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 used as a capping reagent to deactivate unreacted reactive functional groups during chemical synthesis particularly in processes such as oligonucleotide synthesis.

The primary purpose of Capping A is to acetylate residual unreacted amino or other nucleophilic functional groups preventing them from participating in subsequent coupling reactions.

Acetic anhydride is the active acetylating agent while acetonitrile (ACN) acts as the organic solvent that provides a suitable medium for the reaction and facilitates uniform reagent distribution.