The synthesis scale represents the amount of starting material in µmol at the beginning of
synthesis (=loading amount of synthesis column). It is no indication for product yield to be expected!
Yields of full-length oligonucleotide are lower than the starting amount due to various reasons:
- The coupling efficiency of different bases or modifications is not 100%. (For example, the standard coupling efficiency of the 4 “normal” DNA bases is about 98-99,5%.) Coupling of modifications can be as low as 50%. Coupling efficiency is influenced by oligo length, oligo sequence and types of modifications.
- Bio-Synthesis purifies all DNA oligonucleotides by RP-HPLC or PAGE. Thus, the yield decreases again, because a majority of unwanted by-products is removed from the crude oligonucleotide.