Part:BBa_K4665170
Octahedron DNA-origami (3024bp long; 42bp edges)
Biology and Usage
DNA origami is a technique that allows for the fabrication of complex nanostructures through guided DNA folding (Majikes & Liddle, 2021). The process involves designing a long ssDNA molecule, referred to as a scaffold, which acts as a backbone for the assembly. The long strand of ssDNA will then be folded into the wanted format using short ssDNA fragments called staples. Almost any form can be achieved by altering the staple sequences.
For the purpose of our project, Sublimestone, an octahedral 3D lattice form was chosen that acted as a nucleation site for the second module of our project, calcite mineralization.
The staple sequences below were acquired using an algorithm, resulting in the desired octahedral form. The octahedral structure was chosen for its thermodynamic stability, resisting disassembly or rearrangement (Julie et al., 2020). After careful analysis, it was determined that triangular structures have the highest mechanical strength (Tandon, 2021); however, the simplicity of the shape would reduce the surface area needed for nucleation. Hence, the octahedron was chosen as the base of the lattice.
| Row | ID | Type | Sequence |
|---|---|---|---|
| 1 | octa_42nt_A1 | vertex | AGGGCGAAATCTCCAGATTTTTTTGAGTGCTCTT |
| 2 | octa_42nt_A2 | edge | CATTTCTTGATGGCCTCTCAGCATAACCGTCTGGACTCCAACGTCAA |
| 3 | octa_42nt_A3 | vertex | TTAATTGCGGATCCAATTTTTTTTCTTCATTGGC |
| 4 | octa_42nt_A4 | edge | GTTATGGATAAACTTGCGAAAGGTTTCTCCAGTGCAGGGAGTGATCT |
| 5 | octa_42nt_A5 | vertex | ACTTCTTTGCTGCTTGATTTTTTTCCACGTCGAT |
| 6 | octa_42nt_A6 | edge | ACCTGCGCACACATCTTGGTTCAGAGTTCAACAGCTCGTCATACTCC |
| 7 | octa_42nt_A7 | vertex | TCGGACTTCATCTTCGGTTTTTTTTGGTGTGCACTTGGGATAATCTCATA |
| 8 | octa_42nt_A8 | edge | AGGCCCAATGTAGAAACGCAACAGGTGTGG |
| 9 | octa_42nt_A9 | edge | AGAACACCGTTTTTTTTTTTTTTTTTCTCATAGGTGTACTGGAACTCGCTGGACGAGCTTGCTGGCGCAAACATTCTTCC |
| 10 | octa_42nt_A10 | vertex | TGCTGCTGAAGTGCCAGTTTTTTTCTGGACCGTATGGGTTGCGCGCTTCTT |
| 11 | octa_42nt_A11 | edge | TGTGAACTTTGACAGTGTCTTACCGGTGTCACAGACCCCAGTCGTAA |
| 12 | octa_42nt_A12 | vertex | CAGTTCCAACTTGTGCTTTTTTTAGTCTGTGAA |
| 13 | octa_42nt_B1 | vertex | CCTTCATCAACCTCCGATTTTTTTGTGCCTTAACGCTCCTGCCTGAGGAG |
| 14 | octa_42nt_B2 | edge | CCAGCAGCAGTTGAGGACTTAACGTCGATT |
| 15 | octa_42nt_B3 | edge | ACGCTGCGATTTTTTTTTTTTTTTTTCCACACTTAACGAGGCCAACAAAAGTTGAACTCGTCGAATCCACCCTGCCTGC |
| 16 | octa_42nt_B4 | vertex | AAGATTCCGCAGCTCGCTTTTTTTAGACGGTCCTGTGGTTCTCCTGTTGAA |
| 17 | octa_42nt_B5 | edge | TACCCAAGAGTTGGGGGATTCATTGTGATG |
| 18 | octa_42nt_B6 | edge | CGGTGTTCTTTTTTTTTTTTTTTTTTTGGGAGTTTCTGTCTTCCTCCATAGAGGGCGGAACAGCTGATGGTGTACTTCCT |
| 19 | octa_42nt_B7 | vertex | TGCATTCTGTTTCTGGTTTTTTTAGAGAACTTTAGCATCTTCCATTGCTT |
| 20 | octa_42nt_B8 | vertex | GCGCGTAACAGGGCGCGTTTTTTTTCATATGGGGATTCCTTCAGGTTGTC |
| None |