Biomod/2012/TeamSendaiA/Top: Difference between revisions

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<!-- ここから大枠 -->
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<h1>Project</h1>


<div id="head-1">
BIOMOD2012 Team Sendai
</div>


<div id="head-under"></div>
[[Image:スクリーンショット 2012-10-28 8.27.26.png|center|600px]]




<!-- メニューバーの囲い -->
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.
<div id="menu">
{{-}}


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<html><h1><a name="GATE">Sub-project GATE</a></h1></html>
</div>
<h2>Function</h2>
<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"><div id="HOME">
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.
HOME
In order to work as an injector (or extractor) a PORTER system is planted inside this cylinder (see next section).
</div></a>
{{-}}
<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/project"><div id="bottun">
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Experiment
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Team
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<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/link">
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Link
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<br>


<div id="under-line">
</div>


[[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.]]


</div>
<h2>Sub-project GOAL</h2>
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>
<h2>Function</h2>




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.


<!-- ここからイントロダクション -->
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<div id="line2"></div>


<div id="line-title">
{{-}}
<font id="head">Introduction</font>
[[Image:イラストporter.png|center|700px|thumb|PORTER is in charge of the active transporting of the target into GATE.]]
</div>
<div id="line2-5"></div>
<div id="line3"></div>


<div id="line4"></div>
<h2>Sub-project GOAL</h2>
<div id="line5"></div>
The goal of this sub-project is to confirm this Porter system is working by electrophoresis
<div id="line6"></div>
{{-}}


<div id="yohaku"></div>
<div id="kiji-line1"></div>
<div id="kiji">
Recent DNA robots just wait for the target coming.
We are now developing a robot that can catch and store the target you like.
We named the robot D-NApper.
<br>
<br>
<div style="text-align:center;">
<div>
<img src="http://openwetware.org/images/thumb/9/95/Recent_robot.png/800px-Recent_robot.png" width="330px" height="224px">
<img src="http://openwetware.org/images/thumb/a/aa/Dnapperimage.png/800px-Dnapperimage.png" width="405px" height="224px">
</div>
</div>
<br>


To realize D-NApper, we propose "Selector" structure.<br>
"Selector" catches a target distant from D-NApper, and puts it inside, with specificity.<br>
D-NApper can catch various molecules if we modify "Selector".
</div>


<!-- ここまでイントロダクション -->
<html><h1><a name="MEMBRANE">Sub-project MEMBRANE</a></h1></html>
<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.




<div id="yohaku"></div>
[[Image:スライド3.jpg|center|400px|thumb|Our strategy is making liposome indeed cell's membrane]]


<div id="line1"></div>
{{-}}
<div id="line2"></div>
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<font id="head">Abstract</font>
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<div id="line3"></div>


<div id="line4"></div>
<h2>Sub-project GOAL</h2>
<div id="line5"></div>
The goal of this sub-project is to attach gate structure on liposomes and observe them by fluorescence microscope.
<div id="line6"></div>
{{-}}
 
<div id="yohaku"></div>
<div id="kiji-line1"></div>
<div id="kiji">
We're making a molecular robot that can capture an object DNA and put it inside the robot.<br>
Our robot has the function we named "Selector".<br>
<br>
"Selector" is single-stranded DNA which has complementary sequences to the "Target DNA" here and there, and consecutive adenine sequences in other portion. We have three "Selectors", and the inner "Selector" attaches to the target more strongly. When "Selector 1" catches the "Target DNA", the left sequences (which are not complementary and do not attach to the object) make loops. Then the structure shrinks and becomes shorter.<br>
<br>
Thanks to "Selector 1", the robot can select and draw the target DNA close to the robot. Next, "Selector 2" receives the target DNA from "Selector 1". And "Selector 3" receives the target from "Selector 2". Thanks to "Selector 2" and "Selector 3", the robot can deliver only the object inside certainly.<br>
<br>
Then, we will explain the body structure containing these functions.<br>
We design the robot like a tube of hexagonal base. In case it is too difficult to form and observe, we also design a triangle prism body. As for the latter shape, we made the same kind of structure last year. We've acquired some know-how of it.<br>
<br>
We think the robot should have a lid so that nothing would come in from the back. So we arrange "Selectors" symmetrically. <br>
 
</div>
<a href=" http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Legacy--Team Sendai  HP</a>
 
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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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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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