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The codon optimisation challenge

DNA Codon Optimisation
3 minute read


Life's code isn't strictly in DNA, it's also where information is translated into proteins. Consequently, changing a gene's codons can disrupt its protein function. Even the FDA think this topic is important.

What is codon optimisation?

To synthesise a protein, a cell first uses the instructions stored in its DNA to generate messenger RNA (mRNA). mRNA consists of the nucleotides—adenine (A), thymine (U), uracil (G), and cytosine (C).

mRNAs are read in blocks of 3 (codons) by enzymes called ribosomes. During that process, ribosomes incorporate specific amino acids into a growing protein chain, turning DNA's code into a protein.

The curious thing about codons is that they’re synonymous.

With 4 different nucleotides, 64 possible codons exist (4^3 = 64), but proteins are usually only made up of 20 canonical amino acids. In other words, different codons encode the same amino acid. For example, GCU, GCC, GCA, and GCG all code for the amino acid alanine.

Codon redundancy has also resulted in codon usage bias, where different organisms have evolved to use codons at different frequencies. 

In biotechnology, codon optimisation aims to improve protein expression by changing synonymous codons based on an organism’s codon bias before DNA synthesis.

When codon optimisation is needed 

Codon optimisation has become useful for expressing proteins in hosts that do not naturally express that gene. It is common for scientists to express genes from eukaryotes (like humans) in easy-to-propagate systems (like bacteria). 

Humans and bacteria have very different codon usages. So, tweaking a human gene to reflect the codon usage in bacteria can improve protein yields. 

Codon optimisation can certainly increase protein expression. But it can also lead to the production of different protein conformations compared to the natural protein.

Synonymous, but not silent

When you order a specific DNA sequence, providers will check to see if it meets a set of DNA sequence complexity criteria. If the sequence is complex, many companies will reject it as it will be difficult to produce with traditional methods. One way to circumvent this problem is to change the DNA sequence but keep the same string of codons / amino acids.

Yet, synonymous codon swaps can result in a whole host of undesired effects, from disruption of post-translational modification sites to changes in the overall protein conformation, stability, and function.

The challenges of codon optimisation become louder for those developing and manufacturing protein pharmaceuticals - where efficacy and safety are crucial. Codon optimisation can increase immunogenicity and toxicity or reduce activity, potentially stopping life-saving drugs from reaching the market. 

The codon optimisation challenge has also gained interest from the FDA. They identified that changing codons increased mRNA translation and protein levels. But it also led to different protein conformations compared to the wild-type protein. 

The results in this publication have important implications for recombinant protein and gene therapies.


gSynth: Don’t settle for codon (sub)optimisation

A large percentage of DNA sequences are very difficult to produce with traditional synthesis methods. To skirt the problem, companies offer to “optimise” your codons. 

While compromising on codon usage for increased protein production is one thing, changing codon usage because of clunky technology is a major issue for researchers as well as drug developers and manufacturers. Not to mention the potential risks associated with the use of codon-optimised mRNAs to produce therapeutics.  

Unlike other DNA providers, gSynth doesn’t place limits on your synthetic sequence. There are no complexity criteria to meet, no length limitations, and you’ll never be directed to a codon sub-optimisation tool (unless you want one)! 


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