More possibilities than atoms in the universe

If you want to draw the DNA sequence of a protein with 881 amino acids, you will end up with 2x 10⁴²⁰ possibilities to do so (calculating with an average number of 3 triplets per amino acid). We estimate the total number of atoms in the universe to be around 10⁸⁰. So why has nature chosen the mRNA to encode amino acids?

At this stage we cannot supply the answer to this question. But what we definitely know is that codon bias exists. That means that different codons are unequally used in different organisms since varying amounts of individual mRNA's are available.

This codon bias often leads to low expression rates if you transfect your gene of interest in another organism.

How does it work?

1. GENEius assembles the DNA sequence randomly and compares the results to an input codon usage table
2. GENEius harmonises the used codons - frequently used codons are used more often in the resulting gene sequence than less frequently used codons
3. GENEius avoids very rare codons
4. GENEius also checks for bad motifs (read more)
5. GENEius uses a specific algorithm to determine the optimal sequence. Each optimisation step leads to a new DNA sequence.

Try our GENEius system. Since it is integrated in our Ecom shop, you can easily profit from all the advantages each time you order a gene.

Example of codon usage adaption

See the two codon usage tables on the right sidebar.

In a human gene the amino acid arginine is mainly encoded by cgc and cgt (left column, click to enlarge). If E.coli is used  as a host organism for gene expression, the unmodified human sequence will only yield minor amounts of proteins. This small yield reflects the limited number of tRNA available to translate the codons into the respective amino acid sequence.

A vast amount of tRNAs are available if you optimise the codon usage - or better adapt the sequence of the template of origin to the host organism. Using our example above, preferably selecting cgg, aga and agg codons instead will ensure there are sufficient amounts of tRNAs to produce high protein yields.

Small effects make a big difference. The right balance in the codon usage of the host and the original organism's genome is critical for successful gene expression.