DNA

Part:BBa_K4610005:Design

Designed by: Sophie Geierstanger   Group: iGEM23_CCA-San-Diego   (2023-10-07)


Afu8g00370 (Fma-PKS)


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 2043
    Illegal EcoRI site found at 4230
    Illegal SpeI site found at 2241
    Illegal PstI site found at 62
    Illegal PstI site found at 2850
    Illegal PstI site found at 3512
    Illegal PstI site found at 5848
    Illegal PstI site found at 6251
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 2043
    Illegal EcoRI site found at 4230
    Illegal SpeI site found at 2241
    Illegal PstI site found at 62
    Illegal PstI site found at 2850
    Illegal PstI site found at 3512
    Illegal PstI site found at 5848
    Illegal PstI site found at 6251
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 2043
    Illegal EcoRI site found at 4230
    Illegal BglII site found at 1697
    Illegal BglII site found at 1819
    Illegal BglII site found at 5371
    Illegal BglII site found at 6642
    Illegal BamHI site found at 7141
    Illegal BamHI site found at 7342
    Illegal XhoI site found at 686
    Illegal XhoI site found at 1092
    Illegal XhoI site found at 1494
    Illegal XhoI site found at 2298
    Illegal XhoI site found at 3217
    Illegal XhoI site found at 3288
    Illegal XhoI site found at 3493
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 2043
    Illegal EcoRI site found at 4230
    Illegal SpeI site found at 2241
    Illegal PstI site found at 62
    Illegal PstI site found at 2850
    Illegal PstI site found at 3512
    Illegal PstI site found at 5848
    Illegal PstI site found at 6251
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 2043
    Illegal EcoRI site found at 4230
    Illegal SpeI site found at 2241
    Illegal PstI site found at 62
    Illegal PstI site found at 2850
    Illegal PstI site found at 3512
    Illegal PstI site found at 5848
    Illegal PstI site found at 6251
    Illegal NgoMIV site found at 197
    Illegal NgoMIV site found at 4295
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 628
    Illegal BsaI site found at 1239
    Illegal BsaI site found at 4566
    Illegal BsaI site found at 6838
    Illegal BsaI.rc site found at 509
    Illegal BsaI.rc site found at 1123
    Illegal BsaI.rc site found at 6531
    Illegal SapI.rc site found at 1205
    Illegal SapI.rc site found at 2487


Design Notes

In order to increase the rate of transfection, our team has decided to construct two 4 layer chitosan nanocomposites that contain in total 8 DNA sequences rather than one 8 DNA layer nanocomposite. The first chitosan nanocomposite, chitosan nanocomposite A, would contain parts BBa_K4610000, BBa_K4610001, BBa_K4610002, and BBa_K4610003 (in order from outer to inner layer). The second chitosan nanocomposite, chitosan nanocomposite B, would contain BBa_K4610004, BBa_K4610005, BBa_K4610006, and BBa_K4610007 (in order from outer to inner layer).

In the constructed chitosan nanocomposite B, Afu8g00370 is the second innermost layer and is released after the degradation of the Fma-KR (BBa_K4610004) layer. The degradation and release of BBa_K4610005 allows for the release of the BBa_K4610006 part and the subsequent pDNA layers.

Source

The source of Afu8g00370 is the aspergillus fumigatus strain Af293, a saprophytic filamentous fungus. Afu8g00370 is located on chromosome 8. Af293 is a clinically derived strain that was isolated in 1994 from a lung biopsy taken post autopsy from a patient who was developing severe sepsis syndrome. In 1998 it became the first A. fumigatus isolate with a full genome sequence and even in 202, Af293 genome is the only genome sequence of A. fumigatus to have a full physical reconstruction of its chromosomes. Af293 has eight chromosomes, however, Afu8g00370 exists on the 8th chromosome.


References

Guruceaga, X., Perez-Cuesta, U., Abad-Diaz de Cerio, A., Gonzalez, O., Alonso, R. M., Hernando, F. L., Ramirez-Garcia, A., & Rementeria, A. (2019, December 20). Fumagillin, a mycotoxin of aspergillus fumigatus: Biosynthesis, biological activities, detection, and applications. Toxins. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7020470/

Bertuzzi, M., van Rhijn, N., Krappmann, S., Bowyer, P., Bromley, M. J., & Bignell, E. M. (2020, September 17). On the lineage of aspergillus fumigatus isolates in common laboratory use. OUP Academic. https://academic.oup.com/mmy/article/59/1/7/5908083