Phosphoryl transfer reactions involving phosphodiester bonds. In three common variants of this reaction described in this chapter, the nucleophilic hydroxyl group (X–OH) is (1) water, leading to hydrophilic cleavage; (2) the hydroxyl group of a Ser or Tyr residue in the active site of an enzyme, leading to the formation of a covalent phosphodiester linkage to that enzyme at the expense of the existing phosphodiester bond between nucleotides; or (3) the 3′-hydroxyl group of another nucleotide, leading to formation of a new phosphodiester bond at the expense of the existing one. The second and third processes are generally isoenergetic, or nearly so. The closely related phosphoryl transfer reactions leading to formation of phosphodiester bonds in the active sites of DNA and RNA polymerases are illustrated in Chapters 11 and 15, respectively.