Biomod/2012/TeamSendai/Idea

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<div id="Container">   
<div id="Container">   
<h1>Project</h1>
<h1>Project</h1>
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[[Image:Imashun4.png|center|600px]]
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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.
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>
<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>Function</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.
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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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.]]
<h2>Sub-project GOAL</h2>
<h2>Sub-project GOAL</h2>
The goal of this sub-project is to prove this structure is self-assembled by electrophoresis and AFM
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>
<html><h1><a name="PORTER">Sub-project PORTER</a></h1></html>
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[[Image:Porter-picture.png|right|none|400px]]
 
<h2>Function</h2>
<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. </br>
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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>
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.
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.]]
<h2>Sub-project GOAL</h2>
<h2>Sub-project GOAL</h2>
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<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
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<h2>Goal</h2>
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<h2>Function</h2>
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[[Image:Membranerane.png|right|200px|thumb| Picture from "Molecular biology of the CELL" (Bruce Alberts et al.)]]
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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.
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.   
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.
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>
<h2>Sub-project GOAL</h2>
The goal of this sub-project is to attach gate structure on liposomes and observe them by fluorescence microscope.
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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