Codon Optimization

Optimize coding sequences for expression in specific host organisms.

What is Codon Optimization?

Different organisms prefer different codons (three-nucleotide sequences) for the same amino acids. Codon optimization:

• Replaces rare codons with preferred synonymous codons

• Improves translation efficiency

• Can increase protein expression levels

• Maintains the same amino acid sequence

Running Codon Optimization

From the Construct Editor

1. Open a construct in the editor

2. Select a CDS (coding sequence) region

3. Click CO in the right sidebar

4. Configure optimization parameters

5. Click Optimize

Optimization Parameters

• Target organism: Select the expression host

  • E. coli

  • S. cerevisiae

  • CHO cells

  • HEK293

  • And more

• Optimization strategy: Balance between codon usage and other factors

Advanced Options

• Avoid sequences: Restriction sites, splice sites

• GC content: Target range

• Repeat avoidance: Minimize sequence repeats

Viewing Results

After optimization:

• New sequence replaces the original CDS

• Original sequence preserved in history

• Compare before/after in sequence viewer

Optimization Report

View details about the optimization:

• Codon Adaptation Index (CAI) before/after

• GC content change

• Modified codons list

• Removed problematic sequences

Best Practices

When to Optimize

• Expressing genes in heterologous hosts

• Low expression from native sequences

• Synthesizing genes de novo

Considerations

• Rare codons sometimes have biological function

• Consider codon context, not just frequency

• Test multiple optimization strategies

Quality Check

After optimization:

1. Verify amino acid sequence unchanged

2. Check for introduced restriction sites

3. Review GC content

4. Confirm problematic sequences removed

Optimization History

Track optimization runs:

1. Click Runs in the sidebar

2. Find codon optimization runs

3. View parameters and results

4. Compare different optimizations

API Access

Run codon optimization programmatically via the API. See Developer Documentation for details.

Troubleshooting

Optimization Fails

• Verify the region is a valid CDS

• Check that start/stop codons are present

• Ensure sequence length is divisible by 3

Unexpected Results

• Review target organism selection

• Check advanced options for conflicts

• Try different optimization strategies

Next Steps

• Sequence Viewer — View optimized sequences

• Sequence Analysis — Analyze sequence properties

• Simulation — Predict expression