Difference between revisions of "Part:BBa K5143025:Design"

 
 
(2 intermediate revisions by the same user not shown)
Line 7: Line 7:
  
 
===Design Notes===
 
===Design Notes===
−
We worked on the yeast S. cerevisiae that does recombination with small homologous sequences. So, in our case, we modified some sequences in alphafactor and in CBD sequence to avoid recombination between these parts.
+
We worked on the yeast <i> S. cerevisiae </i> that does recombination with small homologous sequences. So, in our case, we modified some sequences in alphafactor and in CBD sequence to avoid recombination between these parts.
  
  
Line 16: Line 16:
  
 
===References===
 
===References===
 +
(1) Ye L, Liu X, Li K, Li X, Zhu J, Yang S, Xu L, Yang M, Yan Y, Yan J. A bioinspired synthetic fused protein adhesive from barnacle cement and spider dragline for potential biomedical materials. Int J Biol Macromol. 2023 Dec 31;253(Pt 5):127125. doi: 10.1016/j.ijbiomac.2023.127125. Epub 2023 Sep 28. PMID: 37776922. <br>
 +
(2) Gilbert, C. et al. Living materials with programmable functionalities grown from engineered microbial co-cultures. Nat Mater 20, 691–700 (2021). A Yeast Modular Cloning (MoClo) Toolkit Expansion for Optimization of Heterologous Protein Secretion and Surface Display in Saccharomyces cerevisiae | ACS Synthetic Biology. https://pubs.acs.org/doi/10.1021/acssynbio.3c00743. <br>
 +
(3) Liljeruhm, J. et al. Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology. Journal of Biological Engineering 12, 8 (2018) <br>
 +
(4) Liu, Z. et al. Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci Rep 7, 2193 (2017). Mukherjee, M. & Wang, Z. Q. A well-characterized polycistronic-like gene expression system in yeast. Biotechnology and Bioengineering 120, 260–271 (2023). Müntjes, K. et al. Establishing Polycistronic Expression in the Model Microorganism Ustilago maydis. Front Microbiol 11, 1384 (2020).

Latest revision as of 17:38, 21 September 2024


Plasmid D


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal suffix found in sequence at 3567
    Illegal EcoRI site found at 1361
    Illegal EcoRI site found at 7006
    Illegal EcoRI site found at 7533
    Illegal PstI site found at 2789
    Illegal PstI site found at 3092
    Illegal PstI site found at 3185
    Illegal PstI site found at 3191
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 1361
    Illegal EcoRI site found at 7006
    Illegal EcoRI site found at 7533
    Illegal SpeI site found at 3568
    Illegal PstI site found at 2789
    Illegal PstI site found at 3092
    Illegal PstI site found at 3185
    Illegal PstI site found at 3191
    Illegal PstI site found at 3582
    Illegal NotI site found at 3575
    Illegal NotI site found at 7539
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 1361
    Illegal EcoRI site found at 7006
    Illegal EcoRI site found at 7533
    Illegal BamHI site found at 1906
    Illegal BamHI site found at 2620
    Illegal XhoI site found at 5171
    Illegal XhoI site found at 7012
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal suffix found in sequence at 3568
    Illegal EcoRI site found at 1361
    Illegal EcoRI site found at 7006
    Illegal EcoRI site found at 7533
    Illegal PstI site found at 2789
    Illegal PstI site found at 3092
    Illegal PstI site found at 3185
    Illegal PstI site found at 3191
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal prefix found in sequence at 7533
    Illegal EcoRI site found at 1361
    Illegal EcoRI site found at 7006
    Illegal SpeI site found at 3568
    Illegal PstI site found at 2789
    Illegal PstI site found at 3092
    Illegal PstI site found at 3185
    Illegal PstI site found at 3191
    Illegal PstI site found at 3582
    Illegal NgoMIV site found at 1876
    Illegal AgeI site found at 1915
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 4280


Design Notes

We worked on the yeast S. cerevisiae that does recombination with small homologous sequences. So, in our case, we modified some sequences in alphafactor and in CBD sequence to avoid recombination between these parts.


Source

The Cp19k is a barnacle gene, MaSp1 is a spider gene, while fwYellow is synthetic.

References

(1) Ye L, Liu X, Li K, Li X, Zhu J, Yang S, Xu L, Yang M, Yan Y, Yan J. A bioinspired synthetic fused protein adhesive from barnacle cement and spider dragline for potential biomedical materials. Int J Biol Macromol. 2023 Dec 31;253(Pt 5):127125. doi: 10.1016/j.ijbiomac.2023.127125. Epub 2023 Sep 28. PMID: 37776922.
(2) Gilbert, C. et al. Living materials with programmable functionalities grown from engineered microbial co-cultures. Nat Mater 20, 691–700 (2021). A Yeast Modular Cloning (MoClo) Toolkit Expansion for Optimization of Heterologous Protein Secretion and Surface Display in Saccharomyces cerevisiae | ACS Synthetic Biology. https://pubs.acs.org/doi/10.1021/acssynbio.3c00743.
(3) Liljeruhm, J. et al. Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology. Journal of Biological Engineering 12, 8 (2018)
(4) Liu, Z. et al. Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci Rep 7, 2193 (2017). Mukherjee, M. & Wang, Z. Q. A well-characterized polycistronic-like gene expression system in yeast. Biotechnology and Bioengineering 120, 260–271 (2023). Müntjes, K. et al. Establishing Polycistronic Expression in the Model Microorganism Ustilago maydis. Front Microbiol 11, 1384 (2020).