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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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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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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:スライド3.jpg|center|400px|thumb|Our strategy is making liposome indeed cell's membrane]]
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<p>
どんな売りを持つチャネルを作りたいのか、そのために何を（DNAを）使って作るのか、その理由は何か。</br>
</br>
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<h1>Why do we use DNA?</h1>
{{-}}
<p>
・自然界にあるチャネルは（タンパク質でできていて？）人間の手で作り変えたりして自在に扱うということは難しい。だから、デザインが可能でsiRNAなどの生体分子と相互作用を持つDNAを使って、チャネルを作ることができれば、チャネル設計（？）の幅が広がるというようなことをまとめていただけると…。（タンパク質とDNAの対比表とか対比図があるとわかりやすいかも）
</p>


<h1>How do we penetrate the Gate to membrane?</h1>
<h2>Sub-project GOAL</h2>
<img src=" http://openwetware.org/images/e/e6/Format_gate_no_tukikata_project.jpg " alt="coreste&tutu " align="left" width="450px" height="290px" >
The goal of this sub-project is to attach gate structure on liposomes and observe them by fluorescence microscope.
<p>
{{-}}
Lipidと親和性のあるコレステロールを使えばいいということを面白おかしく論理的に説明.
どのように貫通するかなど。</br>
（画像はプレゼン用のを拝借したので修正必要。特にHexagonalとかsmall tube とか。絵自体もまだまだ分かりやすくできそうな気が。数式みたいな絵じゃなく、もっと動きのあるものに（アニメーションにしろというわけではない））
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<h1>穴開けただけでチャネル（細胞膜間輸送？）って呼べるの？</h1>
<p>
クーロン力があるから物質だだ漏れにはならない。Gateの内部にDNAの一本鎖並べて、DNAの特異性を利用することで、狙いの分子だけを、一本鎖DNAとの結合エネルギーポテンシャルの坂道に乗せることができる。その一本鎖DNAの列をPoaterと呼ぶことにする。PorterがCellGateのエンジン。みたいなことをうまくまとめる。ここでPorterの説明を終えるつもりで。画像に関してはとりあえず津沢のポテンシャルエネルギーのグラフは必須。
</p>
 
<h1>クーロン力があるならGateに近づけないんじゃない？</h1>
<p>
Porterの一番目を伸ばせばいいみたいなことをキャッチ―な図とともに。筒井さんのシミュレーション映像を貼る。
</p>
 
<h1>私たちが実験で目指したもの</h1>
<img src=" http://openwetware.org/images/c/c8/Format_cell_gate.jpg " alt="hybrid graph" align="left" width="465px" height="315px" >
<p>
ここで初めてMembrane登場？　細胞のモデルとして使っただけ？本物の細胞どうして使わなかったのかという疑問が生まれそう。何かいい理由はないものか。画像はプレゼン用のやつそのままなので改善の余地あり
</br>
（仮の文章↓）
</br>
When we wanted to make cell-gate actually, we had thought this following model which is cell-gate on liposome. （ここでＤ－ＨＥＡＲＴの画像ドーン！）
This model enables us to prove the effect of cell-gate. And to make this model, we divided our project into three parts, Gate itself, Porter (which transports the target in the gate), and Liposome (which is the model of cell membrane).
We have been doing experiment them separately or together. And finally, we want to mix them and prove the effect of cell-gate.
</p>
 
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<h1>Application in future</h1>
<p>
あんなことやこんなことに使えるというのを図入りで。
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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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