Figure 5
From: Gene Composer: database software for protein construct design, codon engineering, and gene synthesis
Use of the degeneracy of the genetic code to silently alter DNA sequences without altering the amino acid sequences. Synonymous codon changes can be categorized as (i) changes to improve DNA cloning features (left box, removal of an EcoR1 site or introduction of a BamH1 site); (ii) changes to improve RNA quality for translation (middle box, removal of a cryptic Shine-Dalgarno site, removal of base repeats, introduction of "ambush" out of frame stop codons, and removal of mRNA hairpin); and (iii) changes to improve RNA stability (right box, removal of RNase or MazF cleavage sites). The DNA encoding a target gene is shown as a solid black line, with sequences of interest in expanded view. Sequence elements with underlined codon triplets which can be altered are shown above the line and the alternative synonymous sequences are shown below the line.