Biomod/2012/UTokyo/KaseiRunners/Test: Difference between revisions

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<p><br><br><br></p>
<p><br><br><br><br></p>
  <ul class="list">
    <li><h3>CONTENTS</h3></li>
    <li><a href="#goal">  1.GOAL</a></li>
    <li><a href="#background">  2.BACKGROUND</a></li>
    <li><a href="#idea">  3.IDEA</a></li>
    <li><a href="#future">  4.FUTURE</a></li>
  </ul>
 
<embed src="Result_2_2_RTile9%2BHT_fps.mov" type="video/quicktime" width=240 height=200> </embed>
 
 
<h1 class="title"><a name="goal">1. Goal</a></h1>
<img src="http://openwetware.org/images/7/7d/Goal_switch.png"  width=400 height=210 style="float:right">
<p class="paragraph">
Our goal is to make an autonomous nano-transporter.
<br>
<br>1. No cargo, no transport.
<br>2. With cargo, run!
</p>
<br>
<h1 class="title"><a name="background">  2.BACKGROUND</a></h1>
<center>
<img src="http://openwetware.org/images/d/db/Background_2.png"  width=530 height=250 style="float:center">
</center>
<br>
 
<p class="paragraph">
In the nanoscale reaction, saving the material is a key issue, as the material resources are limited. To achieve a lean system, we took a method inspired by nature. In the living cell, materials are produced on demand and transported to the place, where these materials are work. To take these advantages, we challenged to make an autonomous nano-transporter using motor protein kinesin. Kinesin has two heads and walks along microtubules processively using energy derived from ATP.
<br>However, without any regulation system, cargo-less kinesin waste the resources (e.g. ATP and kinesin itself). So, we set our goal to construct a nano-transporter having a control system. Recent progress in DNA nanotechnology allow us to design the nano structure transforming its shape. Using the conformation change of DNA nano structure, we planed to control on demand protein production, and transport activity of nano-transporter.
</p>
     
      <h1 class="title"><a name="idea">3.IDEA</a></h1>
<img src="http://openwetware.org/images/c/cf/Idea_3.png"  width="397" height="268" style="float:right">
<h2>Our idea is composed of 5 processes.</h2>
<p class="paragraph">
1. Trigger opens DNA structure.
<br>2. Pure system synthesizes kinesin from template DNA.
<br>3. Cargo is attached to the DNA structure.
<br>4. Kinesins bind the DNA structure.
<br>5. The whole structure walks along the microtubule.
 
</p>
 
 
<h2 class="title">3-1, Trigger opens the DNA structure.</h2>
<center>
<center>
      <img src="http://openwetware.org/images/7/74/Wiki_idea2.png" width="750" height="230" style="float:center">
<img src="http://openwetware.org/images/0/0f/KaseiWiki_result_top.jpg" width=635 height=428>
</center>
</center>
        <p class="paragraph">
<h1 class="title"><a name="video">Video</a></h1>
        Staple strands and another staple with long double-stranded DNA chain (template DNA) assemble in 6 pole cylinder-shaped structure (DNA-tube). This tube has 4 toeholds in its side, which enable to open the tube by addition of the key strands complementary to the toeholds. Template DNA appears from the cylinder.
<center><iframe width="640" height="480" src="http://www.youtube.com/embed/aC_b_WP9bQA" frameborder="0" allowfullscreen></iframe></center>
      </p>
<h1 class="title"><a name="overview">Overview</a></h1>
      <br>
  <p class="paragraph">
<br>
Our research focused on DNA nano-robot which transports cargo in response to external signals. This robot is powered by the active movement of kinesins and only works when triggers cause structure change of DNA tubes. This robot will be applied for efficient transportation in nano-scale devices such as micro total analysis system(micro-TAS).  
<h2 class="title">3-2, Protein is synthesized from dsDNA by pure system.</h2>
      <img src="http://openwetware.org/images/f/f2/Kasei_idea2.png"  width="365" height="407" style="float:right">
        <p class="paragraph">
      Pure system synthesizes protein according to the sequence of the dsDNA released from DNA tube. Pure system is a cell-free protein synthesizing system including RNA polymerase, ribosome, t-RNA and amino acids. These components coordinately perform transcription, translation and aminoacylation with less complex interactions than found in a whole cell. Desired protein (it was kinesin here) is synthesized from the coding region of the dsDNA.
      </p>
     
