Methods of synthesizing oligonucleotides using carbonate protecting groups and alpha-effect nucleophile deprotection
First Claim
1. A method of coupling a nucleoside monomer to a nucleoside, said method comprising:
- (a) coupling a nucleoside monomer having a carbonate protected hydroxyl group and a phosphoramidite group to a free hydroxyl group on the nucleoside, wherein the coupling reaction gives rise to a phosphite triester bond between the nucleoside and the coupled nucleoside monomer; and
(b) removing the carbonate protecting group from the coupled nucleoside monomer with an α
-effect nucleophile reagent through a nucleophilic attack.
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Abstract
The invention provides methods for synthesizing oligonucleotides using nucleoside monomers having carbonate protected hydroxyl groups that are deprotected with α-effect nucleophiles. The α-effect nucleophile irreversibly cleave the carbonate protecting groups while simultaneously oxidizing the internucleotide phosphite triester linkage to a phosphodiester linkage. The procedure may be carried out in aqueous solution at neutral to mildly basic pH. The method eliminates the need for separate deprotection and oxidation steps, and, since the use of acid to remove protecting groups is unnecessary, acid-induced depurination is avoided. Fluorescent or other readily detectable carbonate protecting groups can be used, enabling monitoring of individual reaction steps during oligonucleotide synthesis. The invention is particularly useful in the highly parallel, microscale synthesis of oligonucleotides.
116 Citations
19 Claims
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1. A method of coupling a nucleoside monomer to a nucleoside, said method comprising:
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(a) coupling a nucleoside monomer having a carbonate protected hydroxyl group and a phosphoramidite group to a free hydroxyl group on the nucleoside, wherein the coupling reaction gives rise to a phosphite triester bond between the nucleoside and the coupled nucleoside monomer; and (b) removing the carbonate protecting group from the coupled nucleoside monomer with an α
-effect nucleophile reagent through a nucleophilic attack. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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Specification