Difference between revisions of "Part:BBa K5306003:Design"
 
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<h1> Design Considerations</h1>
 
<h1> Design Considerations</h1>
  
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This coding sequence for nasC has been obtained from the organism <i>Klebsiella oxytoca m5al</i> and has  been codon optimized specifically for our chassise organism <i>Vibrio natriegens</i> using [https://www.benchling.com/ Benchling]and a personal codon optimization table that can be found on our wiki [https://2024.igem.wiki/msp-maastricht/contribution.html Codon Optimization <i>Vibrio natriegens</i>]according to codon frequency taken from Lee et al. (2019).
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This coding sequence for nasC has been obtained from the organism <i>Klebsiella oxytoca m5al</i> and has  been codon optimized specifically for our chassis organism <i>Vibrio natriegens</i> using [https://www.benchling.com/ Benchling]and a personal codon optimization table that can be found on our wiki [https://2024.igem.wiki/msp-maastricht/contribution.html Codon Optimization <i>Vibrio natriegens</i>]according to codon frequency taken from Lee et al. (2019).
  
 
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Latest revision as of 13:41, 30 September 2024

Design Considerations

This coding sequence for nasC has been obtained from the organism Klebsiella oxytoca m5al and has been codon optimized specifically for our chassis organism Vibrio natriegens using Benchlingand a personal codon optimization table that can be found on our wiki Codon Optimization Vibrio natriegensaccording to codon frequency taken from Lee et al. (2019).

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 743
    Illegal XbaI site found at 667
    Illegal XbaI site found at 1011
    Illegal XbaI site found at 1168
    Illegal SpeI site found at 303
    Illegal SpeI site found at 997
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 743
    Illegal SpeI site found at 303
    Illegal SpeI site found at 997
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 743
    Illegal BamHI site found at 1005
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 743
    Illegal XbaI site found at 667
    Illegal XbaI site found at 1011
    Illegal XbaI site found at 1168
    Illegal SpeI site found at 303
    Illegal SpeI site found at 997
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 743
    Illegal XbaI site found at 667
    Illegal XbaI site found at 1011
    Illegal XbaI site found at 1168
    Illegal SpeI site found at 303
    Illegal SpeI site found at 997
  • 1000
    COMPATIBLE WITH RFC[1000]

References

  1. Lee, H. H., Ostrov, N., Wong, B. G., Gold, M. A., Khalil, A. S., & Church, G. M. (2019). Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nature Microbiology, 4(7), 1105–1113. https://doi.org/10.1038/s41564-019-0423-8
  2. Benchling. (2023). Cloud-Based Informatics Platform for Life Sciences R&D. Benchling. https://www.benchling.com/