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

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   <ul class="list">
   <ul class="list">
     <li><h3>CONTENTS</h3></li>
     <li><h3>CONTENTS</h3></li>
     <li><a href="#introduction">  1.INTRODUCTION</a></li>
     <li><a href="#goal">  1.Goal</a></li>
     <li><a href="#idea">  2.IDEA</a></li>
     <li><a href="#background">  2.Background</a></li>
     <li><a href="#goal">  3.GOAL</a></li>
     <li><a href="#idea">  3.IDea</a></li>
     <li><a href="#merit">  4.MERIT</a></li>
     <li><a href="#future">  4.Future</a></li>
    <li><a href="#future">  5.FUTURE</a></li>
   </ul>
   </ul>


  <h1 class="title"><a name="introduction">1.INTRODUCTION</a></h1>
  <h1 class="title"><a name="goal">1. Goal</a></h1>
<img src="http://openwetware.org/images/7/71/120901_uTAS.001.jpg"  width=300 height=250 style="float:right">
<img src="http://openwetware.org/images/7/7d/Goal_switch.png"  width=400 height=210 style="float:right">
<p class="paragraph">
<p class="paragraph">
Micro total analysis system(micro-TAS) caused revolutionary change in nanoscale analysis, as it can remarkably reduce the space, labor and time for chemical process. micro-TAS also holds promise for automatic experiments of chemistry and biology, suggesting the possibility of rapid and simultaneous process with less consumption of reagents. While process efficiency requires miniaturization of its structure, nano-scale fluidity cannot  processed without the application of high pressure. Our research focused on the control of nano-scale transport  powered by DNA-kinesin nano-robot.
Our goal is to make an autonomous nano-transporter.
<br>
<br>1. No cargo, no transport.
<br>2. With cargo, run!
</p>
</p>
      <h1 class="title"><a name="idea">2.IDEA</a></h1>
<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>


<img src="http://openwetware.org/images/d/de/Schemerun.png"  width=300 height=250 style="float:right">
<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[1-5]. 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.
<br>
</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>
<h2>Our idea is composed of 5 processes.</h2>
<p class="paragraph">
<p class="paragraph">
Line 69: Line 83:




<h2 class="title">2-1, Trigger opens DNA structure.</h2>
<h2 class="title">3-1, Trigger opens the DNA structure.</h2>
       <img src="http://openwetware.org/images/3/3c/Kasei_idea1.png" 　width="365" height="342" style="float:right">
<center>
       <img src="http://openwetware.org/images/3/39/Wiki_idea1.png" width="750" height="230" style="float:center">
</center>
         <p class="paragraph">
         <p class="paragraph">
         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.
         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.
       </p>
       </p>
        
       <br>
<h2 class="title">2-2, Protein is synthesized from dsDNA by pure system.</h2>
<br>
       <img src="http://openwetware.org/images/f/f2/Kasei_idea2.png" width="365" height="407" style="float:right">
<h2 class="title">3-2, Protein is synthesized from dsDNA by pure system.</h2>
       <img src="http://openwetware.org/images/7/74/Wiki_idea2.png" width="365" height="407" style="float:right">
         <p class="paragraph">
         <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.
       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>
       </p>
        
        
<h2 class="title">2-3,Combine cargo to DNA tile.</h2>
<h2 class="title">3-3. Combine cargo to the DNA tube.</h2>
       <img src="http://openwetware.org/images/8/85/Kasei_idea3.png"  width="392" height="424" style="float:right">
       <img src="http://openwetware.org/images/8/85/Kasei_idea3.png"  width="196" height="211" style="float:right">
         <p class="paragraph">
         <p class="paragraph">
     Beads with NeutrAvidin(NA) is used as cargo. DNA tile with biotin is attached to this cargo by the non-covalent bond between biotin and NA.
     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.       
This interaction creates DNA tile - beads cargo.       
       </p>
       </p>
        
        
<h2 class="title">2-4, Kinesins bind the DNA structure.</h2>
<h2 class="title">3-4. Kinesins bind to the DNA structure.</h2>
       <img src="http://openwetware.org/images/1/1d/Kasei_idea4.png"  width="392" height="424" style="float:right">
       <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">
       <p class="paragraph">
    Halo-Tag on the tail of kinesin binds to Halo-Tag ligands on the DNA tile, creating the DNA-Kinesin nano-transporter.
  Halo- or SNAP-protein 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>
       </p>
        
