Depurination is defined as the cleavage of the glycosidic bond attaching a purine base to the sugar moiety. Electron withdrawing acyl protecting groups like benzoyl and isobutyryl on the purine amino group(s) destabilize the glycosidic bond, whereas electron donating formamidine protecting groups stabilize the glycosidic bond. The consequence of depurination during oligonucleotide synthesis is the loss of the purine base to form an internucleotide linkage containing the abasic sugar at that position. This site is stable during further synthesis cycles but, upon deprotection with basic reagents, the oligonucleotide is cleaved at that position leading to two shorter fragments. The fragment towards the 5’ terminus still contains the DMT group. If DMT-ON purification is being used, the depurinated fragments are co-purified along with the full length product as truncated oligonucleotides.
The most commonly used dA-CE Phosphoramidite containing benzoyl protecting groups suffers substantial degradation by depurination after excessive exposure to TCA. At the same time, two depurination resistant dA monomers, protected with diethylformamidine (def) and dimethylacetamidine (dma), are essentially stable to depurination during the same exposure to TCA.
Both new depurination resistant dA monomers (def and dma protected), were rapidly deprotected in ammonium hydroxide and are fully compatible with regular deprotection strategies. Def-protected-dA was rapidly deprotected with AMA at 65° in 20 minutes, which makes it fully compatible with regular AMA deprotection. In contrast, the dma-protected-dA required 80 minutes with AMA at 65° for complete deprotection.
Dmf-dG is also a depurination resistant CE Phosphoramidite with the isobutyryl group of the original monomer replaced with dimethylformamidine (dmf).
Although depurination does occur in regular oligonucleotide synthesis, the degradation is at an extremely low level. However in certain other circumstances, depurination may become more significant, such as synthesis of long oligos, chip-based synthesis, and large-scale synthesis.