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 B2 is used as a capping reagent in solid-phase oligonucleotide synthesis to block unreacted reactive sites on the growing chain.

Its purpose is to prevent incomplete or unreacted chains from undergoing further coupling reactions thereby reducing the formation of unwanted truncated by-products and improving the purity of the final product.

Capping B2 is a solution containing 60% lutidine in acetonitrile where lutidine acts as a basic organic component and acetonitrile serves as the solvent. The reagent is typically introduced during the capping step to chemically deactivate unreacted functional groups before the synthesis proceeds to the next cycle.