Coding
Fast Super

Part:BBa_K1506002:Design

Designed by: Sam Krug, Clay Swackhamer, Ashlee Smith, Emily Sileo   Group: iGEM14_Penn_State   (2014-10-01)


Design Notes

Codon_usage_table.JPG


Fast codons show a positive correlation between frequency and TIR, slow codons show a negative correlation. Codons whose frequency increases with TIR are defined as fast codons. Those with declining frequency in relation to TIR are slow codons, and those with no correlation are defined as independent of TIR. This can be viewed in the figure above as the slope of the graphs for each codon showing ratio and TIR. If ratio increases with TIR, the codon is fast, and the graph displays positive slope. Slow codons slow negative slope, and TIR independent codons show essentially no slope.


Source

We designed the coding sequence in MatLab using the software to break up the initial coding sequence and then substitute each codon for the fastest translation rate for that specific amino acid. After these were designed, we ordered them as gBLOCKS from IDT DNA. Custom software was developed to take the coding sequence of Superfolder GFP (part BBa_I746916) and replace all codons with “fast” degenerate codons.


References

Ng, C. Y., Farasat, I., Zomorrodi, A. R., Maranas, C. D. & Salis, H. M. Model-guided construction and optimization of synthetic metabolism for chemical product synthesis. Synthetic Biology Engineering Research Center Spring Retreat (2013), Berkeley, CA.

Optimized Superfolder GFP - only fast codons


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 664
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 664
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 664
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 664
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 664
  • 1000
    COMPATIBLE WITH RFC[1000]