title: 2,2-Bis(ethoxycarbonyl)- and 2-(alkylaminocarbonyl)-2-cyano-substituted 3-(pivaloyloxy)propyl groups as biodegradable phosphate protections of oligonucleotides.
abstract: Oligonucleotides bearing biodegradable phosphate protecting groups have been synthesized on a solid support. For this purpose, two dimeric building blocks, viz. 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2,2-bis(ethoxycarbonyl)-3-(pivaloyloxy)propyl]-P-thiothymidylyl-(3',5')-thymidine 3'-[O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite] (1) and 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2-cyano-2-(2-phenylethylaminocarbonyl)-3-(pivaloyloxy)propyl]thymidylyl-(3',5')-thymidine 3'-(H-phosphonate) (2), were prepared. Phosphoramidite 1 was incorporated into an phosphorothioate oligothymidylate sequence on a base-labile hydroquinone-O,O'-diacetic acid linker (Q-linker) and on a photolabile 4-alkoxy-5-methoxy-2-nitrobenzyl carbonate linker (11). H-Phosphonate 2 was, in turn, incorporated into an oligothymidylate sequence only on the photolabile linker. Kinetics of the removal of the protecting groups by porcine liver esterase and subsequent retro aldol condensation/phosphate elimination were then studied. While the pro-oligonucleotide that contained only one phosphate protection gave the deprotected phosphorothioate oligonucleotide in a quantitative yield, the enzymatic step was markedly decelerated upon increasing the number of protection groups, and hence chain cleavage started to compete.
authors.affiliation: Department of Chemistry, University of Turku, FIN-20014 Turku, Finland. paipoi@utu.fi
authors.forename: Päivi
authors.initials: P
authors.lastname: Poijärvi
authors.forename: Petri
authors.initials: P
authors.lastname: Heinonen
authors.forename: Pasi
authors.initials: P
authors.lastname: Virta
authors.forename: Harri
authors.initials: H
authors.lastname: Lönnberg
mesh_terms: D001673:Biodegradation, Environmental; D009841:Oligonucleotides / Q000138:chemical synthesis*; D063065:Organophosphonates / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry*; D011407:Propane / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D063065:Organophosphonates; D010710:Phosphates; D011407:Propane