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The General Introduction of Codon Optimization

Optimal gene expression relies on systematic design of the gene, vector, host system, and culture conditions. Efficient expression is achieved when the gene, vector, and host system are synergistically constituted. Codon optimization algorithm plays a critical role. With our extensive experience in synthetic biology, Synbio Technologies has pioneered codon optimization technology. By optimizing the sequence design, NGCodon enhances protein expression efficiency, ensuring more rational and effective genetic expression.

The codon optimization platform takes into consideration the following factors (not limited):

• Cryptic splice sites
• Poly(N)
• Internal RBS sites
• Repeats
• GC content
• Codon preference
• Hairpin structure
• RNA secondary structures
• Translation initiation and termination efficiency
• Killer sequences

Highlights

Proprietary Algorithm
Customizable Optimization Solutions
Improved Protein Expression
Free Tools for Fast Optimization
Wide Range of Optimizable Species

Case Study

I. Optimization of Codons to Resemble Preferred Codon Usage for a Particular Organism

The X and Y axis in the graph below (Figure 1) represent the genetic codons and its relative usage frequency of codons respectively. The codon usage (orange bars) is rather dispersed compared to the optimized one (green bars). Synbio technologies has a proprietary NGCodon optimization algorithm that greatly improves codon usage efficiency and satisfies different customers’ requirements.

Figure 1. Comparison of codon usage frequencies before and after optimization

II. Improved Protein Expression Level after Codon Optimization

The target protein was expressed in E.Coli system after codon optimization.

Figure 2. SDS-PAGE results showing target protein expression before and after codon optimization

FAQs

What are the methods of peptide synthesis?

The standard methods of peptide synthesis are solid-phase synthesis, liquid-phase synthesis, and combinatorial chemistry.

Why are the peptides invisible in the vials?

1. Low Concentration: The concentration of peptide might be too little to be seen with the naked eyes.

2. Lyophilization: Peptides are often lyophilized into a powder which can appear as a thin, invisible film at the bottom or sides of the vial.

3. Clear or White Appearance: Some peptides are clear or white, blending in with the vial and making them hard to see.

4. Solubility: If the peptide is dissolved in a solution, it may be completely clear, making it invisible.

What purity does my peptide need to be?

1. Research and Development: For basic research, a purity of 70-90% is often sufficient.
2. Biological Assays: For cell-based assays or biochemical studies, a higher purity, typically around 95%, is preferred to ensure accurate results.
3. Therapeutic Applications: For clinical or therapeutic use, peptides usually need to be of very high purity, often exceeding 98-99% to meet regulatory standards and ensure safety and efficacy.
4. Mass Spectrometry: For mass spectrometry analysis, high purity, often ≥95%, is essential to avoid interference from contaminants.

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