Codon Optimization

It is recommended to compare the codon usage of the bacterial host and the protein of interest: Rare codons such as AGG, AGA, CUA, AUA, CCC, and GGA could be a problem in E. coli. Amino acids may be encoded by more than one codon, and each organism carries its own bias in the usage of the 61 available amino acid codons. In each cell, the tRNA population closely reflects the codon bias of the mRNA. If the mRNA of heterologous target genes is intended to be over expressed in E. coli, differences in the codon usage can impede translation due to the demand for one or more tRNAs that may be rare or lacking in the host. Insufficient tRNA pools can lead to translational stalling, premature translation termination, translation frameshift and amino acid misincorporation. Codon usage optimization and gene synthesis may improve the situation. Synthetic genes are available for less than $1 per base now. It provides the most suitable techniques for codon optimization.

Codon Optimization vs. Codon plus strain?

Beside codon optimization, use of codon plus strains is another way of optimizing codon usage in bacteria. Codon plus strains are transformed for one or two rare tRNA genes. However, the over expression of these genes are usually weak and therefore reduce the ability of prodution of your target protein.

In conclusion, synthetic gene with codon optimization technology improves drastically the protein expression in E. Coli without any side effects.

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