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 used as a capping reagent in oligonucleotide synthesis particularly during solid-phase synthesis to cap unreacted reactive sites on the growing oligonucleotide chain.

Its primary purpose is to prevent unreacted hydroxyl groups from participating in subsequent synthesis cycles thereby reducing the formation of deletion sequences and improving the purity of the final oligonucleotide product.

In this formulation acetonitrile serves as the solvent while 26-lutidine and N-methylimidazole provide the basic and catalytic environment required for efficient capping. The solution reacts with unreacted sites so that they can no longer undergo further chain elongation.