Use of the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) and related protecting groups in oligoribonucleotide synthesis: stability of internucleotide linkages to aqueous acid

Open Access
Publisher Website
Google Scholar
Abstract
The internucleotide linkage of uridylyl-(3′→5′)-uridine (r[UpU]) does not undergo detectable hydrolytic cleavage or migration in ca. 24 hr in 0.01 mol dm-3 hydrochloric acid (pH 2.0) at 25°C. However, unlike r[UpU] and previously examined relatively high molecular weight oligoribonucleotides, oligouridylic acids are very sensitive to aqueous acid under the latter conditions (pH 2.0, 25°C). Thus when the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) group is used to protect the 2′-hydroxy functions in the synthesis of r[(Up)9U] and r[(Up)19U], the final unblocking process must be carried out above pH 3 if hydrolytic cleavage and migration are to be avoided. It is demonstrated that the rate of acid-catalyzed hydrolysis of the internucleotide linkages of oligoribonucleotides is sequence dependent. As Fpmp groups may be virtually completely removed from average partially-protected oligoribonucleotides within ca. 24 hr at pH 3 and 25°C, it is concluded that Fpmp is a suitable 2′-protecting group even in the synthesis of particularly acid-sensitive sequences.