Coding

Part:BBa_M36402:Design

Designed by: Walter Roper, Theresa Sievert, Connor Gonzalez   Group: Stanford BIOE44 - S11   (2015-10-25)

Salicylic Acid to Methyl Salicylate Actuator #2


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 652
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 232


Design Notes

A consideration we had in regards to plasmid design was the optimization of codons. Our sequence was taken from a pre-existing part (BBa_J45005) taken from the IGEM registry. We then condon optimized this particular DNA sequence for E.coli expression using IDT's Codon Optimization Tool. This way the protein will be more efficiently translated and make more of the desired product. Also, we made sure to remove different restriction sites that would interfere with the creation or function of the enzyme, namely BsaI and SapI which is used by DNA 2.0 for Electra cloning.

Source

The plasmid vector we used was adopted from an already existing plasmid backbone for E.Coli constructed by the company DNA 2.0. Since we used an existing part within their parts catalog it allowed us to have a longer sequence for our genetic code. The original genetic sequence used for the project was taken from a pre-registered IGEM part which we took and then made slight alterations using Integrate DNA Technologies' codon optimization software to get rid of restriction sites and palindrome sequences.

This part is derived from salicylic acid carboxyl methyltransferase(SAMT) from Clarkia breweri.

References

Part:BBa_J45005, who created the actual part that we adapted to fit our project. https://www.idtdna.com/CodonOpt https://www.dna20.com/resources/genedesigner