Biomod/2012/UTokyo/UT-Hongo: Difference between revisions

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#description {
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       <div style="float: right; width=270px; margin-left: 24px; padding: 5px; border: 1px solid #666; border-style: dashed;">
<img src="http://openwetware.org/images/e/e8/Biomod-2012-UTokyo-UT-Hongo-Idia-4.jpg" width="350px"></img>
        <img src="http://openwetware.org/images/a/a3/2012_BIOMOD_UT-HONGO_DNA_shell.gif" width="270px"></img>
<p style="font-size: 100%; font-weight: bold; margin-left: auto; margin-right: auto; text-align: center">fig1. Schematic of Medical DNA Shell system</p>
<p style="font-size: 100%; font-weight: bold; margin-left: auto; margin-right: auto; text-align: center">Fig1. Schematic animation of DNA Shell</p>
       </div>
       </div>
       <p id="desc-first">Methodologies to apply DNA for building precisely controlled nanostructures have greatly developed over the recent years. Our focus for BIOMOD is to utilize DNA to make a shell like structure which can capture molecules inside the shell-like body, as if a shellfish is eating its prey. Entrapment of the substrate was detected by the numerous florescent molecules that are attached to the body. This research may become a foundation for using DNA to mimic catalytic activity of enzymes.</p>
       <p id="desc-first">Our focus for BIOMOD is to utilize DNA to make a shell like structure which can capture molecules inside the body, as if a shellfish is capturing its prey. The device, named DNA Shell, can exhibit functionalities such as highly sensitive detection, enzyme protection, and attachment to solid surfaces. All these new functionalities are the results of this new capturing mechanism that we call the "Shell Mechanism" and the feasibility of modifications on the DNA structure. The functionalities of the DNA shell, along with the enzyme that is captured, may allow us to open up new fields of applications in chemical and medical applications, such as bioreactors and biomolecules detection. </p>
       <br style="clear: both;">
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        <img src="http://openwetware.org/images/1/1e/Biomod-2012-utokyo-uthongo-anime.gif" width="350px"></img>
<img src="http://openwetware.org/images/1/19/Biomod_anime.gif" width="350px"></img>
<p style="font-size: 100%; font-weight: bold; margin-left: auto; margin-right: auto; text-align: center">Fig2. Schematic animation of the DNA Shell system</p>
       </div>
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       <p>Medical functions such as detection of diseases with small amount of blood are possible by using microfluidics. For example, detecting and sensing the concentration of Thrombin which causes blood coagulation is possible by using Shell and microfluidics developed by our team. In the future, we will develop medical DNA Shell system for monitoring components of blood, detecting diseases, inputting medicine by DNA Shell, computing system integrated in microfluidics.</p>
       <p>The DNA shell is made of three domains of DNA origamis. The two domains would be used to capture enzymes, and the last domain would be used to be attached to a solid surface as is shown in Fig.2.
Our experiments were done using a certain protein called Streptavidin. To widen the types of enzymes that could be captured in the DNA Shell, it needs to more works to be done to find different aptamers that bind specifically to certain enzymes. However, with such developments, we hope and strongly believe that this nano-device would give innovative boost to the enzyme application.
</p>
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       <h2>YouTube</h2>
       <h2>YouTube</h2>
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<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro"><img src="http://openwetware.org/images/d/d7/Biomod-2012-UTokyo-UT-Hongo_Design_Thumb.jpeg" class="mythumb" alt="" /></a></p>
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro"><img src="http://openwetware.org/images/4/4d/Biomod-2012-UTokyo-UT-Hongo_Design_Thumb_2.jpeg" class="mythumb" alt="" /></a></p>
<h2>Motives</h2>
<h2>Motives</h2>
<p></p>
<p>The great scope of our research is to make a DNA origami structure that has functionalities similar to that of enzymes... however, that is far too much for students to do in one summer. Therefore, we chose to narrow down to making the structure which can bind to certain molecules and capture it, just like enzymes makes specific bondings to make ES complex.</p>
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<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Function"><img src="http://openwetware.org/images/a/a0/Biomod-2012-UTokyo-UT-Hongo-outline-2.jpg" class="mythumb" alt="" /></a></p>
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Design"><img src="http://openwetware.org/images/a/a0/Biomod-2012-UTokyo-UT-Hongo-outline-2.jpg" class="mythumb" alt="" /></a></p>
<h2>Design</h2>
<h2>Design</h2>
<p></p>
<p>In this section, we describe how we designed our DNA shell which efficiently capture the target molecules and be observed with dramatic change in the fluorescence when it closes. Furthermore, we show the simulation for hybridization of DNA shell.</p>
       </div>
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       <div class="column3 column">
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<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly"><img src="http://openwetware.org/images/4/45/Biomod-2012-UToky%E2%80%8Bo-UT-Hongo-2012aug31no3x1_h.011m0.5.jpg" class="mythumb" alt="" /></a></p>
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Result"><img src="http://openwetware.org/images/4/45/Biomod-2012-UToky%E2%80%8Bo-UT-Hongo-2012aug31no3x1_h.011m0.5.jpg" class="mythumb" alt="" /></a></p>
<h2>Result</h2>
<h2>Result</h2>
<p>In this section, we write about the result of our experiment. We can classify the experiment that we performed roughly into four themes:
<p>In this section, we write about the results of our experiment. We can classify the experiments that we performed roughly into four themes:
<ol>
<ol>
<li>Assembly of the DNA Shell</li>
<li>Assembly of the DNA Shell</li>
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<li>Supporting Enzyme</li>
<li>Supporting Enzyme</li>
</ol>
</ol>
We describe the part which I was able to confirm by each experiment.</p>
We describe the part which we was able to confirm by each experiment.</p>
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<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method"><img src="" class="mythumb" alt="" /></a></p>
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method"><img src="http://openwetware.org/images/b/b6/Biomod-2012-utokyo-uthongo-top-AFM.JPG" class="mythumb" alt="" /></a></p>
<h2>Method</h2>
<h2>Method</h2>
<p></p>
<p>We did some experiments for indicating the characteristics of our DNA shell. In this section, the method was described. Also, we write about equipments and reagents. </p>
       </div>
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       <div class="column2 column">
       <div class="column2 column">
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork"><img src="http://openwetware.org/images/2/20/Biomod-2012-utokyo-uthongo-Future-work-thumb.png" class="mythumb" alt="" /></a></p>
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork"><img src="http://openwetware.org/images/2/20/Biomod-2012-utokyo-uthongo-Future-work-thumb.png" class="mythumb" alt="" /></a></p>
<h2>Future Work</h2>
<h2>Progress & Beyond</h2>
<p> We aim to make a device that has wider usage than an enzyme.
<p> We aim to make a device that has wider application than an enzyme.
By putting together DNA Shell, certain target substances, and an enzyme, you can bring functionality or selectivity to the enzyme.
By putting together DNA Shell, certain target substances, and an enzyme, you can bring functionality or selectivity to the enzyme.
It will become possible thanks to the diversity of DNA Shell. </p>
It will become possible thanks to the diversity of DNA Shell. </p>
       </div>
       </div>
       <div class="column3 column">
       <div class="column3 column">
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team"><img src="" class="mythumb" alt="" /></a></p>
<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team"><img src="http://openwetware.org/images/5/5a/Biomod-2012-utokyo-uthongo-team-photo.jpg" class="mythumb" alt="" /></a></p>
<h2>Team</h2>
<h2>Team</h2>
<p>About Us</p>
<p>About Us. Please see also <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement" style="color: white">Acknowledgement</a>. </p>
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Latest revision as of 03:19, 31 August 2013

