| Products/Services Used | Details | Operation |
|---|---|---|
| Codon Optimization | SyGS v1.0 is a computational sequence-refactoring tool that automates the standardization of gene sequences to have the broadest compatibility with current synthetic biology cloning strategies (Fig 1). The program searches for restriction sites used in BioBrick (EcoRI, XbaI, SpeI, PstI, ApoI, MfeI, AvrII, NheI, NsiI, SbfI, NotI), BglBrick (EcoRI, BglII, BamHI, XhoI), MoClo (BsaI, BbsI, MlyI), and GoldenBraid (BsaI, BsmBI, BtgZI) cloning. Additionally, all E. coli chi sites are removed to reduce recombination 20 and enable further engineering22. All start codons are unified to ATG and all stop codons are set to TAA. NdeI sites are also removed for ease of assembly analysis and cloning at the ATG start codon. Once identified, silent mutations to a codon within each targeted site are made to an alternative codon with its choice based on removing the target site and matching the statistics of the codon usage of the organism [http://www.genscript.com/tools/codon-frequency-table], although a minimal algorithm can be used to remove all sites by changing one codon to its most frequently used codon (Table 1). | Get A Quote |
Four cloning standards in synthetic biology are BioBrick, BglBrick, MoClo and GoldenBraid, with each requiring their constitutive parts be compatible with the associated restriction enzymes. To standardize parts for the broadest usage, it would be useful to synthesize genes that are simultaneously compatible with all 4 popular assembly strategies. Here it is shown that using a defined set of rules, implemented in a computational program, any protein coding sequence can be made compatible with all four standards by silent mutations. Using a coding sequence as an input, all BioBrick, BglBrick, MoClo, and GoldenBraid restriction sites and chi recombination hot spots can be destroyed with silent mutations that appr... More
