Rewriting Natural Decoding Rules by De Novo Genome Synthesis

Genetic incorporation of unnatural amino acids allows expansion of the chemical, physical, and biological properties of proteins and thereby of life itself. One possible way of expanding incorporation to several unnatural amino acids simultaneously is by synthesising a new genome with artificially re-defined decoding rules. This requires the de novo construction of a viable, synthetic, recoded genome, with a reduced number of codons.
To facilitate the synthesis of a whole genome, we have developed an efficient, specific, and iterative method in E. coli to replace defined genomic fragments with synthetic DNA (replicon excision enhanced recombination, REXER). We have employed this method to empirically test several codon compression schemes in vivo and the method should allow replacement of the entire 4.6-Mb E. coli genome in around 15 or less iterated REXER steps.