Biomod/2011/TeamJapan/Tokyo: Difference between revisions

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[[Image:Free moving mode figure.jpg|250px|center]]
[[Image:Free moving mode figure.jpg|250px|center]]
|To realize functional autonomous molecular robot, the robot needs to be able to move at all times because it guarantees the molecular robot not to stop and become uncontrollable. Furthermore, this characteristic is very useful for moving molecular robot to the area. We make “free moving mode” to give DNA ciliate the character. In free moving mode, DNA ciliate moves freely and at random in almost all the space. We use Brownian motion to move DNA ciliate in this mode.  
|:[[Biomod/2011/TeamJapan/Tokyo/Project/Free_moving_mode|The free moving mode]] is utilizing Brownian motion. We changed the size of DNA ciliate and observed the DNA ciliate movement by Brownian motion.
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|width="300px"|[[Image:Track walking mode figure.jpg|left|280px]]
|width="300px"|[[Image:Track walking mode figure.jpg|left|280px]]
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:The purpose of the track walking mode is to move DNA ciliate directionally<br>on the track.
:[[Biomod/2011/TeamJapan/Tokyo/Project/Track_walking_mode|The track walking mode]] is utilizing deoxyribozyme activity for substrate. We checked deoxyribozyme activity and simulated DNA ciliate's movement on micrometer-sized track and confirmed the track walking mode by simulation.
:To achive this mode, we needed to come up with the mechanism of walking and the way to make DNA tracks.
:We chose the "Deoxyribozyme-substrate reaction" to solve the mechanism of walking. And we also chose the microchannel to solve the problem of making of DNA tracks.  
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|width="320px"|[[image:Tokyo-gathering1.png|300px|center]]
|width="320px"|[[image:Tokyo-gathering1.png|300px|center]]
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:In the light-irradiated gathering mode, DNA ciliates gather at a specific area responding to UV irradiation. This mode is achieved by UV-switching DNA devices and observation of gathering DNA ciliates.
:[[Biomod/2011/TeamJapan/Tokyo/Project/Light_irradiated_gathering_mode|The light-irradiated mode]] is utilizing UV-switching DNA. We checked the "UV-switching system" and confirmed DNA ciliate trapping at one spot.
:The UV-switching DNA device has the stem-loop structure which has UV-responsive bases, azobenzenes. Before UV-irradiattion, this DNA device doesn’t trap deoxyribozyme legs of DNA ciliate. After UV irradiation, azobenzenes are isomerized and the DNA device traps deoxyribozyme legs of DNA ciliate. By this reaction, DNA ciliates gather at UV-irradiated area. By using this system, we think DNA’s movement can be controlled.
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<div id="navigation"> <div id="menu" style="position:static"> <ul> <li><a class="aMain" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo">Home</a></li> <li><a class="aTeam" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Team/Students">Team</a></li> <li><a class="aProject" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Project</a> <!-- <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Overview</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/introduction">Introduction</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Model">Model</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Devices">Devices</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Modes">Modes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Results</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> </ul> --> <li><font color="#ffffff">Results</font> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Experiments</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Design</a></li> </ul></li> <!-- <li><a class="Simulation" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a class="DNA design" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Designs</a></li> --> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Protocols">Protocols</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Lab.notebook">Notes</a></li> <li><a class="aNotebook" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sponsors/">Sponsors</a></li> <li><a class="aSitemap" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sitemap">Sitemap</a></li>

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Project overview

<html><body> <table width="100%"> 

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<td>

<i>We developed an autonomous micrometer-sized molecular robot,“DNA ciliate,toward a highly functional molecular robot like living cells.</i><br><br> &nbsp;A living cell is an ultimate highly functional molecular robot. The high functionality is caused by not only its various nanometer-sized functional molecules but also its “micrometer-sized” body that has enough space to possess the molecules. However, the size of already-developed molecular nano-robots is too small to include multiple functions. Toward highly functional molecular robots, it is required to construct molecular robots with micrometer-sized body. Here, we propose an autonomous DNA-based molecular robot “DNA ciliate”. A natural ciliate has a micrometer-sized body with cilia and achieves various functions such as autonomous motion with the cilia, phototaxis, etc. DNA ciliate has a micrometer-sized body with many DNAs as cilia, and it can switch three different modes in response to its external environment: the free moving mode, tracks walking mode, and light-irradiated gathering mode. We believe our concept will promote the construction of highly functional molecular robots like cells in future.</td> 　　<td align="top"><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Over_view"><img src="http://openwetware.org/images/9/9c/DNA_ciliate概念図.png" border=1 width="400" height="300"></a> 

  <font size="3" color="#000066"><i><strong>

<font size="3" color="#00ff66">“DNA ciliate”</font> has three independent functional modes. </strong></i></font></td> 

</tr>

</table> <center> <iframe width="420" height="315" src="http://www.youtube.com/embed/uejCuQWG07A" frameborder="0" allowfullscreen></iframe> </center> </body></html>

DNA ciliate body

DNA ciliates'body
To create DNA ciliate, a micrometer-sized body and its motor are indispensable. We chose DNA as a material for the motor because DNA is the most suitable material that is nanometer-sized and easy to be attached to micrometer-sized objects by various surface modifications. The micrometer-sized body is required to be micrometer-sized, homogeneous, and easy to attach DNA.


1. Free moving mode

 :The free moving mode is utilizing Brownian motion. We changed the size of DNA ciliate and observed the DNA ciliate movement by Brownian motion.


2. Track walking mode
The track walking mode is utilizing deoxyribozyme activity for substrate. We checked deoxyribozyme activity and simulated DNA ciliate's movement on micrometer-sized track and confirmed the track walking mode by simulation.


3. Light-irradiated gathering mode
The light-irradiated mode is utilizing UV-switching DNA. We checked the "UV-switching system" and confirmed DNA ciliate trapping at one spot.
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