Codon optimization is crucial for achieving high-level expression of target genes by considering factors such as transcription efficiency, translation efficiency, and protein folding. The document outlines how codon usage bias and mRNA structure impact translation efficiency, and highlights the Codon Adaptation Index (CAI) and Codon Correlation Index (CCI) as metrics for optimizing gene expression. Creative Biogene offers solutions to various protein expression challenges through effective codon optimization.

1. Codon optimization technology
Tel: 1-631-626-9181 Fax: 1-631-614-7828
Email: info@creative-biogene.com
Website: http://www.creative-biogene.com

2. Codon optimization is one of the key steps in achieving
the high level expression of target gene. There are some key
factors for consideration including transcription efficiency,
translation efficiency, gene synthesis and protein folding.
Creative Biogene can optimize almost perfectly these key
factors in codon optimization.

3. A B
Some necessary consideration factors in codon optimization

4. mRNA
C D

5. tRNA abundance
Owing to different tRNAs identify several synonymous
codons and the content of these synonymous tRNAs are
different, therefore, the efficiency of translation also depends
on the number of tRNA. Preferred codons are those that can
base pair optimally with the most abundant tRNA. Generally
this involves Watson - Crick pairing or, when bases are
modified in the tRNA, some modifications in optimal binding
occur.

6. Codon usage bias
There are obvious biases of synonymous codon in bacteria,
Escherichia coli, yeast and some expression systems of higher
biological. This can directly affect the efficiency of translation. So
when one gene is expressed in a heterologous system, the codon
usage bias should be taken into account.

7. Complete mRNA structure
Next to 5’UTR and 3’UTR, The complete mRNA structure
also has significant effect on the process of protein translation.
Recently, from the systematic study of major factors which affect
the protein expression, we know that the folding of mRNA,
especially the mRNA structure near the RBS, plays an important
role in protein expression. For example, the level of protein
expression can be greatly improved by reducing the secondary
structure near the start codon.

8. The theory of gene design
Codon adaptation index (CAI)
CAI measures the proximity between the codon which is used by one gene
and the codon which is used in gene with high expression. CAI is between
0 and 1. The closer that the CAI is to 1, the higher level of gene expression
is. In general, CAI>0.8 means that gene expression has a high level.
Codon correlation index (CCI)
Researches show that codon correlation of specific host exert considerable
influence on the expression of heterologous genes. Codon correlation, such
as codon usage, double codon usage, dynamic of translation phase and GC
content, describe an integrated evolutionary environment characteristic of
species codon selection.

9. Codon optimization can solve the problem of protein expression as follow:
◆ Can not be expressed in heterologous systems;
◆ Expression level was very low;
◆ Unable to fold properly;
◆ Lose functional activity.