Why are alkaline phosphatases used in cloning protocols? What is a typical protocol for dephosphorylation of nucleic acids?
Alkaline phosphatases are used to dephosphorylate the 5' ends of DNA. In cloning, it is used to prevent self-ligation of vector DNA. Standard ligation of DNA with ligase requires a 5' phosphate to be present on at least one of the ends being joined. When a DNA insert containing phosphates on both 5' termini is added to a dephosphorylated vector, the insert will be efficiently ligated into the vector, but the vector will not be able to self-ligate. Thus, dephosphorylation of vector lowers the number of background colonies containing vector without insert.