Biomod/2012/TeamSendai/Idea

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<h1>Project</h1>
<h1>Project</h1>
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[[Image:スライド1.JPG|center|600px]]
 
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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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So we decided to separate our project into several part and do experiment parallelly.
 
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Our experiment separates three parts; Gate part, Porter part, and Membrane part.
 
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Gate part is the group making the Cell-gate itself.
 
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Porter part is the group making the function to transport the target in the channel.</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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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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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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And we also establish simmulation group that verifies each structure theoretically.
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<h1>Project GATE</h1>
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<html><h1><a name="GATE">Sub-project GATE</a></h1></html>
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[[Image:Gate.png|right|none|400px]]
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  <h2>Function</h2>
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  <h2>Goal</h2>
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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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GATE is the gatekeeper that allows only the target to enter the cell.
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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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Electric repulsions from the negative charge of the DNA backbone inhibit NOT desired DNA from entering GATE.
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<h1>Project PORTER</h1>
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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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[[Image:Porterget.png|right|none|400px]]
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<h2>Goal</h2>
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<h2>Sub-project GOAL</h2>
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PORTER is in charge of the active transporting of the target into 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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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.
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Inner Porters that have higher affinity than the first Porter pull the target inside GATE step by step.
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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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<h1>Project MEMBRANE</h1>
 
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<h2>Goal</h2>
 
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[[Image:Membranerane.png|right|200px|thumb| reference from "the CELL"]]
 
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As active transporter, "CELL-GATE" should work in a cell membrane. Thus, a implementation module for inserting it to membranes was designed.
 
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DNA sequences with a hydrophobic molecule (cholesterol) are situated outside and around GATE. 
 
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We used liposome (artificial lipid vesicle) as a model cell membrane.
 
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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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<h2>Sub-project GOAL</h2>
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The goal of this sub-project is to confirm this Porter system is working by electrophoresis
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<h1>Application in future</h1>
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Finally, this project aims to attach to a real cell and transport a substance to cell and from cell. Of course, this channel may have medical use. Also, it may be used for bringing some substances which are difficult to bring back from cell nowadays. In our project "CELL-GATE", we used liposome as a model of a cell membrane, but if we consider that the "CELL-GATE" is attached to liposome, it can be used as molecular robot. This robot may be used as a cleaning robot or medical sprinkling robot.
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</div>
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<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
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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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[[Image:スライド3.jpg|center|400px|thumb|Our strategy is making liposome indeed cell's membrane]]
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<h2>Sub-project GOAL</h2>
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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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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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