This algorithm determines the Shine-Dalgarno (SD) and Anti-Shine-Dalgarno (ASD) sequences for development of orthogonal ribosomes.
Steps 4 and 5 Details
Calculate binding energies of all remaining candidate ASD with the wild-type SD sequence; discard those with less than -1 kcal binding energies. (Switched from Chubiz and Rao method[1] to improve time-efficiency).
Function description: narrow_crossbinding
This function again determines the wild type ASD and SD sequences for an organism. It then determines the binding energies between all of the candidate ASD sequences and the wild-type SD sequence. Those candidates with binding energies less than -1 kcal/mol are discarded, because this means that the orthogonal ribosomes produced using those ASD sequences are more likely to bind with the host’s SD sequence, which means they would not be truly orthogonal (separate from the host’s own resources) in nature. The concept is illustrated in figure 5 below.
Figure S3. Ensure orthogonality of chosen sequences.
