Reagents and methods used in deprotection of 3'-O-amino polynucleotides

A method of synthesizing a polynucleotide, the method comprising the steps of:

• (a) providing initiators which are polynucleotides having each a free 3′-hydroxyl;
• (b) repeating in a reaction mixture, until the polynucleotide is formed, cycles of:
• (i) contacting under elongation conditions the initiators or elongated fragments having free 3′-hydroxyls with a 3′-O—NH2 nucleoside triphosphate and a polymerase, so that the initiators or elongated fragments are elongated by incorporation of a 3′-O-amino nucleoside triphosphate to form 3′-O-amino elongated fragments, and
• (ii) deprotecting the elongated fragments to form elongated fragments having free 3′-hydroxyls;
• wherein the deprotecting is performed by contacting the elongated fragments with an effective amount of at least one phosphonate compound, wherein at least one phosphonate compound is: