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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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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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The goal of this sub-project is to prove this structure is self-assembled by electrophoresis and AFM
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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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The goal of this sub-project is to confirm this Porter system is working by electrophoresis
   
{{-}}
<h1>Project</h1>
<img src=" http://openwetware.org/images/c/c8/Format_cell_gate.jpg " alt="hybrid graph" align="left" width="465px" height="315px" >
<p>
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. When we test the effect
of the artificial channel, we use liposome as a model of
a cell membrane. In short, our goal in this experiment is
THIS! (画像) Our experiment separates three parts; channel structure part,
carry system part, and liposome part.(画像)
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<h1>Gate</h1>
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<img src="http://openwetware.org/images/9/94/Gate.png " alt="hybrid graph" align="left" width="400px" height="300px" >
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>
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>
In the Gate, "Porter" which transport the target is planted. So Gate can connect the inside and outside. </br>
We can use the Gate as an injector or extractor.</br>
The simulation that the targets actually enter in the Gate is here.(simlationへのリンクを！..)</br>
We considered about annealing situation of the Gate and did electrophoresis and AFM for observing the Gate.</br>
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>
<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
<p>
<h2>Function</h2>
<img src="http://openwetware.org/images/e/eb/Porterget.png " alt="hybrid graph" align="left" width="465px" height="315px" >
As active transporter, "CELL-GATE" should work in a cell membrane. Thus, a implementation module for inserting it to membranes needs to be designed.
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.  
DNA sequences with a hydrophobic molecule (cholesterol) are attached outside and around GATE.
If we design that the DNA binds the target more stable than former one, and if next DNA binds more stable than it…,
We use a liposome (artificial lipid vesicle) as a model for the cell membrane.
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.（Designページporterへのリンクを!...） And simulation of suitable Porter length.（simulationへの以下略）




[[Image:スライド3.jpg|center|400px|thumb|Our strategy is making liposome indeed cell's membrane]]


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<h1>Membrane</h1>
<h2>Sub-project GOAL</h2>
<p>
The goal of this sub-project is to attach gate structure on liposomes and observe them by fluorescence microscope.
<img src="http://openwetware.org/images/4/4b/Membranerane.png " alt="hybrid graph" align="left" width="300px" height="350px" >
{{-}}
We make liposome by using lipid, and utilize liposome as model of cell-membrane.
reference from "the CELL"
</p>
 
 
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<h1>Application in future</h1>
<p>
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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Latest revision as of 19:42, 27 October 2012

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<body> <div id="Container"> <!-- Menu --> <ul id="menu"> <li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Home</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea ">Project</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design">Design</a> </li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation">Simulation</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment ">Experiment</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Future Application">Future Application</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Diary">Diary</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Team ">Team</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/Tohoku/Team Sendai/header"></a> </li>

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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.

<html><h1><a name="GATE">Sub-project GATE</a></h1></html>

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.

Sub-project GOAL

The goal of this sub-project is to prove this structure is self-assembled by electrophoresis and AFM

<html><h1><a name="PORTER">Sub-project PORTER</a></h1></html>

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. <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.



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


<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>

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


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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