Difference between revisions of "Team:HK SKHLPSS/Design"

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{{HK_SKHLPSS}}
 
{{HK_SKHLPSS}}
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<html>
 
<html>
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<div class="column full_size">
 +
  <h1>Design</h1>
 +
  <p>
 +
    Since our previous studies only focused on 2-dimensional structure of nano-device, we would like to explore the feasibility of a 3-dimensional structure of nano-device.
 +
  </p>
 +
  <p>
 +
    In our design, eight single-stranded DNAs are used to form a DNA Nano-Cube. This cube is designed so that one side of the cube is originally open. We fit in the corresponding base pairs of this side so that the presence of the target H3N2 virus strands would induce the closing of the cube and lead to the formation of G-quadruplex.
 +
  </p>
 +
  <p>
 +
    The eight oligos we chose and the nano-cube we designed are listed below as reference.
 +
  </p>
  
 +
  <table>
 +
    <tbody>
 +
      <th>
 +
        <td>Tetra forming Oligo</td>
 +
        <td>Sequence</td>
 +
        <td>Size (nucleotide)</td>
 +
      </th>
  
 +
      <tr>
 +
        <td>Oligo1</td>
 +
        <td>TCG GCC GCG CGG TTC CGG TGC CCC CTT CGG CGC CCG TCT TGC GGT CCG GGG TTG CAG GAC GCC GT</td>
 +
        <td>65</td>
 +
      </tr>
  
 +
      <tr>
 +
        <td>Oligo2</td>
 +
        <td><span style="background-color: #4BFF00;">AAG CAA TGA TGG TCT T</span>TT TCC GCG GGC CCG TTC CCC GGA CCG CTT GGG CAG CCT GGT TCC AGC CAC GGC T</td>
 +
        <td>70</td>
 +
      </tr>
  
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<div class="column full_size">
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      <tr>
−
<h1>Design</h1>
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        <td>Oligo3</td>
−
<p>
+
        <td>TCG CCG GGT GGG TTG AGT GGC GCC CTT GGG GGC ACC GGT TGG CAG GCG GCG T</td>
−
Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
+
        <td>52</td>
−
</p>
+
      </tr>
  
−
<p>
+
      <tr>
−
This page is different to the "Applied Design Award" page. Please see the <a href="https://2017.igem.org/Team:HK_SKHLPSS/Applied_Design">Applied Design</a> page for more information on how to compete for that award.
+
        <td>Oligo4</td>
−
</p>
+
        <td><span style="background-color: #FEFF03;">GGG TTG GGT TT</span>C GGG CCC GCG GTT GCC GCG GCA GGT TCG CCG CCT GCC TTC GGC GTC CTG CT</td>
 +
        <td>62</td>
 +
      </tr>
  
−
</div>
+
      <tr>
 +
        <td>Oligo5</td>
 +
        <td>TCC GCG CGG CCG TTT AGG CCC GGC GTT CCC CGG CCG CCT</td>
 +
        <td>39</td>
 +
      </tr>
  
−
<div class="column half_size">
+
      <tr>
−
<h5>What should this page contain?</h5>
+
        <td>Oligo6</td>
−
<ul>
+
        <td>TCG CCG GGC CTA <span style="background-color: #FEFF03;">TTT GGG TAG GG</span></td>
−
<li>Explanation of the engineering principles your team used in your design</li>
+
        <td>23</td>
−
<li>Discussion of the design iterations your team went through</li>
+
      </tr>
−
<li>Experimental plan to test your designs</li>
+
−
</ul>
+
  
−
</div>
+
      <tr>
 +
        <td>Oligo7</td>
 +
        <td>TCC TGC CGC GGC TTG CCG TGG CTG GTT CGC CGC GGC CCT TCC CAC CCG GCG TTG GCG GCC GGG GTT T<span style="background-color: #F60016;">AT TAA TAG AAT TAT CC</span></td>
 +
        <td>83</td>
 +
      </tr>
 +
 
