Fig. 2. Mechanisms for solid-phase oligonucleotide synthesis and depurination.

A, Schematic representation of phosphoramidite solid-phase oligonucleotide synthesis. The method sequentially adds 5ʹ-dimethoxytrityl-protected nucleoside phosphoramidites 4 upon activation by tetrazole to ensure sequence-specific strand elongation^35–39. The steps of the process include a synthesis cycle comprising: protonation (step a), detritylation (step b), tetrazole activation and coupling (step c), capping of unreacted nucleotides on the resin (step d), oxidation (step e), detritylation (step f), which is repeated n times (step g), and followed by cleavage from the support (step h) and deprotection (step i) to yield a desired DNA 10. B, Mechanism of acid-catalysed depurination as a common side reaction in chemical synthesis^62–64,163, comprising protonation (step j), depurination (step k), hydrolysis (step l) and elimination (step m). Resulting apurinic site 14 owing to the loss of a purine base (for example, adenine 13) is readily hydrolysed (steps c and d) during the basic work-up steps required for removing base protecting group (PG).