Methods and compounds for polynucleotide synthesis

• US 20060247430A1
• Filed: 04/29/2005
• Published: 11/02/2006
• Est. Priority Date: 04/29/2005
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc., The Board of Regents of the University of Colorado (University of Colorado System)
• Original Assignee: Agilent Technologies, Inc., The Board of Regents of the University of Colorado (University of Colorado System)
• Inventors: Caruthers, Marvin H., Dellinger, Douglas J., Dellinger, Geraldine, Kupihar, Zoltan
• Granted Patent: US 7,572,907 B2
• Time in Patent Office: Days
• US Class Current: 536/25.330
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

Abstract

Methods of forming polynucleotides are disclosed.

Claims

1. A method of forming polynucleotides, comprising:

providing a structure X selected from;

where R1 is selected from substituted carbonyls, substituted silanes and functional groups, where the functional group is selected from carbonate, ester, amide, carbamate, silane, siloxane, orthoester, acetal, and ketal;

where R2 is selected from benzyl, substituted benzyl, phenyl, substituted phenol, tertiary alkyl, and substituted tertiary alkyl;

where B comprises purine and pyrimidine bases and analogs thereof;

wherein n is from 1 to 350; and

wherein ●

is a substrate; and

oxidizing and deprotecting structure X simultaneously, wherein the aqueous buffer solution comprises an oxidant and a nucleophile at a pH of about 6 to 10.

2. The method of claim 1, wherein the aqueous buffer solution is selected from hydrogen peroxide, peracids, performic acid, peracetic acid, perbenzoic acid, chloroperbenzoic acid, hydroperoxides, butylhydroperoxide, benzylhydroperoxide, phenylhydroperoxide, and combinations thereof.

3. The method of claim 1, wherein the aqueous buffer solution comprises hydrogen peroxide.

4. The method of claim 1, wherein R1 is selected from oxycarbonate, aryl ester, alkyl ester, alkyl silane, aryl silane, alkylsiloxane, arylsiloxane, alkylarylsilane, and alkylarylsiloxane.

5. The method of claim 1, wherein R2 is selected from alkylbenzyl, dialkylbenzyl, trialkylbenzyl, thioalkylbenzyl, phenylthiobenzyl, dithioalkylbenzyl, trithioalkylbenzyl, thioalkylhalobenzyl, alkyloxybenzyl, dialkyloxybenzyl, halobenzyl, dihalobenzyl, trihalobenzyl, and esterifiedsalicyl.

6. The method of claim 1, wherein R1 is selected from oxycarbonate, aryl ester, alkyl ester, alkyl silane, aryl silane, alkylsiloxane, arylsiloxane, alkylarylsilane, and alkylarylsiloxane, and wherein R2 is selected from alkylbenzyl, dialkylbenzyl, trialkylbenzyl, thioalkylbenzyl, phenylthiobenzyl, dithioalkylbenzyl, trithioalkylbenzyl, thioalkylhalobenzyl, alkyloxybenzyl, dialkyloxybenzyl, halobenzyl, dihalobenzyl, trihalobenzyl, and esterifiedsalicyl.

7. The method of claim 1, wherein the pH of the aqueous buffer solution is about 6.5 to 8.5.

8. The method of claim 1, wherein the pH of the aqueous buffer solution is about 6.5 to 8.

9. The method of claim 1, wherein the pH of the aqueous buffer solution is about 7 to 8.

10. The method of claim 1, wherein oxidizing and deprotecting is an irreversible process.

11. The method of claim 1, wherein oxidizing and deprotecting produces a product selected from: