Solid phase synthesis of oligonucleotides using carbonate protecting groups and alpha-effect nucleophile deprotection

• US 6,222,030 B1
• Filed: 06/22/1999
• Issued: 04/24/2001
• Est. Priority Date: 08/03/1998
• Status: Expired due to Term

• Current Assignee: Agilent Technologies, Inc., The Board of Regents of the University of Colorado (University of Colorado System)
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Betley, Jason R., Caruthers, Marvin H., Dellinger, Douglas J.
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/338,179
• Time in Patent Office: 672 Days
• Field of Search: 435/6, 536/22.1, 536/23.1, 536/24.3, 536/25.3, 536/25.31, 536/25.23, 536/25.34
• US Class Current: 536/25.3
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

The invention provides a method for synthesizing oligonucleotides using carbonate protection of hydroxyl groups and nucleophilic deprotection reagents. The deprotection reagents irreversibly cleave the carbonate protecting groups while simultaneously oxidizing the intemucleotide phosphite triester linkage, and can be used 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. Reagents and kits for carrying out the aforementioned method are provided as well.

Claims

1. A method for synthesizing oligonucleotides which comprises (a) condensing the 3′

-OH or 5′

-OH group of a support-bound nucleoside or oligonucleotide with a monomeric nucleoside phosphoramidite having a carbonate-protected hydroxyl group, to provide an intermediate in which the support-bound nucleoside or oligonucleotide is bound to the monomeric nucleoside through a phosphite triester linkage, and (b) treating the intermediate provided in step (a) with a deprotecting reagent effective to convert the carbonate-protected hydroxyl group to a free hydroxyl moiety and simultaneously oxidize the phosphite triester linkage to give a phosphotriester linkage.

2. The method of claim 1, wherein steps (a) and (b) are carried out in aqueous solution.

3. The method of claim 1, wherein step (b) is conducted at neutral to mildly basic pH.

4. The method of claim 3, wherein the deprotecting reagent used in step (b) comprises a nucleophile having a nucleophilic site and a lone electron pair on an atom adjacent to the nucleophilic site.

5. The method of claim 3, wherein step (b) is conducted at a pH of less than about 10.

6. The method of claim 1, wherein the nucleophile is a peroxide.

7. The method of claim 6, wherein the peroxide is an inorganic peroxide of the formula M⁺OOH⁻

, wherein M⁺ is a counterion.

8. The method of claim 7, wherein the counterion is selected from the group consisting of H⁺, Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺.

9. The method of claim 6, wherein the peroxide is an organic peroxide of the formula ROOH, wherein R is hydrocarbyl optionally substituted with one or more nonhydrocarbyl substituents and optionally containing one or more nonhydrocarbyl linkages.

10. The method of claim 9, wherein the peroxide has the structure of formula (V), (VI) or (VII)

in which R⁴ through R¹⁰ are hydrocarbyl optionally substituted with one or more nonhydrocarbyl substituents and optionally containing one or more nonhydrocarbyl linkages.

11. The method of claim 6, wherein the peroxide is one of t-butyl hydroperoxide, m-chloroperoxybenzoic acid, and mixtures thereof.

12. The method of claim 4, wherein step (b) is conducted at a pH that is greater than the pKa of said nucleophile.

13. The method of claim 1, wherein steps (a) and (b) are repeated until an oligonucleotide having a desired sequence and length is provided.

14. The method of claim 1, wherein synthesis is conducted in the 3′

-to-5′

direction, and step (a) involves condensation at the 5′

-OH of the support-bound nucleoside or oligonucleotide.

15. The method of claim 14, wherein the monomeric nucleoside phosphoramidite has the structure of formula (II)

wherein:

B is a purine or pyrimidine base;

R is hydrido or hydroxyl;

R¹ is COOR³, wherein R³ is substituted or unsubstituted hydrocarbyl;

R² has the structure (III)

 

wherein X is NQ¹Q² in which Q¹ and Q² are independently selected from the group consisting of alkyl, aryl, aralkyl, alkaryl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl or cycloalkynyl, optionally containing one or more nonhydrocarbyl linkages and optionally substituted on one or more available carbon atoms with a nonhydrocarbyl substituent, or wherein Q¹ and Q² are linked to form a mono- or polyheterocyclic ring, and Y is hydrido or hydrocarbyl.

16. The method of claim 15, wherein X is di(lower alkyl)amino or morpholino and Y is selected from the group consisting of lower alkyl, electron-withdrawing β

-substituted aliphatic, electron-withdrawing substituted phenyl, and electron-withdrawing substituted phenylethyl.

17. The method of claim 16, wherein Y is selected from the group consisting of methyl, β

-cyanoethyl and 4-nitrophenylethyl.

