Difference between revisions of "Part:BBa K3634002:Design"

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===Design Notes===
 
===Design Notes===
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Initially, part BBa_K814001 (Minnesota iGEM, 2012) was taken and the sequence found to include a single EcoR1 illegal restriction site at bp 805. The appropriate synonymous mutation was made in silico to remove this site (a807g). This allowed for the part to be used at RFC[10] and RFC[1000] standard without codon optimisation. The sequence was then optimised using the IDT codon optimiser tool. This resulted in a new PstI and EcoR1 illegal restriction sites at bp 233 and 787 respectively. The appropriate synonymous mutation was then made in silico to remove this additional site (g231c & a789g). This allowed for the part to be used at RFC[10] and RFC[1000] standard with codon optimisation.
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Initially, part BBa_K814001 (Minnesota iGEM, 2012) was taken and the sequence found to include a single EcoR1 illegal restriction site at bp 805. The appropriate synonymous mutation was made in silico to remove this site (a807g). This allowed for the part to be used at RFC[10] and RFC[1000] standard without codon optimisation. The sequence was then optimised using the IDT codon optimiser tool. This resulted in a new PstI and EcoR1 illegal restriction sites at bp 233 and 787 respectively. The appropriate synonymous mutation was then made in silico to remove these additional site (g231c & a789g). This allowed for the part to be used at RFC[10] and RFC[1000] standard with codon optimisation.
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===Source===
 
===Source===
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IDT Codon Optimisation Tool - https://eu.idtdna.com/CodonOpt
 
IDT Codon Optimisation Tool - https://eu.idtdna.com/CodonOpt
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Balskus, E.P, Walsh, C.T. 2010. The Genetic and Molecular Basis for Sunscreen Biosynthesis in Cyanobacteria. Science. 329 (5999): p1653-1656. DOI: 10.1126/science.1193637

Latest revision as of 19:49, 20 July 2020


ATP-Grasp (ATPG) (Codon Optimised for E.coli)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Initially, part BBa_K814001 (Minnesota iGEM, 2012) was taken and the sequence found to include a single EcoR1 illegal restriction site at bp 805. The appropriate synonymous mutation was made in silico to remove this site (a807g). This allowed for the part to be used at RFC[10] and RFC[1000] standard without codon optimisation. The sequence was then optimised using the IDT codon optimiser tool. This resulted in a new PstI and EcoR1 illegal restriction sites at bp 233 and 787 respectively. The appropriate synonymous mutation was then made in silico to remove these additional site (g231c & a789g). This allowed for the part to be used at RFC[10] and RFC[1000] standard with codon optimisation.

Source

The initial genomic sequence came from Anabaena variabilis ATCC 29413 which can be obtained from part BBa_K814001 (Minnesota iGEM, 2012). The part sequence was then optimised for our chosen chassis organism, E.coli, using the IDT codon optimisation tool.

References

Minnesota iGEM 2012 - https://parts.igem.org/Part:BBa_K814001

IDT Codon Optimisation Tool - https://eu.idtdna.com/CodonOpt

Balskus, E.P, Walsh, C.T. 2010. The Genetic and Molecular Basis for Sunscreen Biosynthesis in Cyanobacteria. Science. 329 (5999): p1653-1656. DOI: 10.1126/science.1193637