Biomod/2012/TeamSendai/Idea

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<h1>Project</h1>
<h1>Project</h1>
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<h2>motivation</h2>
 
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<p>
 
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We want to make an artificial channel.</br>
 
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If we make an artificial channel, it is desirable that the channel can carry selectively </br>
 
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and actively only what we want to carry.</br>
 
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Also, it is desirable that the channel can change its function and shape artificially.</br>
 
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Think of these things, we think it is best to make this structure with DNA-origami.</br>
 
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If we use DNA, the shape of the channel is changeable as we like.</br>
 
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Also, the carry structure that through the channel is possible by using DNA’s complementarity, </br>
 
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so we decided to use DNA to make the structure.</br>
 
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</br>
 
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<h2>Experiment goal </h2>
 
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[[Image:Format_D-Heart.jpg|none|400px]]
 
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<p>
 
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When we test the effect of the Cell-gate, we use liposome as a model of a cell membrane. </br>
 
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We have to make liposome and confirm the effect of the Cell-gate.</br>
 
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So finally, we will make molecular robot which is Cell-gate on liposome and transport the object inside or outside liposome.</br>
 
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In short, our goal in this experiment is following. (D-Heart画像)</br>
 
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</br>
 
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</br>
 
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</br>
 
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<h2>Three experiment parts</h2>
 
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<img src=" http://openwetware.org/wiki/Image:Cellgate3part.png " alt="hybrid graph" width="400px" height="350px" align="left">
 
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[[Image:Format_cell_gate.jpg|none|400px]]
 
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<p>
 
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But on experiment, it is not smart that proceeing our project in order. </br>
 
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Luckily, large number of people in our team(and most of us are fresh!). </br>
 
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So we decided to separate our project into several part and do experiment parallelly.  </br>
 
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Our experiment separates three parts; Gate part, Porter part, and Membrane part.</br>
 
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(3つのグループに分かれてる画像端っこにシミュレーション班もいるよ的な感じで)</br>
 
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Gate part is the group making the Cell-gate itself.</br>
 
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Porter part is the group making the function to transport the target in the channel.</br>
 
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Membrane part is the group making liposome by using lipid.</br>
 
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To separate our project and finally mix, we aim to gain our achievement. </br>
 
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And we also establish simmulation group that verifies each structure theoretically.</br>
 
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</br>
 
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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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</br>
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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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<h2>Function</h2>
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</br>
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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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<h2>Sub-project GOAL</h2>
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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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<html><h1><a name="PORTER">Sub-project PORTER</a></h1></html>
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<h2>Function</h2>
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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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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.
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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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<h1>Gate</h1>
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<h2>Sub-project GOAL</h2>
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<p>
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The goal of this sub-project is to confirm this Porter system is working by electrophoresis
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<img src="http://openwetware.org/images/9/94/Gate.png " alt="hybrid graph" align="left" width="400px" height="300px" >
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[[Image:Gate.png|right|400px]]
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We will make the gate made of DNA origami! DNA origami is the way how to fold DNA and make structure investigated by Paul Rothemund.</br>
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So we decided to make the tube structure as the Gate using DNA origami. Consideration for the form of the Gate is written on Design page "Gate".(ここにデザインページGATEへのリンクを!..)</br>
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In the Gate, "Porter" which transport the target is planted. So Gate can connect the inside and outside. </br>
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We can use the Gate as an injector or extractor.</br>
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The simulation that the targets actually enter in the Gate is here.(simlationへのリンクを!..)</br>
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We considered about annealing situation of the Gate and did electrophoresis and AFM for observing the Gate.</br>
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Consideration for annealing situation and experiment results is here(ここにexperimentのリンクを!..)</br>
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<h1>Porter</h1>
 
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<img src="http://openwetware.org/images/e/eb/Porterget.png " alt="hybrid graph" align="left" width="465px" height="315px" >
 
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[[Image:Porterget.png|right|400px]]
 
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We thought to make DNA Porter which is function to transport the target in channel. One of the characteristic of DNA is to bind another DNA comprementary sequence to it.
 
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If we design that the DNA binds the target more stable than former one, and if next DNA binds more stable than it…,
 
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the target moves to most complementary sequence DNA.
 
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We thought this characteristic of DNA can be utilized the power of channel.
 
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This channel can make us transport the object selectively and actively independent of concentration gradient.
 
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We deceided to make the Porter made of DNA.
 
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DNA sequence of Porter is here.(Designページporterへのリンクを!...) And simulation of suitable Porter length.(simulationへの以下略)
 
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We did electrophoresis to confirm working of DNA. Experiment method and result is here.(experiment he no rinku wo!)
 
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<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
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</p>
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<h2>Function</h2>
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As active transporter, "CELL-GATE" should work in a cell membrane. Thus, a implementation module for inserting it to membranes needs to be designed.
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DNA sequences with a hydrophobic molecule (cholesterol) are attached outside and around GATE. 
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We use a liposome (artificial lipid vesicle) as a model for the cell membrane.
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<h1>Membrane</h1>
 
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<p>
 
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<!--
 
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<img src="http://openwetware.org/images/4/4b/Membranerane.png " alt="hybrid graph" align="left" width="300px" height="350px" >
 
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[[Image:Membranerane.png|right|200px]]
 
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reference from "the CELL" (画像の下に置きたいセリフ) </br>
 
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In this project, We make the model of cell membrane and aim that the channel penetrate it. </br>
 
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Because using cell membrane immediately is hard. </br>
 
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We make liposome by using lipid. </br>
 
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Liposome is the membrane made of lipid and utilize liposome as model of cell-membrane. </br>
 
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Consideration making situation of liposome is here.(リンクおね) </br>
 
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And experiment method and result is here.(ここからリンクよろ) </br>
 
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</p>
 
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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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<br clear="left">
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<h1>Application in future</h1>
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<h2>Sub-project GOAL</h2>
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<p>
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The goal of this sub-project is to attach gate structure on liposomes and observe them by fluorescence microscope.
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Finally, this project aims to attach to real cell and
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{{-}}
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transport a substance to cell and from cell. Of cause,
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this channel can be applied to medical use. Also, it can
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be used for bring some substance which it is difficult
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to bring back now from cell. In this experiment, we used
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liposome as a model of a cell membrane, but if we consider
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the channel attached liposome as one robot, the robot can
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use to cleaner robot or medical sprinkling robot.
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</p>
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Current revision


Team Sendai Top

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.

Sub-project GATE

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.
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

Sub-project PORTER

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.
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.
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


Sub-project MEMBRANE

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
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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