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 reaction and dilution solvent mixture in organic and solid-phase synthesis processes particularly where a polar organic solvent containing a basic component is required.

Its purpose is to provide a controlled solvent environment and basic medium that can help dissolve reagents maintain suitable reaction conditions and facilitate reactions involving pyridine-sensitive or pyridine-mediated chemistry.

Solvent Mix Pyridine in ACN consists of 60% pyridine and 40% acetonitrile by volume. Pyridine acts as a basic polar organic component and can also function as a reagent or catalyst in certain reactions while acetonitrile serves as a polar aprotic solvent that helps adjust the overall solvent properties and viscosity of the mixture.