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Codon optimization is the cloning of DNA for protein expression according to the codon usage bias of the organism in which the protein will be expressed. This optimization is necessary to maximize the production of recombinant protein from one organism in another organism, such as E. coli. Amino acids are encoded by sequences of three nucleotides called “codons” and one amino acid will be encoded by multiple codons. For example, glycine has four codons: GGU, GGC, GGA, and GGG. Transfer RNAs (tRNA) recognize the codons and incorporate the correct amino acid during translation. Organisms that replicate rapidly, like E. coli, have genomes that prefer certain codons to simplify translation. E. coli produces few tRNAs that recognize the other “rare” codons, such as GGA for glycine. When expressing the DNA of another organism in E. coli, translation can be significantly slowed, error prone, or can fail if rare codons are abundant. Codon optimization involves the replacement of rare codons, like GGA, with the favored codons of the expression organism, like GGG for E. coli glycine, during cloning. Codon optimization extends to the selection of expression strain as well. If cloning with alternative codons is not feasible, codon optimization can be achieved through the use of expression strains engineered to produce increased levels of rare codons, such as BL21 (DE3) Codon Plus E. coli, or insect or reticulocyte expression are other alternatives. (Credit: Brooke Anderson-White)
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