<h2 class="title">3-3. Combine cargo to the DNA tube.</h2>
      <img src="http://openwetware.org/images/8/85/Kasei_idea3.png" width="196" height="211" style="float:right">
        <p class="paragraph">
    Beads with NeutrAvidin (NA) are used as model cargo. While there are no singals (key DNA in our projet), the tube can't bind to the cargo. Therefore the tube just diffuse in the solution. Once the signal binds to the tube, the conformational change of the tube is occured. And the hidden biotin appeared, allowing the tube to bind to the cargo (Beads) through biotin - avidin interaction.     
      </p>
     
<h2 class="title">3-4. Kinesins bind to the DNA structure.</h2>
      <img src="http://openwetware.org/images/3/3e/Wiki_idea4.png"  width="294" height="318" style="float:right">
      <img src="http://openwetware.org/images/3/39/Wiki_idea4_2nd.png"  width="294" height="170" style="float:right">
 
      <p class="paragraph">
    Snap-Tag on the tail of kinesins binds to Snap-Tag ligands on the DNA tile, creating the DNA-kinesin conjugate. Kinesins can transport the cargo on the DNA tube.
<br>DNA structure works well to keep kinesins in line, otherwise they are attached to the cargo randomly. This regulation leads to the kinesins walking toward the same direction.
  <br>Furthermore, this DNA-Kinesin conjugate can be switched on by the cargo binding. Once cargoes are attached, it starts to walk on microtubule filament.
      </p>
     
<h2 class="title">3-5. DNA-kinesin nano-robot transports the specified cargo to destination.</h2>
    <img src="http://openwetware.org/images/4/44/Wiki_idea5.png"  width="389" height="390" style="float:right">
      <p class="paragraph">
    Regulated movement of the nano-robot enables lean transport.  
      </p>
     
   
    <h1 class="title"><a name="future">4.FUTURE</a></h1>
<p class="paragraph">
<img src="http://openwetware.org/images/5/5b/Future.jpg"  width="500" height="390" style="float:right">
 
 
comiing soon
</p>
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Revision as of 21:03, 27 October 2012

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　<img src="http://openwetware.org/images/d/df/Top_rogo_kasei.jpg" width=800px height=100px> 

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</center> <center> 

<ul class="menu"  >  
  <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners" >home</a>
     <ul>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners#video">video</a></li>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners#overview">overview</a>
    </ul>
   </li>
  <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Project" >project</a>
    <ul>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Project#goal">goal</a></li>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Project#background">background</a>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Project#idea">idea</a></li>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Project#future">future</a></li>
    </ul>
  </li>
  <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Result" >result</a>
    <ul  class="result">
    <li><a class="resultttt" href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Result#r1">  1. open</a></li>
    <li><a class="resultttt" href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Result#r2">  2. pure</a></li>
    <li><a class="resultttt" href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Result#r3">  3. cargo</a></li>
    <li><a class="resultttt" href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Result#r4">  4. kinesin</a></li>
    <li><a class="resultttt" href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Result#r5">  5. run</a></li>
    </ul>
  </li>
  <li><a class="others">others</a>
     <ul>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/MeetingSummary">study</a></li>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Process">process</a></li>
    <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Reference">reference</a></li>
    </ul>
  </li>
  <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/KaseiRunners/Team" >team</a></li>
  </ul>
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<img src="http://openwetware.org/images/0/0f/KaseiWiki_result_top.jpg" width=635 height=428>

<a name="video">Video</a>

<iframe width="640" height="480" src="http://www.youtube.com/embed/aC_b_WP9bQA" frameborder="0" allowfullscreen></iframe>

<a name="overview">Overview</a>

  

Our research focused on DNA nano-robot which transports cargo in response to external signals. This robot is powered by the active movement of kinesins and only works when triggers cause structure change of DNA tubes. This robot will be applied for efficient transportation in nano-scale devices such as micro total analysis system(micro-TAS).

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