> Moreover, a DNA molecule with changed codons is slightly different chemically at that place - which means a protein that might have previously attached there

> Moreover, a DNA molecule with changed codons is slightly different chemically at that place - which means a protein that might have previously attached there for some reason now might not. That shouldn't be a big concern. For one I think they only altered the base pairs inside the codons of the open reading frames. Most of the important protein binding during transcription and translation happens on regions outside the open reading frames which they left unaltered. Additionally the codons that code for the same amino acid share 2 out of the 3 bases, so they only had to alter a single base, which is usually not enough to change functionality a lot espacially when their main functional property is being translated. Disclaimer: I only have access to abstract right now