        
<h2 class="title">2-5, DNA-kinesin nano-robot transports the specified cargo to destination.</h2>
<h2 class="title">3-5. DNA-kinesin nano-robot transports the specified cargo to destination.</h2>
     <img src="http://openwetware.org/images/7/78/Kasei_idea5.png" width="389" height="390" style="float:right">
     <img src="http://openwetware.org/images/4/44/Wiki_idea5.png" width="389" height="390" style="float:right">
       <p class="paragraph">
       <p class="paragraph">
     Regulated movement of nano-robot enables lean transport .
     Regulated movement of the nano-robot enables lean transport.  
       </p>
       </p>
        
        
<h1 class="title"><a name="goal">3.GOAL</a></h1>
      
 
     <h1 class="title"><a name="future">4.FUTURE</a></h1>
     <p class="paragraph">・Design and produce a DNA nanostructure with template DNA.
    <br>・Open our DNA nanostructure with key strands.
    <br>・Obtain that kinesins through PURE system and template DNA.
    <br>・Observe kinesins are attached to our DNA nanostructure.
    <br>・Observe a cargo is attached to our DNA nanostructure.
    <br>・Observe the combined structure walk along the microtubule.
</p>
     <h1 class="title"><a name="merit">4.MERIT</a></h1>
<p class="paragraph">
<p class="paragraph">
The elegance of our method is to...
<img src="http://openwetware.org/images/5/5b/Future.jpg"  width="400" height="312" style="float:right">
<br>・regulate transcription and translation reactions with DNA nanostructure.
<br>
<br>・keep kinesins in line by DNA origami.
<br>
<br>・use chaperones for full length yield of kinesin - halo tag hybrid protein.
  In the future, nano-medical  device will check our health and cure diseases. DNA runner may work in such nano-medical device. For more information, watch our YouTube.
</p>
    <h1 class="title"><a name="future">5.FUTURE</a></h1>
<p class="paragraph">
As was described earlier, this study can be applied for efficient transportation within micro TAS.
Beyond the micro TAS application, our device can act as an intelligent DNA robot in the future. It can accept multiple signals and produce corresponding proteins.
</p>
</p>


<p class="paragraph" style="clear:right">
<br><br><br><br>1 Hess H. and Vogel V., Molecular shuttles based on motor proteins:
active transport in synthetic environments. Rev. Mol. Biotechnol, 82,
67-85 (2001)
<br>2.Nitta T and Hess H. Dispersion in active transport by kinesin-powered
molecular shuttles. Nano Lett, 5, 1337-1342 (2005)
<br>3. van den Heuvel MG. and Dekker C. Motor proteins at work for
nanotechnology. Science, 317, 333-6 (2007).
<br>4 Yokokawa R. et al., Simultaneous and Bidirectional Transport of
Kinesin-Coated Microspheres and Dynein-Coated Microspheres on
Polarity-Oriented Microtubules. Biotechnol Bioeng, 101, 1-8 (2008).
<br>5. Hiyama S. et al., Biomolecular-Motor-Based Nano- or Microscale
Particle Translocations on DNA Microarrays. Nano Lett, 9, 2407-2413 (2009)
<p>
</body>
</body>
</html>
</html>

Revision as of 21:01, 27 October 2012

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<div  class="maintitle">

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

</div>

</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>
</center>

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 <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>

<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[1-5]. 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. <br> </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> 

      <img src="http://openwetware.org/images/3/39/Wiki_idea1.png"  width="750" height="230" style="float:center">

</center> 

       <p class="paragraph">
       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.
     </p>
     <br>

<br> <h2 class="title">3-2, Protein is synthesized from dsDNA by pure system.</h2> 

      <img src="http://openwetware.org/images/7/74/Wiki_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">
  Halo- or SNAP-protein 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="400" height="312" style="float:right"> <br> <br> 

In the future, nano-medical  device will check our health and cure diseases. DNA runner may work in such nano-medical device. For more information, watch our YouTube.

</p>

<p class="paragraph" style="clear:right">

<br><br><br><br>1 Hess H. and Vogel V., Molecular shuttles based on motor proteins: active transport in synthetic environments. Rev. Mol. Biotechnol, 82, 67-85 (2001) <br>2.Nitta T and Hess H. Dispersion in active transport by kinesin-powered molecular shuttles. Nano Lett, 5, 1337-1342 (2005) <br>3. van den Heuvel MG. and Dekker C. Motor proteins at work for nanotechnology. Science, 317, 333-6 (2007). <br>4 Yokokawa R. et al., Simultaneous and Bidirectional Transport of Kinesin-Coated Microspheres and Dynein-Coated Microspheres on Polarity-Oriented Microtubules. Biotechnol Bioeng, 101, 1-8 (2008). <br>5. Hiyama S. et al., Biomolecular-Motor-Based Nano- or Microscale Particle Translocations on DNA Microarrays. Nano Lett, 9, 2407-2413 (2009) <p> </body> </html>

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