Difference between revisions of "Part:BBa K4665170"

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3) M13 PS for phage particle export.  
 
3) M13 PS for phage particle export.  
 
4) modified M13 origin to serve as the ssDNA synthesis terminator.
 
4) modified M13 origin to serve as the ssDNA synthesis terminator.
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 +
===Characterisation===
  
  

Revision as of 15:36, 9 October 2023


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 (Julin 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
21 octa_42nt_B9 edge CCGCTACCACCACAGTGTAGCGGTCACGCT
22 octa_42nt_B10 edge CGGTGTTCTTTTTTTTTTTTTTTTTTAGAAAGCGAAAGGAGCGGGCGCTAGGGGCGAACGTGGCGAACGATGGTAATGCG
23 octa_42nt_B11 vertex CTTATAAATCAAATCATTTTTTTAGTTTTTTGGGGTCGAGGCTTATCGGC
24 octa_42nt_B12 vertex TCGCGGATGTTTCAGGTTTTTTTTCAGCAGCCTTGGCCGAAAGGAAGGGA
25 octa_42nt_C1 edge TCAGATCGTCACTTCAGTTCCCTGAGTGCT
26 octa_42nt_C2 edge CGGTGTTCTTTTTTTTTTTTTTTTTTGATCAGTGTGAACACAGCACCCACGAGTGCGGCTCTGGGACGACCAACGTGAGT
27 octa_42nt_C3 vertex ACAGAATGCATAGTATGTTTTTTTGTGAGTCCTTCAAGGACTCGAGATTGG
28 octa_42nt_C4 edge CAGTTTCTGGCGGTCAAAGCCTTTTCCTCCAGAGCTTGACAGTCATC
29 octa_42nt_C5 vertex CTTGACGGGAGCAGGTTTTTTTTCACCGAACAG
30 octa_42nt_C6 vertex ACTTCTCCCTTCCCAGATTTTTTTTGCTGACCTTGTCTGTACTTCAGGAT
31 octa_42nt_C7 edge CAGAGAAGCAGTAATGAGTTTCCTTCCAAGGATTCTTGAATGGCACA
32 octa_42nt_C8 vertex TGTGTTACCAGGATCTTTTTTTTGTGATGGGAA
33 octa_42nt_C9 vertex CCTGCGTGGCTGCAAATTTTTTTTATTCGTCCAGTTCGGGCCAGATCGTT
34 octa_42nt_C10 edge ATTGGTTGCGCGATTGTTGAGGTTGTAGTCACAGTGAGTTGCGAATG
35 octa_42nt_C11 vertex AGTGAGTGGGACTGAATTTTTTTTCACGGATGG
36 octa_42nt_C12 vertex ATGGGACATTTTCCAGTTTTTTTTCTTGCACAGTGCTGGTTGAGTGTTG
37 octa_42nt_D1 edge GTGGGCCACTTTTTTTTTTTTTTTTTTCCAGTTTGGAACAAGAGTCCACCCATAGCCCGAGATAGGCCACTACGTGA
38 octa_42nt_D2 edge ACCATCACCCAAAAGAGAAATCGGCAAAATCC
39 octa_42nt_D3 vertex GTGATCGGGTCCTCAATTTTTTTACAAGTAGGTCTTAGATGTTAGTATA
40 octa_42nt_D4 edge TCGCAGCGTTTTTTTTTTTTTTTTTCTGCTCCAATTTGTTCACCAGCTGCTTCGGAAGATGTGTCGTGATCTGTTCG
41 octa_42nt_D5 edge GCCAAGCACTGGGTCCCCAGAATACCGGACTC
42 octa_42nt_D6 edge AGAACACCGTTTTTTTTTTTTTTTTTGTTAGCCTCCTCAAACACCTGCTTCTTTGATCTGATTAGGATTTTAATCAGA
43 octa_42nt_D7 edge GCGTCAAATTGCTTTCGACACAGCTGTTCATA
44 octa_42nt_D8 vertex CAGCTGCTCAAACAGATTTTTTTCAGAGTTGATACCAATTTCCTTGGTA
45 octa_42nt_D9 edge GAGGTGAAGTGTAATGAGGTAACACTTGTC
46 octa_42nt_D10 edge ACGCTGCGATTTTTTTTTTTTTTTTATTTCCTGAACCTCTCAGGACGGTGACCGCTCTTGTTCAGTCATTGAAGATG
47 octa_42nt_D11 edge GCCACGAGCTGTTGTACAATGTGGCTCTCATT
48 octa_42nt_D12 vertex AGGGAAGGCATGATGCTTTTTTTTGCGGAAATCTTCAGCAACCCCAAGC
49 octa_42nt_E1 edge TCTGGTCCAGCCTGAGACGGCGCTCAGCAC
50 octa_42nt_E2 vertex AGATTCCTCTGCTCTTTTTTTTTTGGGCAGGGCTCCGGTCCTCATAGTC
51 octa_42nt_E3 edge CACCACCAGCCACTTCAGCTCATTGTCTGG
52 octa_42nt_E4 edge AACTCTCGAAAGCCAGCCCCCGATTTAGAG
53 octa_42nt_E5 edge TTCGAGGCTTCATGCGATGTCCTTCCAATC
54 octa_42nt_E6 vertex CTTGATCAGTAAACCCTTTTTTTACTTTCTCTGAATACTCGTTGAGGCT
55 octa_42nt_E7 edge GTGGCCCACTTTTTTTTTTTTTTTTAGGGATAACAATCTTATATTTGTCGCTGTTCTCCGCGGACTCGTGCCAATTC
56 octa_42nt_E8 edge ATCAGAAACTGACAGGGGAACAGATCCAGCCA
57 octa_42nt_E9 edge GTGGCCCACTTTTTTTTTTTTTTTTCAGCCAGGTTTCGACGTTATTGGATGTTCTTCATCTCCAGGCGTGCTTAGAC
58 octa_42nt_E10 edge TTCTCATCGCAGGGTCTCACGCACTCCTTCAG
59 octa_42nt_E11 edge GTGGCCCACTTTTTTTTTTTTTTTTGCGCTGGCATCTCTGCAATTGGTCTCTTCTCCTCCAGGAATGGTCCTTCTTG
60 octa_42nt_E12 edge ATATCTGTCGCTGCGCCGATGAAGTAGAAGCG
61 octa_42nt_F1 edge TCGCAGCGTTTTTTTTTTTTTTTTTTCTTCGTAGGTACCTATTAAAGAACGTATCAGGGCGGAATCCCTGCTGGAAC
62 octa_42nt_F2 edge AGAACACCGTTTTTTTTTTTTTTTTTGCT
63 octa_42nt_F3 edge GTGGGCCACTTTTTTTTTTTTTTTTACCACTCCCATCCTCAAAGCGGCGCTTACCAGGGACTGATGGGCCCACAATC
64 octa_42nt_F4 edge ACGCTGCGATTTTTTTTTTTTTTTTATAGCCTGTGTCAAGTCAACCATCTGACCTCAACTCTCCCAGGCCCATCTTC
65 octa_42nt_F5 edge GTGGGCCACTTTTTTTTTTTTTTTTCTCAGAGCCTGGACCTTGAGGGCTCTGGAGTTCTCTTGACATGGTATTCAGC
66 octa_42nt_F6 edge CGGTGTTCTTTTTTTTTTTTTTTTTTGTCTGGATCTGCATGATTCTTCCCATACACGAGGATCAATGCGTCCTGGATG
67 octa_42nt_F7 edge GTGGGCCACTTTTTTTTTTTTTTTTAGGATGACTTCGGCTCCTTTACCTGCAGTTCACCTTGAATCCCTCGGAATAG
68 octa_42nt_F8 edge TCGCAGCGTTTTTTTTTTTTTTTTTTCGGAACCCTAAAGGGGCGCTGGCAACCCGCCGCGTGCCGTAAAGCACTAAA
69 octa_42nt_F9 edge GTGGCCCACTTTTTTTTTTTTTTTTTCGCCCACCTGGTTGCCCCACAAATCCACCCTGGGGCAGGAGGCATCTATTG
70 octa_42nt_F10 edge TCGCAGCGTTTTTTTTTTTTTTTTTGGCAGACCCAGCAACACCTCAGATTGCTTTCCTGACCAGAGATGTGCCGCGA
71 octa_42nt_F11 edge AGAACACCGTTTTTTTTTTTTTTTTTGAGCTGCGTCCGGTCAAGGGCACCTTACTTCATTGGGTCCACAGCTCCCTGA
72 octa_42nt_F12 edge ACGCTGCGATTTTTTTTTTTTTTTTAGCAGGTCATCGTCCAGGATGGTCAGAGGTTGTGAACTGGCCCAAGATCTCC