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<li class="toppage"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></li> <li class="motives"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></li> <!-- <li class="design"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Function">Design</a></li> --> <li class="result"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a> <ul class="submenu"> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Assembly of the DNA Shell</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Capturing_ability">Capturing Ability</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Immobilizing_on_microfluidic_device">Immobilizing on microfluidic device</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Supporting_Enzyme">Supporting Enzyme</a></li> </ul> </li> <li class="method"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></li> <li class="futurework"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></li> <li class="team"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></li> <li class="acknowledgement"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></li> 

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<p style="font-size: 100%; font-weight: bold; margin-left: auto; margin-right: auto; text-align: center">Fig1. Schematic animation of DNA Shell</p> 

     </div>
     <p id="desc-first">Our focus for BIOMOD is to utilize DNA to make a shell like structure which can capture molecules inside the body, as if a shellfish is capturing its prey. The device, named DNA Shell, can exhibit functionalities such as highly sensitive detection, enzyme protection, and attachment to solid surfaces. All these new functionalities are the results of this new capturing mechanism that we call the "Shell Mechanism" and the feasibility of modifications on the DNA structure. The functionalities of the DNA shell, along with the enzyme that is captured, may allow us to open up new fields of applications in chemical and medical applications, such as bioreactors and biomolecules detection.  </p>
     <br style="clear: both;">
     <div style="float: left; margin-right: 24px; margin-top: 12px;width=350px; padding: 5px; border: 1px solid #666; border-style: dashed;">

<img src="http://openwetware.org/images/1/19/Biomod_anime.gif" width="350px"></img> <p style="font-size: 100%; font-weight: bold; margin-left: auto; margin-right: auto; text-align: center">Fig2. Schematic animation of the DNA Shell system</p> 

     </div>
     <p>The DNA shell is made of three domains of DNA origamis. The two domains would be used to capture enzymes, and the last domain would be used to be attached to a solid surface as is shown in Fig.2.

