A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. An example is found in the linking of two pentose (5 carbon sugar) rings to a phosphate group by strong, covalent ester bonds. Each ester bond is formed by a condensation reaction in which water is lost. This bond is a key structural feature of the backbone of DNA and RNA and links the 3’ carbon of one nucleotide to the 5’ carbon of another to produce the strands of DNA and RNA.
Phosphodiester Bond Formation
In phosphodiester formation, two hydroxyl (OH) groups on the phosphate molecule bind to the 3’ and 5’ carbons on two independent pentose sugars. These are two condensation reactions, so two molecules of water are produced. The phosphate is then bonded to the sugars by two ester bonds, hence the nomenclature of phosphodiester bond. This reaction is catalysed by ligases, such as DNA ligase during DNA replication.
A representation of the reaction is shown in the diagram below.
Phosphodiester Bond Hydrolysis
In phosphodiester hydrolysis, water is dissociated into H+ and OH-. The OH- acts as a nucleophile in the reaction. The reaction is catalysed by phosphodiesterase.
The mechanism of this reaction is given below.