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<h1>Project</h1>


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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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<html><h1><a name="GATE">Sub-project GATE</a></h1></html>
<h2>Function</h2>
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).
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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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<h2>Sub-project GOAL</h2>
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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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<html><h1><a name="PORTER">Sub-project PORTER</a></h1></html>
<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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[[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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The goal of this sub-project is to confirm this Porter system is working by electrophoresis
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<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
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<h2>Function</h2>
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.


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<h1>Team Sendai</h1>
<p>Tohoku University</p>
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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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<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Top">Top</a></li>
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Project">Project</a></li>
<li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendaiA/Results_%26_Discussion">Experiment</a></li>
<li><a href=" http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/diary">Diary</a></li>
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<h2>Abstract</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.
<p>
{{-}}
&nbsp;All the creatures on Earth are made of cells. The exterior and the interior of the cell are compartmentalized by biomembranes. A nanodevice that is able to actively transport only the specific oligonucleotide through the biomembrane has a great potential to deliver siRNA into the cell or to extract mRNA expressed in the cell.　Here, we decided to create a novel device with such a function. We have designed a cylindrical injector/extractor device made of DNA origami. Inside the cylinder, a cascade of single stranded DNAs is planted. Once the outer-most ssDNA binds to a target oligonucleotide,　the target is passed to the inner-ones one by one because of the higher bonding energy assigned to the inner ones. We also investigate how the cylinder penetrates the biomembrane by using liposome as a model membrane.
</p>
<p><img src="http://openwetware.org/images/4/46/Format_D-Heart.jpg" alt="D-Heart" width="800" height="610"/></p>
 
<p>
<strong>Selector</strong>: Single stranded DNA. Once the outer-most ssDNA binds to a target,　the target is passed to the inner-ones one by one.</br>
<strong>Gate</strong>: Cylindrical structure connecting the inside and outside like gates. A cascade of the "Selector" is planted in this. We can use this as an injector or extractor.</br>
<strong>Membrane</strong>: The exterior and the interior of the cell are compartmentalized by biomembranes. We use liposome as a model membrane.</br>
</p>
 
 
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<li><a href=" http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/diary">Diary</a></li>
<li><a href=" http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/member">Team</a></li>
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<address>Copyright (C) Team Sendai, All rights reserved.</address>
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Latest revision as of 18:28, 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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<div id="ttop"> <a href="#top" class="page_top" onfocus="this.blur();" onclick="scrollTo(0,0); return false;" title="Top"></a></div>

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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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