To get the ssDNA sequence a pScaf phagemid with insert for generating DNA origami was used. This phagemid was constructed by Nafisi et al., (2018). They converted pUC18 into a pagemid for custom ssDNA production by adding four components: 1) a full-length M13 origin for ssDNA initiation. 2) Kpnl and BamHl restriction sites for insert cloning. 3) M13 PS for phage particle export. 4) modified M13 origin to serve as the ssDNA synthesis terminator.

Characterisation

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 919
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 919
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 738
    Illegal BglII site found at 1310
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 919
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 919
    Illegal NgoMIV site found at 132
  • 1000
    COMPATIBLE WITH RFC[1000]


References

Julin, S., Keller, A., & Linko, V. (2022). Dynamics of DNA Origami Lattices. Bioconjugate Chemistry, 34(1), 18-29. https://doi.org/10.1021/acs.bioconichem.2c00

Majikes, J.M. & Liddle, J.A. (January 8, 2021). DNA Origami Design: A How-To Tutorial. Journal of Research of the National Institute of Standards and Technology, 126:126001. https://doi.org/10.6028/jres.126.001

Nafisi, P. M., Aksel, T., Douglas, S. M. (2018) Construction of a novel phagemid to produce custom DNA origami scaffolds, Synthetic Biology, Volume 3, Issue 1, https://doi.org/10.1093/synbio/ysy015

Tandon, S. et al. (August 2021). Experimental investigation on tensile properties of the polymer and composite specimens printed in a Triangular pattern. Journal of manufacturing Process, 68A: 706-715. https://doi.org/10.1016/j.jmapro.2021.05.074