What is a phosphoramidite?

A phosphoramidite is the actual building block we use to chemically synthesize oligonucleotides. It usually consists of a protected nucleoside with a 3’ phosphitylating reagent, where phosphorus is in the trivalent state and protected with a stable amine and ester. The amine is activated during synthesis with acid, producing a good leaving group. The phosphorus is then attacked by the 5’ hydroxyl of the growing oligonucleotide chain. After coupling, the phosphorus is oxidized to the pentavalent phosphorus state using iodine and water.