Methods of synthesizing oligonucleotides using carbonate protecting groups and alpha-effect nucleophile deprotection
First Claim
1. A method of synthesizing an oligonucleotide on a solid support comprising:
- (a) coupling a nucleoside monomer having a protected hydroxyl group to a free hydroxyl group on a support-bound nucleoside monomer, wherein the hydroxyl group on the coupled nucleoside monomer is protected with a carbonate protecting group and the coupling reaction gives rise to a phosphite triester bond between the support-bound nucleoside monomer and the coupled nucleoside monomer; and
(b) contacting the coupled nucleoside monomer with an alpha-effect nucleophile to simultaneously (i) irreversibly remove the carbonate protecting group, and (ii) oxidize the phosphite triester linkage to a phosphotriester linkage.
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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.
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30 Claims
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1. A method of synthesizing an oligonucleotide on a solid support comprising:
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(a) coupling a nucleoside monomer having a protected hydroxyl group to a free hydroxyl group on a support-bound nucleoside monomer, wherein the hydroxyl group on the coupled nucleoside monomer is protected with a carbonate protecting group and the coupling reaction gives rise to a phosphite triester bond between the support-bound nucleoside monomer and the coupled nucleoside monomer; and (b) contacting the coupled nucleoside monomer with an alpha-effect nucleophile to simultaneously (i) irreversibly remove the carbonate protecting group, and (ii) oxidize the phosphite triester linkage to a phosphotriester linkage. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30)
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Specification