Difference between revisions of "Team:HK SKHLPSS/Design"
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<td>Oligo1</td> | <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>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>Oligo2</td> | <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><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>Oligo3</td> | <td>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>Oligo4</td> | <td>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>Oligo5</td> | <td>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>Oligo6</td> | <td>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>Oligo7</td> | <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>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>Oligo8</td> | <td>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>Target</td> | <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><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> | ||
Revision as of 09:20, 4 October 2017
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 |
