Due to the redundant nature of the DNA code more than one triplet codon can code for an amino acid e.g. Arginine - CGT, CGC, CGA, CGG, AGA, AGG. The frequency of these codons differs across species. It is therefore possible to optimize a DNA sequence so it contains the same frequency of codons as seen in the organism where the gene will be expressed. The optimization also helps in the reduction of high GC regions and repeat regions in the gene.

This type of optimization is only possible however when the gene to be synthesized (or part of it) is coding for a protein sequence and therefore has codons that can be manipulated in this way. A non-coding stretch of DNA does not contain codons coding for an amino acid and therefore an optimization exploiting the redundancy of DNA cannot be done.