Biomod/2012/UTokyo/UT-Hongo

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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 style="text-align: right"> <a href="http://openwetware.org/index.php?title=Biomod/2012/UTokyo/UT-Hongo&action=edit">edit this page</a> </div> 

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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> 

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     <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, substrate protection, and attachment to solid surfaces. All these new functionalities are the result 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 fields of applications in chemical and medical applications, such as in bioreactors and in biomolecule detection.  </p>
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<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 Medical DNA Shell system</p> 

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     <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 attach 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, there needs to be more work 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/d/d7/Biomod-2012-UTokyo-UT-Hongo_Design_Thumb.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 a 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 can 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 result of our experiment. We can classify the experiment 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 I 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 indicate the characteristic of our DNA shell. In this section, the method was described. Also, we wrote about the equipments and the 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>Future Work</h2> <p> We aim to make a device that has wider usage 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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   <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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<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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     Copyright (C) 2012 | Design by Yuichi Nishwiaki | BIOMOD Team UT-Hongo
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