For each synthesis cycle up to 1 to 2 % of free 5-hydroxy groups remain after the phosphoramidite coupling step has been completed. By running a subsequent Capping step using an anhydride these free hydroxyl groups are converted to acetates and are hindered from further chain elongation and formation of long oligonucleotides with incorrect sequences. For optimal acetylation a solution of acetic anhydride in Tetrahydrofuran or acetonitrile (Capping A) will be mixed in situ during reaction with a catalytic acting solution of N-methylimidazole (Capping B). Additives such as pyridine and lutidine function as mild bases to enhance the efficiency of the capping reaction.

it is generally used as a capping reagentsolution in chemical synthesis and polymer or oligonucleotide processing to deactivate or cap unreacted reactive functional groups.

The main purpose of Capping B is to react with residual unreacted reactive groups and prevent them from participating in subsequent reactions thereby improving the selectivity and quality of the desired product.

The N-methylimidazole (NMI) acts primarily as a nucleophilic catalystbase and promotes the capping reaction while THF serves as the organic solvent to provide a homogeneous reaction medium.