Synbio Technologies’ Codon Optimization Strategy

Translation is the last step in protein synthesis that results in stable proteins from DNA replication, mRNA transcription and modification in cells. Codon optimization aims to increase the yield of protein expression in different organisms by rebalancing usage of synonymous codons. High quality protein has a wide range of applications, including study of protein structure and function, biological research, clinical medicine.

Higher protein yield in turn can be a valuable feature in a wide range of applications, including…

  • Codon usage bias
  • There are 64 codons in total, 61 codons encode 20 amino acids and the remaining 3 are stop codons. Redundant codons exist for most amino acids; multiple different codons encode the same amino acid. In general, the expression of heterologous proteins is negatively correlated with the occurrences of rare codons. In simpler terms, when the codon usage of a target protein in its native organism differs significantly from the average codon usage of the expression host, this could cause problems during expression. Therefore, an effective solution is to replace rare codons in the original sequences with major codons that are preferred in the host.

  • The secondary structure of mRNA
  • Translation refers to the conversion of nucleic acid sequences into amino acid sequences, and is greatly affected by complex secondary structures in mRNA. The translation of codons in the non-structural part of the α-helix is the rate-determing step in the translational process. Identifying the hairpin structure in an mRNA can lead to significant optimizations of translational efficiency for that mRNA.

  • Changing regulatory elements and restriction sites
  • The process of optimizing protein expression is affected by many factors: not only basic DNA transcription and translation, but also a series of regulatory elements. By incorporating signal peptides, tags, other regulatory elements, or appropriate restriction sites during gene synthesis, expression of synthetic genes in heterologous host organisms can be significantly improved.

Synbio Technologies NGTM Codon Optimization software can intelligently optimize codon usage to effectively improve protein expression, in order to better meet the needs of scientific research and industrial production.