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.

Capping B is applied during the capping step of automated oligonucleotide synthesis to treat unreacted reactive sites on the solid support after the coupling reaction.

Its primary purpose is to chemically block unreacted 5-hydroxyl groups so that they cannot participate in subsequent coupling cycles. This helps prevent the formation of truncated or deletion oligonucleotide sequences and improves the purity of the desir

The solution contains acetonitrile as the solvent pyridine as a basic component and N-methylimidazole as a catalyst mixed in a 503020 volume ratio. Together these components provide the chemical environment required for efficient acetylation and capping of unreacted sites.