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

 
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= Design =
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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.
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  <h1>Design</h1>
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  <p>
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    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.
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  </p>
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  <p>
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    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.
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  <p>
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    The eight oligos we chose and the nano-cube we designed are listed below as reference.
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  <table>
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[[File: Design_1.jpg |thumbnail| 800px | center | Fig.3. The nano-cube is designed according to Watson & Crick’s principle. Under guanine-riched sequence, it is able to bind with specific target strand to form a G-quadruplex. The G-quadruplex will enhance the peroxidase activity of hemin and lead to the peroxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) giving a colorimetric signal. The degree of peroxidase activity indicates the concentration of the target.]]
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    <tbody>
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      <th>
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        <td>Tetra forming Oligo</td>
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        <td>Sequence</td>
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        <td>Size (nucleotide)</td>
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      </th>
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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.
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The eight oligos we chose and the nano-cube we designed are listed below as reference.
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  <table class="table table-hover table-bordered" style="font-size: 1em">
 
       <tr>
 
       <tr>
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         <td>Oligo1</td>
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        <th style="text-align: center" width="25%">Cubic forming Oligo</th>
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        <th style="text-align: center">Sequence</th>
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        <th style="text-align: center" width="15%">Size (nucleotide)</th>
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      </tr>
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      <tr style="font-size: 0.8em">
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         <td style="text-align: center">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>TCG GCC GCG CGG TTC CGG TGC CCC CTT CGG CGC CCG TCT TGC GGT CCG GGG TTG CAG GAC GCC GT</td>
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         <td>65</td>
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         <td style="text-align: center">65</td>
 
       </tr>
 
       </tr>
  
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Oligo2</td>
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         <td style="text-align: center">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><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>
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         <td>70</td>
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         <td style="text-align: center">70</td>
 
       </tr>
 
       </tr>
  
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Oligo3</td>
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         <td style="text-align: center">Oligo3</td>
 
         <td>TCG CCG GGT GGG TTG AGT GGC GCC CTT GGG GGC ACC GGT TGG CAG GCG GCG T</td>
 
         <td>TCG CCG GGT GGG TTG AGT GGC GCC CTT GGG GGC ACC GGT TGG CAG GCG GCG T</td>
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         <td>52</td>
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         <td style="text-align: center">52</td>
 
       </tr>
 
       </tr>
  
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Oligo4</td>
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         <td style="text-align: center">Oligo4</td>
 
         <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><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>
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         <td>62</td>
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         <td style="text-align: center">62</td>
 
       </tr>
 
       </tr>
  
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Oligo5</td>
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         <td style="text-align: center">Oligo5</td>
 
         <td>TCC GCG CGG CCG TTT AGG CCC GGC GTT CCC CGG CCG CCT</td>
 
         <td>TCC GCG CGG CCG TTT AGG CCC GGC GTT CCC CGG CCG CCT</td>
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         <td>39</td>
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         <td style="text-align: center">39</td>
 
       </tr>
 
       </tr>
  
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Oligo6</td>
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         <td style="text-align: center">Oligo6</td>
 
         <td>TCG CCG GGC CTA <span style="background-color: #FEFF03;">TTT GGG TAG GG</span></td>
 
         <td>TCG CCG GGC CTA <span style="background-color: #FEFF03;">TTT GGG TAG GG</span></td>
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         <td>23</td>
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         <td style="text-align: center">23</td>
 
       </tr>
 
       </tr>
  
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Oligo7</td>
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         <td style="text-align: center">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>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>
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         <td>83</td>
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         <td style="text-align: center">83</td>
 
       </tr>
 
       </tr>
  
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Oligo8</td>
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         <td style="text-align: center">Oligo8</td>
 
         <td>TGG GCC GCG GCG TTC CAG GCT GCC CTT GAC GGG CGC CGT TGG GCG CCA CTC T</td>
 
         <td>TGG GCC GCG GCG TTC CAG GCT GCC CTT GAC GGG CGC CGT TGG GCG CCA CTC T</td>
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         <td>52</td>
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         <td style="text-align: center">52</td>
 
       </tr>
 
       </tr>
 
          
 
          
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       <tr>
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       <tr style="font-size: 0.8em">
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         <td>Target</td>
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         <td style="text-align: center">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><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>
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         <td>36</td>
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         <td style="text-align: center">36</td>
 
       </tr>
 
       </tr>
  
 
     </tbody>
 
     </tbody>
 
   </table>
 
   </table>
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The colours show how the oligos bind with each other. We used DNA sequence mimicking the RNA sequence to do the test first because of stability problem.  
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      <p>
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        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.
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      </p>
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       <p>
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         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.
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  <table class="table table-hover table-bordered" style="font-size: 1em">
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       </p>
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       <tr>
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         <th style="text-align: center" width="20%">Oligo</th>
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        <th style="text-align: center">Sequence</th>
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        <th style="text-align: center" width="15%">Size (nucleotide)</th>
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       </tr>
  
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      <tr style="font-size: 0.8em">
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        <td style="text-align: center">Target (RNA)</td>
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        <td>GGA UAA UUC UAU UAA UCA UGA AGA CCA UCA UUG CUU</td>
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        <td style="text-align: center">36</td>
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      </tr>
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After obtaining positive result in using DNA sequence, we would also like to check whether our design could successfully bind with RNA of H3N2 virus. Hence, the above RNA sequence of H3N2 virus was ordered for further study.
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      <h5>What should this page contain?</h5>
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      <ul>
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        <li>Explanation of the engineering principles your team used in your design</li>
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        <li>Discussion of the design iterations your team went through</li>
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        <li>Experimental plan to test your designs</li>
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The above DNA and RNA strand are sponsored by <I>Integrated DNA Technologies</I>.
  
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{{HK_SKHLPSS_FOOTER}}
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      <h5>Inspiration</h5>
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        <li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
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        <li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
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        <li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
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      </ul>
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Latest revision as of 12:49, 1 November 2017

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JUDGING FORM

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.

Fig.3. The nano-cube is designed according to Watson & Crick’s principle. Under guanine-riched sequence, it is able to bind with specific target strand to form a G-quadruplex. The G-quadruplex will enhance the peroxidase activity of hemin and lead to the peroxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) giving a colorimetric signal. The degree of peroxidase activity indicates the concentration of the target.


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.

Cubic 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

The colours show how the oligos bind with each other. We used DNA sequence mimicking the RNA sequence to do the test first because of stability problem.

Oligo Sequence Size (nucleotide)
Target (RNA) GGA UAA UUC UAU UAA UCA UGA AGA CCA UCA UUG CUU 36

After obtaining positive result in using DNA sequence, we would also like to check whether our design could successfully bind with RNA of H3N2 virus. Hence, the above RNA sequence of H3N2 virus was ordered for further study.

The above DNA and RNA strand are sponsored by Integrated DNA Technologies.