Team:Hong Kong HKU/Design
Project
Design
Our design is a tetrahedral nanostructure for diagnostic purposes.
It consists of five oligonucleotides (oligos, O1 to O5) with lengths ranging from 30 to 97 nucleotides.
The oligos are assembled by heating at 95ºC for 5 minutes and then cooled to 25ºC.
The details of the DNA nanostructure assembly can be found in here.
The oligo sequences are shown below:
| Tetra forming Oligo | Sequence | Size (nucleotide) |
|---|---|---|
| Oligo 1 | CTACTAGCTGCACGACGTAGTGGGTTGGGTCTAACTCCACTGGGTAGGGTCGT CGAGCTCACGTGCGTCACGCGCGATAGTCGAGTGCTGCTGAGTA |
97 |
| Oligo 2 | CTACGAGTGATGACGAGACATGTGACAGTGCACACTATGTGCGCTCATCGCAC GATAGCAGACGACG |
67 |
| Oligo 3 | TGACGCACGTGAGCACTGCTATCGTGCGATGAGCGCACATAGACTGACACACG CATGACGCTATCGCAGCACGACTATCGCGCG |
84 |
| Oligo 4 | GTCTCGTCATCACACGTGCAGCTAGTAGTACTCAGCAGCACAGCTGCGATAGC GTCATGCGTGTGTCAGAGTGCACTGTCACAT |
84 |
| Oligo 5 | ATGGCACCCAGTGGAGTTAGACCCTGATTG | 30 |
To test our design, we used a miRNA sequence found in patients who have high risks of acquiring Huntington disease. The miRNA is expected to displace O5 from the tetrahedral structure. With Oligo 5 displaced, steric hindrance within the tetrahedron would hence be reduced. Oligo 1 would then be able to fold into a G-quadruplex structure, which serves as a DNAzyme to catalyze the reaction between hemin, ABTS and hydrogen peroxide, which gives a green color. The sequence of the miRNA for Huntington disease used for testing is shown below:
| Input Oligo | Sequence | Size (nucleotide) |
|---|---|---|
| Input | CAATCAGGGTCTAACTCCACTGGGTGCCAT | 30 |
| RNA Input | CAAUCAGGGUCUAACUCCACUGGGUGCCAU | 30 |
For future development as a diagnostic tool with broader applications, part of the DNA sequence can be altered for the detection of other miRNAs for various diseases.
