All parts non-native to E. coli were codon optimised using the IDT codon optimisation tool (https://eu.idtdna.com/CodonOpt). Codon optimisation ensures that the codons within our parts correspond to the codon bias of our chassis. The pre-existing biobricks for the parts used are listed below, as well as the codon optimised replacement created by our team.
|Part Name||Pre-existing BioBrick||Codon Optimised Replacement|
|3-Dehydroquinate Synthase (DHQS)||BBa_K814000||BBa_K3634000|
|Nonribosomal Peptide Synthetase (NRPS)||BBa_K814003||BBa_K3634003|
|Heme Oxygenase (ho1)||BBa_K2328062||BBa_K3634007|
|Phycocyanobilin:Ferredoxin Oxidoreductase (pcyA)||BBa_I15009||BBa_K3634008|
For some of these parts, in silico site-directed mutagenesis was carried out as to remove illegal BioBrick standard restriction sites introduced by the IDT codon optimisation tool.
Alongside creating new codon optimised parts, we also added additional information from the literature to the following parts:
- BBa_K1725400 *
- BBa_K1725410 *
- BBa_K1725420 *
* the UirS/UirR system formed part of our early gene circuit design but was omitted from our final design.