Biomod/2012/TeamSendai/Idea

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<h2>Motivation</h2>
<h2>Motivation</h2>
We want to make an artificial channel.If we make an artificial channel, it is desirable that the channel can carry selectively and actively only what we want to carry. Also, it is desirable that the channel can change its function and shape artificially.  
We want to make an artificial channel.If we make an artificial channel, it is desirable that the channel can carry selectively and actively only what we want to carry. Also, it is desirable that the channel can change its function and shape artificially.  
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Think of these things, we think it is best to make this structure with DNA-origami.
Think of these things, we think it is best to make this structure with DNA-origami.
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If we use DNA, the shape of the channel is changeable as we like.
If we use DNA, the shape of the channel is changeable as we like.
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Also, the carry structure that through the channel is possible by using DNA’s complementarity, so we decided to use DNA to make the structure.
Also, the carry structure that through the channel is possible by using DNA’s complementarity, so we decided to use DNA to make the structure.
<h2>Experiment goal </h2>
<h2>Experiment goal </h2>
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<img src="http://openwetware.org/images/4/46/Format_D-Heart.jpg" alt="D-Heart" width="400px" align="left"><br>
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When we test the effect of the Cell-gate, we use liposome as a model of a cell membrane. We have to make liposome and confirm the effect of the Cell-gate. So finally, we will make molecular robot which is Cell-gate on liposome and transport the object inside or outside liposome. In short, our goal in this experiment is following.  
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(画像の名称が違っている)
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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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<h2>Three experiment parts</h2>
<h2>Three experiment parts</h2>
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[[Image:Format_cell_gate.jpg|right|none|400px]]
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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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But on experiment, it is not smart that proceeing our project in order.  
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Luckily, large number of people in our team(and most of us are fresh!).  
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[[Image:Format_cell_gate.jpg|none|400px]]
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So we decided to separate our project into several part and do experiment parallelly.
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<p>
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Our experiment separates three parts; Gate part, Porter part, and Membrane part.
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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>
+
(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)
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So we decided to separate our project into several part and do experiment parallelly. </br>
+
 
-
Our experiment separates three parts; Gate part, Porter part, and Membrane part.</br>
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Gate part is the group making the Cell-gate itself.
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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>
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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Membrane part is the group making liposome by using lipid.
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To separate our project and finally mix, we aim to gain our achievement.
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</br>
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And we also establish simmulation group that verifies each structure theoretically.
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<h1>Gate</h1>
<h1>Gate</h1>
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[[Image:Gate.png|right|none|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.
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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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So we decided to make the tube structure as the Gate using DNA origami. Consideration for the form of the Gate is written on [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design#Gate ''' Design page "Gate"'''].
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[[Image:Gate.png|right|400px]]
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In the Gate, "Porter" which transport the target is planted. So Gate can connect the inside and outside.
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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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We can use the Gate as an injector or extractor.
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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 [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation '''here'''].
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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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We considered about annealing situation of the Gate and did electrophoresis and AFM for observing the Gate.
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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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Consideration for annealing situation and experiment results is [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment '''here'''].
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<h1>Porter</h1>
<h1>Porter</h1>
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<p>
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[[Image:Porterget.png|right|none|400px]]
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<!--
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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.  
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…,  
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.
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.  
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.
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.
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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DNA sequence of Porter is [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design#Porter '''here''']. And [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation '''  simulation'''].  
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We did electrophoresis to confirm working of DNA. Experiment method and result is [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment#Porter '''here'''].
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<h1>Membrane</h1>
<h1>Membrane</h1>
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<p>
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[[Image:Membranerane.png|right|200px|thumb| reference from "the CELL"]]
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もっといい画像はないか
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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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In this project, We make the model of cell membrane and aim that the channel penetrate it.  
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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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Because using cell membrane immediately is hard.
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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>
+
We make liposome by using lipid.  
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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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Liposome is the membrane made of lipid and utilize liposome as model of cell-membrane.
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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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Consideration making situation of liposome is [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design#Membrane '''here'''].
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</p>
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And experiment method and result is [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment#Membrane '''here'''].
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{{-}}
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<br clear="left">
 
