Biomod/2012/UTokyo/UT-Hongo
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<div style="height: 60px; margin-bottom: 18px;"> <div style="float: left; width: 250px; padding: 3px; background-color: white;"> <a href="http://biomod.net/"><img src="http://openwetware.org/images/8/82/Biomod2012-logo.png" width="250px" height="50px"></img></a> </div> <div style="float: right; width: 240px; padding: 3px; background-color: white;"> <a href="http://www.u-tokyo.ac.jp/en/" target="_blank"><img src="http://www.u-tokyo.ac.jp/en/images/banner/UT-logo.gif" width="234" height="60" border="0" alt="The University of Tokyo"></img></a> </div> </div>
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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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<div id="description"> <div style="float: right; width=270px; margin-left: 24px; padding: 5px; border: 1px solid #666; border-style: dashed;"> <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 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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<div id="youtube"> <h2>YouTube</h2> <div id="video"><center><iframe width="853" height="480" src="http://www.youtube.com/embed/f3hSqLA3ICA" frameborder="0" allowfullscreen></iframe></iframe></center></div> </div>
</div> <div id="navi"> <h2>Links</h2> <p style="margin-bottom: 15px"></p> <div id="row1" class="block-container"> <div class="column1 column">
<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>
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<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>
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<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>
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<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>
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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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<div id="sitemap"> <h2 style="border-bottom: none;">BIOMOD 2012 Team UT-Hongo</h2> <hr> <div id="footer-contents"> <div class="footer-section" id="section1">
<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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<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>
</div> </div> <p id="copyright"> Copyright (C) 2012 | Design by Yuichi Nishwiaki | BIOMOD Team UT-Hongo </p> <br style="clear: both;"> </div>
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