Biomod/2012/UTokyo/UT-Hongo

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(3 intermediate revisions not shown.)
Line 115: Line 115:
<p style="font-size: 100%; font-weight: bold; margin-left: auto; margin-right: auto; text-align: center">Fig1. Schematic animation of DNA Shell</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">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 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>
+
       <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;">
       <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;">
       <div style="float: left; margin-right: 24px; margin-top: 12px;width=350px; padding: 5px; border: 1px solid #666; border-style: dashed;">
Line 121: Line 121:
<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>
<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>
       </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 attach to a solid surface as is shown in Fig.2.  
+
       <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, 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.
+
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>
</p>
       <br style="clear: both">
       <br style="clear: both">
Line 138: Line 138:
     <div id="row1" class="block-container">
     <div id="row1" class="block-container">
       <div class="column1 column">
       <div class="column1 column">
-
<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>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>
+
<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>
       <div class="column2 column">
       <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>
<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>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>
+
<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>
       <div class="column3 column">
       <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>
<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>
Line 164: Line 164:
<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>
<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>We did some experiments for indicating the characteristic of our DNA shell. In this section, the method was described. Also, we wrote about the equipments and the reagents. </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>
       </div>
       <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>Progress & Beyond</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>

Revision as of 10:42, 29 October 2012

The University of Tokyo


edit this page

Fig1. Schematic animation of DNA Shell

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.


Fig2. Schematic animation of the DNA Shell system

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.


YouTube

edit this footer

Views
Personal tools