active transporting of the target into GATE.]]


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<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
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<h2>Function</h2>
   
As active transporter, "CELL-GATE" should work in a cell membrane. Thus, a implementation module for inserting it to membranes needs to be designed.
<!-- Menu -->
DNA sequences with a hydrophobic molecule (cholesterol) are attached outside and around GATE.
<ul id="menu">
We use a liposome (artificial lipid vesicle) as a model for the cell membrane.
<li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Top</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/Simulation">Simulation</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/Experiment ">Experiment</a>
<ul>
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Method">Method</a>
<ul>
<li>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Porter">Porter</a>
<li>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Cylinder">Cylinder</a> </li>
<li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result# Vesicle">Vesicle</a>
</li>
</ul>
</li>
<li>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result">Result</a>
<ul>
<li>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Porter">Porter</a>
<li>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result#Cylinder">Cylinder</a> </li>
<li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Result# Vesicle">Vesicle</a>
</li>
</ul>
</li>
</ul>
</li>
<li>
<a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Achievement">Achievement</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/TeamSendai/FAQ">FAQ</a>
</li>
</ul>


<h1>Goal</h1>
<p style="text-align:center;">
<em><strong>"We create a channel made of DNA!" </em></strong>
</p>
<img src="http://openwetware.org/images/9/9c/Hybri_graph_format_small.jpg" alt="hybrid graph" align="right" width="240px" height="194px" >
<p>
私たちはDNAを使ってチャネルを作りたい。</br>
標的分子との結合を考えて、いくつかの一本鎖DNAを進めたい方向に行くほど結合が強くなるように設計することで、物質の移動を行える。この標的分子とのハイブリダイゼーションを使った物質の移動をチャネルの動力に利用できれば、濃度勾配などに依存しない物質の輸送が行える。濃度勾配に頼ると、物質を移動させるのに長い時間がかかっていたり、そもそも移動ができなかったものも、ハイブリダイゼーションを利用した方法ならば、移動を促進したり、濃度勾配だけでは不可能だった移動も可能になる。
</p>
<img src="http://openwetware.org/images/9/97/Graph_all.jpg" alt="graph" width="980px" height="231px">


[[Image:スライド3.jpg|center|400px|thumb|Our strategy is making liposome indeed cell's membrane]]


<h1>Problem & Solution</h1>
{{-}}
<h2>Problem</h2>
<p>
私たちはチャネルの動力だけでなく、物質の通り道となる部分もDNAで作ったTubeにしたい。DNAでチャネルを作るとき、問題が二つある。</br>
一つはDNAが電荷を持つということ。</br>
もう一つはどのようにしてDNAの構造体を細胞膜に貫通させるかということである。
</p>
<h2>Solution of charges of DNA</h2>
<img src="http://openwetware.org/images/f/f0/Format_porter_idea.jpg" alt="porter idea" align="right" width="600px" height="241px">
<p>
DNAは負の電荷を持つ。したがって、DNAを使ってチャネルを作ると、ブラウン運動では越えられないクーロン力の壁ができてしまう。この壁を越えるために、私たちはチャネルの入口から一本鎖DNAを長く伸ばすことにした。さらに、こうすることにより、標的分子の濃度が少ない状況での、捕集率の向上が望まれる。
<br clear="right">
</p>


<h2>How to penetrate the tube</h2>
<h2>Sub-project GOAL</h2>
<img src="http://openwetware.org/images/0/0b/スクリーンショット_2012-10-15_1.11.35.png" alt="modified tube" align="left"　width="350px" height="217px">
The goal of this sub-project is to attach gate structure on liposomes and observe them by fluorescence microscope.
<img src=" http://openwetware.org/images/5/5e/スクリーンショット_2012-10-15_1.22.38.png " alt="modified tube" align="left"　width="350px" height="217px">
{{-}}
<p>
Tubeを脂質二重膜に貫通させるために、私たちはコレステロールを修飾したDNAを用いた。このDNAをTubeの側面に取り付けることで、Tubeは脂質膜上に取りつくことができるようになるだろうと考えられる。また、コレステロール修飾したDNAを生やすだけでは、貫通するのか、それとも脂質膜上に浮いた状態になるのかは制御できない。そのため、Tubeの片側にわざとM13を余らせて、脂質膜に近づいたらモーメントを得て、取りつく角度が修正されるように設計してある。</br>
</br>
</br>
私たちはcylinderとvesicleを混ぜただけではvesicle(脂質)の非特異吸着性によってcylinderがvesicle表面にべたべたと貼りついてしまって刺さらないと考えた。そこで、cylinderにコレステロールを修飾した(図で示す)。これは、コレステロールのカルボキシル基がリン脂質と結合するため、cylinderがvesicle刺さりやすくなると考えたからである。</br>
(↑筒チームのアイデア？)
<br clear="left">
</p>
 
<h1>Application in future</h1>
<p>
あんなことやこんなことに使える。
</p>
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Latest revision as of 19:42, 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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Project



We decided to divide our project into several subprojects to do experiments in parallel. The sub-projects are GATE, PORTER, and MEMBRANE projects. We also have SIMULATION project to evaluate design of each sub-project.

<html><h1><a name="GATE">Sub-project GATE</a></h1></html>

Function

GATE is the gatekeeper that allows only the target to enter the cell. Actually, is cylindrical DNA nanostructure connecting the inside and outside of membrane like a channel. Because GATE is made of DNA origami, electric repulsions caused by the negative charge of the DNA backbone prevent not desired DNA from entering GATE. In order to work as an injector (or extractor) a PORTER system is planted inside this cylinder (see next section).


GATE is the gatekeeper that allows only the target to enter the cell.

Sub-project GOAL

The goal of this sub-project is to prove this structure is self-assembled by electrophoresis and AFM

<html><h1><a name="PORTER">Sub-project PORTER</a></h1></html>

Function


PORTER is in charge of the active transporting of the target into GATE. It is composed of single stranded DNA (ssDNA) sequences. Each ssDNA sequence is called Porter. These Porters are designed to transfer target DNA strands into (or out from) the membrane. <html></br></html> The first Porter is likely to be outside GATE because of its electric repulsion. Furthermore, the first Porter catches the target DNA and pull it inside the GATE by hybridizing with it. Inner Porters that have higher affinity than the previous Porter pull the target inside GATE step by step.



PORTER is in charge of the active transporting of the target into GATE.

Sub-project GOAL

The goal of this sub-project is to confirm this Porter system is working by electrophoresis


<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>

Function

As active transporter, "CELL-GATE" should work in a cell membrane. Thus, a implementation module for inserting it to membranes needs to be designed. DNA sequences with a hydrophobic molecule (cholesterol) are attached outside and around GATE. We use a liposome (artificial lipid vesicle) as a model for the cell membrane.


Our strategy is making liposome indeed cell's membrane


Sub-project GOAL

The goal of this sub-project is to attach gate structure on liposomes and observe them by fluorescence microscope.

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