Our experiments were done using a certain protein called Streptavidin. To widen the types of enzymes that could be captured in the DNA Shell, it needs to more works to be done to find different aptamers that bind specifically to certain enzymes. However, with such developments, we hope and strongly believe that this nano-device would give innovative boost to the enzyme application. </p> 

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<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro"><img src="http://openwetware.org/images/4/4d/Biomod-2012-UTokyo-UT-Hongo_Design_Thumb_2.jpeg" class="mythumb" alt="" /></a></p> <h2>Motives</h2> <p>The great scope of our research is to make a DNA origami structure that has functionalities similar to that of enzymes... however, that is far too much for students to do in one summer. Therefore, we chose to narrow down to making the structure which can bind to certain molecules and capture it, just like enzymes makes specific bondings to make ES complex.</p> 

     </div>
     <div class="column2 column">

<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Design"><img src="http://openwetware.org/images/a/a0/Biomod-2012-UTokyo-UT-Hongo-outline-2.jpg" class="mythumb" alt="" /></a></p> <h2>Design</h2> <p>In this section, we describe how we designed our DNA shell which efficiently capture the target molecules and be observed with dramatic change in the fluorescence when it closes. Furthermore, we show the simulation for hybridization of DNA shell.</p> 

     </div>
     <div class="column3 column">

<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Result"><img src="http://openwetware.org/images/4/45/Biomod-2012-UToky%E2%80%8Bo-UT-Hongo-2012aug31no3x1_h.011m0.5.jpg" class="mythumb" alt="" /></a></p> <h2>Result</h2> <p>In this section, we write about the results of our experiment. We can classify the experiments that we performed roughly into four themes: <ol> <li>Assembly of the DNA Shell</li> <li>Capturing Ability</li> <li>Immobilizing on microfluidic device</li> <li>Supporting Enzyme</li> </ol> We describe the part which we was able to confirm by each experiment.</p> 

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<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method"><img src="http://openwetware.org/images/b/b6/Biomod-2012-utokyo-uthongo-top-AFM.JPG" class="mythumb" alt="" /></a></p> <h2>Method</h2> <p>We did some experiments for indicating the characteristics of our DNA shell. In this section, the method was described. Also, we write about equipments and reagents. </p> 

     </div>
     <div class="column2 column">

<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork"><img src="http://openwetware.org/images/2/20/Biomod-2012-utokyo-uthongo-Future-work-thumb.png" class="mythumb" alt="" /></a></p> <h2>Progress & Beyond</h2> <p> We aim to make a device that has wider application than an enzyme. By putting together DNA Shell, certain target substances, and an enzyme, you can bring functionality or selectivity to the enzyme. It will become possible thanks to the diversity of DNA Shell. </p> 

     </div>
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<p><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team"><img src="http://openwetware.org/images/5/5a/Biomod-2012-utokyo-uthongo-team-photo.jpg" class="mythumb" alt="" /></a></p> <h2>Team</h2> <p>About Us. Please see also <a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement" style="color: white">Acknowledgement</a>. </p> 

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   <h2 style="border-bottom: none;">BIOMOD 2012 Team UT-Hongo</h2>
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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#description">Abstract</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#youtube">YouTube</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#navi">Links</a></li> </ul> 

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     <div class="footer-section" id="section2">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Focus">Focus</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Idea_of_DNA_Shell">Idea</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Functionalities_Exhibited">Funcitonalities</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Conceptual_Blueprint_of_the_Structure">Blueprint</a></li>

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Design">Design</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Adding_functionality">Function</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Result">Result</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Experiments</a></li>

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#AFM">AFM</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Photometer">Photometer</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Electrophoresis">Electrophoresis</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Ultraviolet_Irradiation">Others</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Reagent">Reagent</a></li> </ul> 

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#Variety_of_Target_Substances">Target Variety</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#DNA_Shell_with_Functionality">Functionalization</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#Shell_with_the_DNA_Hybridization_Circuits">Circuits</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#A_Device_more_than_Shell_and_Enzyme">Conclusion</a></li>

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Info">Info</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Team_members">Members</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Graduate_and_Post-Doctoral_Mentors">Mentors</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Team_Photos">Photos</a></li>

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<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Mentor">Mentor</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Professors">Professors</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Sponsors">Sponsors</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Special_Thanks">Special Thanks</a></li> </ul> 

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