<h1>Application in future</h1>
<h1>Application in future</h1>
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<p>
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Finally, this project aims to attach to real cell and transport a substance to cell and from cell. Of cause, this channel can be applied to medical use. Also, it can be used for bring some substance which it is difficult to bring back now from cell. In this experiment, we used
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Finally, this project aims to attach to real cell and
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liposome as a model of a cell membrane, but if we consider the channel attached liposome as one robot, the robot can use to cleaner robot or medical sprinkling robot.
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transport a substance to cell and from cell. Of cause,
+
-
this channel can be applied to medical use. Also, it can
+
-
be used for bring some substance which it is difficult
+
-
to bring back now from cell. In this experiment, we used
+
-
liposome as a model of a cell membrane, but if we consider
+
-
the channel attached liposome as one robot, the robot can
+
-
use to cleaner robot or medical sprinkling robot.
+
-
</p>
+
</div>
</div>

Revision as of 13:25, 26 October 2012

Team Sendai Top

Contents

Project

Motivation

We want to make an artificial channel.If we make an artificial channel, it is desirable that the channel can carry selectively and actively only what we want to carry. Also, it is desirable that the channel can change its function and shape artificially. Think of these things, we think it is best to make this structure with DNA-origami. If we use DNA, the shape of the channel is changeable as we like. Also, the carry structure that through the channel is possible by using DNA’s complementarity, so we decided to use DNA to make the structure.

Experiment goal

When we test the effect of the Cell-gate, we use liposome as a model of a cell membrane. We have to make liposome and confirm the effect of the Cell-gate. So finally, we will make molecular robot which is Cell-gate on liposome and transport the object inside or outside liposome. In short, our goal in this experiment is following. (画像の名称が違っている)

Three experiment parts

But on experiment, it is not smart that proceeing our project in order. Luckily, large number of people in our team(and most of us are fresh!). So we decided to separate our project into several part and do experiment parallelly. Our experiment separates three parts; Gate part, Porter part, and Membrane part.

(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)

Gate part is the group making the Cell-gate itself.

Porter part is the group making the function to transport the target in the channel.</br>

Membrane part is the group making liposome by using lipid.

To separate our project and finally mix, we aim to gain our achievement. And we also establish simmulation group that verifies each structure theoretically.

Gate

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.

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". In the Gate, "Porter" which transport the target is planted. So Gate can connect the inside and outside.

We can use the Gate as an injector or extractor.

The simulation that the targets actually enter in the Gate is here.

We considered about annealing situation of the Gate and did electrophoresis and AFM for observing the Gate.

Consideration for annealing situation and experiment results is here.

Porter

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.

If we design that the DNA binds the target more stable than former one, and if next DNA binds more stable than it…,

the target moves to most complementary sequence DNA.

We thought this characteristic of DNA can be utilized the power of channel.

This channel can make us transport the object selectively and actively independent of concentration gradient.

We deceided to make the Porter made of DNA.

DNA sequence of Porter is here. And simulation.

We did electrophoresis to confirm working of DNA. Experiment method and result is here.


Membrane

reference from "the CELL"
reference from "the CELL"

もっといい画像はないか

In this project, We make the model of cell membrane and aim that the channel penetrate it.

Because using cell membrane immediately is hard.

We make liposome by using lipid.

Liposome is the membrane made of lipid and utilize liposome as model of cell-membrane.

Consideration making situation of liposome is here.

And experiment method and result is here.


Application in future

Finally, this project aims to attach to real cell and transport a substance to cell and from cell. Of cause, this channel can be applied to medical use. Also, it can be used for bring some substance which it is difficult to bring back now from cell. In this experiment, we used liposome as a model of a cell membrane, but if we consider the channel attached liposome as one robot, the robot can use to cleaner robot or medical sprinkling robot.

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