 +
      <tr>
 +
        <td>Oligo8</td>
 +
        <td>TGG GCC GCG GCG TTC CAG GCT GCC CTT GAC GGG CGC CGT TGG GCG CCA CTC T</td>
 +
        <td>52</td>
 +
      </tr>
 +
       
 +
      <tr>
 +
        <td>Target</td>
 +
        <td><span style="background-color: #F60016">GGA TAA TTC TAT TAA T</span>CA TG<span style="background-color: #4BFF00">A AGA CCA TCA TTG CTT</span></td>
 +
        <td>36</td>
 +
      </tr>
 +
 
 +
    </tbody>
 +
  </table>
  
−
<div class="column half_size">
 
−
<h5>Inspiration</h5>
 
−
<ul>
 
−
<li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
 
−
<li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
 
−
<li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
 
−
</ul>
 
 
</div>
 
</div>
 +
</html>
  
 +
  <!--
 +
      <p>
 +
        Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
 +
      </p>
  
 +
      <p>
 +
        This page is different to the "Applied Design Award" page. Please see the <a href="https://2017.igem.org/Team:HK_SKHLPSS/Applied_Design">Applied Design</a> page for more information on how to compete for that award.
 +
      </p>
  
−
</html>
+
 
 +
    <div class="column half_size">
 +
      <h5>What should this page contain?</h5>
 +
      <ul>
 +
        <li>Explanation of the engineering principles your team used in your design</li>
 +
        <li>Discussion of the design iterations your team went through</li>
 +
        <li>Experimental plan to test your designs</li>
 +
      </ul>
 +
 
 +
    </div>
 +
 
 +
    <div class="column half_size">
 +
      <h5>Inspiration</h5>
 +
      <ul>
 +
        <li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
 +
        <li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
 +
        <li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
 +
      </ul>
 +
    </div>
 +
  -->

Revision as of 07:06, 4 October 2017

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HK_SKHLPSS

Design

Since our previous studies only focused on 2-dimensional structure of nano-device, we would like to explore the feasibility of a 3-dimensional structure of nano-device.

In our design, eight single-stranded DNAs are used to form a DNA Nano-Cube. This cube is designed so that one side of the cube is originally open. We fit in the corresponding base pairs of this side so that the presence of the target H3N2 virus strands would induce the closing of the cube and lead to the formation of G-quadruplex.

The eight oligos we chose and the nano-cube we designed are listed below as reference.

Tetra forming Oligo Sequence Size (nucleotide)
Oligo1 TCG GCC GCG CGG TTC CGG TGC CCC CTT CGG CGC CCG TCT TGC GGT CCG GGG TTG CAG GAC GCC GT 65
Oligo2 AAG CAA TGA TGG TCT TTT TCC GCG GGC CCG TTC CCC GGA CCG CTT GGG CAG CCT GGT TCC AGC CAC GGC T 70
Oligo3 TCG CCG GGT GGG TTG AGT GGC GCC CTT GGG GGC ACC GGT TGG CAG GCG GCG T 52
Oligo4 GGG TTG GGT TTC GGG CCC GCG GTT GCC GCG GCA GGT TCG CCG CCT GCC TTC GGC GTC CTG CT 62
Oligo5 TCC GCG CGG CCG TTT AGG CCC GGC GTT CCC CGG CCG CCT 39
Oligo6 TCG CCG GGC CTA TTT GGG TAG GG 23
Oligo7 TCC TGC CGC GGC TTG CCG TGG CTG GTT CGC CGC GGC CCT TCC CAC CCG GCG TTG GCG GCC GGG GTT TAT TAA TAG AAT TAT CC 83
Oligo8 TGG GCC GCG GCG TTC CAG GCT GCC CTT GAC GGG CGC CGT TGG GCG CCA CTC T 52
Target GGA TAA TTC TAT TAA TCA TGA AGA CCA TCA TTG CTT 36