Allyl Group as a Protecting Group for Internucleotide Phosphate and Thiophosphate Linkages in Oligonucleotide Synthesis:  Facile Oxidation and Deprotection Conditions

Abstract

[reaction: see text] The allyl group, which serves as a protecting group for an internucleotide bond for both phosphates and phosphorothioates, can be easily removed by good nucleophiles under weakly basic or neutral conditions. For a practical synthesis on solid support, camphorsulfonyloxaziridine was used as the oxidizing agent for synthesizing DNA, while the Beaucage reagent was used for preparing phosphorothioate oligomers. Both types of oligonucleotides were easily deprotected by concentrated ammonium hydroxide containing 2% mercaptoethanol.

Synthesis of polyphosphodiesters by ring‐opening polymerization of cyclic phosphates bearing allyl phosphoester protecting groups

“…Finally, the selective deprotection of the polyphosphate was studied. In the previous work of Manoharan et al in the field of nucleotide synthesis, the allyl‐protecting group was cleaved by an aqueous solution of concentrated ammonium hydroxide. This deprotecting agent is not suitable because polyphosphates could be degraded by hydroxides and we could expect a high risk of backbone degradation.…”

DNA Duplex Stability of the Thio-Iso-Guanine•Methyl-Iso-Cytosine Base Pair

“…Here, the oxidizing agent was changed from 0.02 M I 2 /THF to 0.5 M (camphorylsulfonyl)-oxaziridine/CH 3 CN. [11] Lastly, oligonucleotides-containing iso-Gs were deprotected with DTT/NH 4 OH instead of NH 4 OH alone. Oligonucleotides were synthesized with an ABI 391 or 394 synthesizer.…”

Strategies Useful for the Chemical Synthesis of Oligonucleotides and Related Compounds

“…Therefore, more reliable methods applicable under nonbasic and nonaqueous conditions have been developed to date. These include the use of a tert-butyl hydroperoxide (TBHP)/toluene solution in acetonitrile [34,35] [36], (1S)-(+)-(10-camphorsulfonyl)oxaziridine (CSO) [37,38] in acetonitrile, 2-butanone peroxide in dichloromethane [39], and N-bromosuccinimide (NBS)-dimethylsulfoxide (DMSO) in acetonitrile [40]. Among these approaches, TBHP in toluene and 2-butanone peroxide oxidation are most recommended.…”

“…This is problematic, especially when the synthesis is conducted on a large scale for the production of therapeutic agents such as phosphorothioates. Thus, the ISIS group developed a method of deprotecting the allyl group by use of concentrated ammonia containing 2% mercaptethanol instead of using the Pd(0) catalyst [59].…”