Biomod/2012/TeamSendai/Idea

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<h1>Projct Gate</h1>
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<h1>Projct GATE</h1>
  [[Image:Gate.png|right|none|400px]]
  [[Image:Gate.png|right|none|400px]]
  <h2>Goal</h2>
  <h2>Goal</h2>
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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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GATE is the gatekeeper that allows only the target to enter the cell.
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Electric repulsions of the negative charge of DNA backbone inhibit NOT desired DNA from coming in the Gate.
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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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In the Gate, "Porter" which transport the target is planted. So Gate can connect the inside and outside.
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We can use the Gate as an injector or extractor.
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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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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 [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment '''here'''].
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<h1>Project Porter</h1>
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<h1>Project PORTER</h1>
[[Image:Porterget.png|right|none|400px]]
[[Image:Porterget.png|right|none|400px]]
<h2>Goal</h2>
<h2>Goal</h2>
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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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PORTER is the module for active transporter of the target in the GATE.
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The first Porter reaches the outside of the electric repulsion of the Gate, and pulls the target DNA inside the Gate by using hybridization energy.
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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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Inner Porters that have higher affinity than the first Porter push the target inside the Gate step by step.
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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 [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>Project Membrane</h1>
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<h1>Project MEMBRANE</h1>
<h2>Goal</h2>
<h2>Goal</h2>
[[Image:Membranerane.png|right|200px|thumb| reference from "the CELL"]]
[[Image:Membranerane.png|right|200px|thumb| reference from "the CELL"]]
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もっといい画像を
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As active transporters, the "CELL GATE" should work in membrane. Thus, a implementation module for inserting to membranes was designed.
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DNA with a hydrophobic molecule, cholesterol, hybridized around the GATE.
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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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We used liposome (artificial lipid vesicle) as a model cell membrane.
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Because using cell membrane immediately is hard.
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We make liposome by using lipid.
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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 [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design#Membrane '''here'''].
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And experiment method and result is [http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment#Membrane '''here'''].
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Revision as of 02:28, 27 October 2012

Team Sendai Top

Contents

Project

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.

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.

Projct GATE

Goal

GATE is the gatekeeper that allows only the target to enter the cell. Electric repulsions of the negative charge of DNA backbone inhibit NOT desired DNA from coming in the Gate.


Project PORTER

Goal

PORTER is the module for active transporter of the target in the GATE. The first Porter reaches the outside of the electric repulsion of the Gate, and pulls the target DNA inside the Gate by using hybridization energy. Inner Porters that have higher affinity than the first Porter push the target inside the Gate step by step.


Project MEMBRANE

Goal

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

As active transporters, the "CELL GATE" should work in membrane. Thus, a implementation module for inserting to membranes was designed. DNA with a hydrophobic molecule, cholesterol, hybridized around the GATE. We used liposome (artificial lipid vesicle) as a model cell membrane.


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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