Codon Optimization
- Keeping GC ratio around 50%;
- Remove cis-acting DNA sequences such as internal TATA-boxes, chi-sites, and ribosomal entry sites AGGAGG, AGGAGGT, TAAGGAGG; AT-rich or GC-rich sequence stretches; repeat sequences; and RNA
- secondary structures
- ATAAGA to ATCCGT; AGAATA to CGCATT; ATAAGG to ATTCGT; AGAAGG to CGTCGC
- Add two stop codons TAATAA
- Append another strong terminator to the end of your DNA sequence
Transcriptional Efficacy:
GC content CpG dinucleotides content Cryptic splicing sites Negative CpG islands SD sequence TATA boxes Terminal signal
Translation Efficiency:
Codon usage bias GC content mRNA secondary structure Premature PolyA sites RNA instability motif (ARE) Stable free energy of mRNA Internal chi sites and ribosomal binding sites
Protein Refolding:
Codon usage bias Interaction of codon and anti-codon Codon-context RNA secondary structures