DNA

Part:BBa_K4610004:Design

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


Afu8g00490 (Fma-KR)


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 741
    Illegal PstI site found at 806
    Illegal PstI site found at 1501
    Illegal PstI site found at 1996
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 741
    Illegal PstI site found at 806
    Illegal PstI site found at 1501
    Illegal PstI site found at 1996
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 741
    Illegal XhoI site found at 634
    Illegal XhoI site found at 677
    Illegal XhoI site found at 994
    Illegal XhoI site found at 1643
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 741
    Illegal PstI site found at 806
    Illegal PstI site found at 1501
    Illegal PstI site found at 1996
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 741
    Illegal PstI site found at 806
    Illegal PstI site found at 1501
    Illegal PstI site found at 1996
    Illegal NgoMIV site found at 2204
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1399
    Illegal BsaI site found at 3095
    Illegal BsaI.rc site found at 274


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 A, BBa_K4610004 is the first layer of pDNA which will be assembled by complex coacervation. It’s degradation causes the degradation and release of the 2nd layer, BBa_K4610005.

Source

The source of Afu8g00490 is the aspergillus fumigatus strain Af293, a saprophytic filamentous fungus. Afu8g00490 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, Afu8g00490 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