Difference between revisions of "Part:BBa K3409013:Design"

 
 
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===Design Notes===
 
===Design Notes===
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Used the Salis Lab Algorithm to predict the Translation Initiation Rates of each start codon (according to different combinations of Promoters and Ribosome Binding Sites) to make sure the mRNA was translated in similar levels to the native MccPDI gene cluster. The presence of all 5 genes from the cluster are essential for appropriate expression and secretion of Microcin PDI.  
+
Used the Salis Lab Algorithm to predict the Translation Initiation Rates of each start codon (according to different combinations of Promoters and Ribosome Binding Sites) to make sure the mRNA was translated in similar levels to the native MccPDI gene cluster. The presence of all 5 genes from the cluster are essential for appropriate expression and secretion of Microcin PDI.
  
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[[File:MccPDI Cluster Construct ionis paris TIR.png|border|750px]]
  
  
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===References===
 
===References===
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Espah Borujeni, A., Channarasappa, A. S., & Salis, H. M. (2014). Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Research, 42(4), 2646–2659. https://doi.org/10.1093/nar/gkt1139

Latest revision as of 08:52, 19 October 2020


Microcin PDI gene cluster


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
    Illegal NheI site found at 1498
    Illegal NheI site found at 1521
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Used the Salis Lab Algorithm to predict the Translation Initiation Rates of each start codon (according to different combinations of Promoters and Ribosome Binding Sites) to make sure the mRNA was translated in similar levels to the native MccPDI gene cluster. The presence of all 5 genes from the cluster are essential for appropriate expression and secretion of Microcin PDI.

MccPDI Cluster Construct ionis paris TIR.png


Source

This is a composite part including all 5 genes of the MccPDI cluster: the mcpM, mcpI, and mcpA coding regions encoded in BBa_K3409003, BBa_K3409004, BBa_K3409005 respectively, mcpD coding region encoded in BBa_K3409006, mcpB coding region encoded in BBa_K3409007.

References

Espah Borujeni, A., Channarasappa, A. S., & Salis, H. M. (2014). Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Research, 42(4), 2646–2659. https://doi.org/10.1093/nar/gkt1139