18. The method of claim 15, wherein R¹ is selected from the group consisting of o-nitrophenylcarbonyl, p-phenylazophenylcarbonyl, phenylcarbonyl, p-chlorophenylcarbonyl, 5′

-(α

-methyl-2-nitropiperonyl)oxycarbonyl (“

MeNPOC”

), 9-fluorenylmethylcarbonyl (“

Fmoc”

), 2,2,2-trichloro-1,1-dimethylcarbonyl (“

TCBOC”

) and cyano-substituted lower alkyl carbonates.

19. The method of claim 16, wherein R¹ is selected from the group consisting of o-nitrophenylcarbonyl, p-phenylazophenylcarbonyl, phenylcarbonyl, p-chlorophenylcarbonyl, 5′

-(α

-methyl-2-nitropiperonyl)oxycarbonyl (“

MeNPOC”

), 9-fluorenylmethylcarbonyl (“

Fmoc”

), 2,2,2-trichloro-1,1-dimethylcarbonyl (“

TCBOC”

) and cyano-substituted lower alkyl carbonates.

20. The method of claim 17, wherein R¹ is selected from the group consisting of o-nitrophenylcarbonyl, p-phenylazophenylcarbonyl, phenylcarbonyl, p-chlorophenylcarbonyl, 5′

-(α

-methyl-2-nitropiperonyl)oxycarbonyl (“

MeNPOC”

), 9-fluorenylmethylcarbonyl (“

Fmoc”

), 2,2,2-trichloro-1,1-dimethylcarbonyl (“

TCBOC”

) and cyano-substituted lower alkyl carbonates.

21. The method of claim 15, wherein R³ comprises a moiety that becomes fluorescent or colored upon cleavage of the carbonate —

OCOOR³.

22. The method of claim 1, wherein synthesis is conducted in the 5′

-to-3′

direction, and step (a) involves condensation at the 3′

-OH of the support-bound nucleoside or oligonucleotide.

23. The method of claim 22, wherein the monomeric nucleoside phosphoramidite has the structure of formula (X)

wherein:

B is a purine or pyrimidine base;

R is hydrido or hydroxyl;

R¹ is COOR³, wherein R³ is substituted or unsubstituted hydrocarbyl;

R² has the structure (III)

 

wherein X is NQ¹Q² in which Q¹ and Q² are independently selected from the group consisting of alkyl, aryl, aralkyl, alkaryl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl or cycloalkynyl, optionally containing one or more nonhydrocarbyl linkages and optionally substituted on one or more available carbon atoms with a nonhydrocarbyl substituent, or wherein Q¹ and Q² are linked to form a mono- or polyheterocyclic ring, and Y is hydrido or hydrocarbyl.

24. The method of claim 23, wherein X is di(lower alkyl)amino or morpholino and Y is selected from the group consisting of lower alkyl, electron-withdrawing β

-substituted aliphatic, electron-withdrawing substituted phenyl, and electron-withdrawing substituted phenylethyl.

25. The method of claim 24, wherein Y is selected from the group consisting of methyl, β

-cyanoethyl and 4-nitrophenylethyl.

26. The method of claim 23, wherein R¹ is selected from the group consisting of o-nitrophenylcarbonyl, p-phenylazophenylcarbonyl, phenylcarbonyl, p-chlorophenylcarbonyl, 5′

-(α

-methyl-2-nitropiperonyl)oxycarbonyl (“

MeNPOC”

), 9-fluorenylmethylcarbonyl (“

Fmoc”

), 2,2,2-trichloro- 1,1-dimethylcarbonyl (“

TCBOC”

) and cyano-substituted lower alkyl carbonates.

27. The method of claim 24, wherein R¹ is selected from the group consisting of o-nitrophenylcarbonyl, p-phenylazophenylcarbonyl, phenylcarbonyl, p-chlorophenylcarbonyl, 5′

-(α

-methyl-2-nitropiperonyl)oxycarbonyl (“

MeNPOC”

), 9-fluorenylmethylcarbonyl (“

Fmoc”

), 2,2,2-trichloro-1,1-dimethylcarbonyl (“

TCBOC”

) and cyano-substituted lower alkyl carbonates.

28. The method of claim 25, wherein R¹ is selected from the group consisting of o-nitrophenylcarbonyl, p-phenylazophenylcarbonyl, phenylcarbonyl, p-chlorophenylcarbonyl, 5′

-(α

-methyl-2-nitropiperonyl)oxycarbonyl (“

MeNPOC”

), 9-fluorenylmethylcarbonyl (“

Fmoc”

), 2,2,2-trichloro- 1,1-dimethylcarbonyl (“

TCBOC”

) and cyano-substituted lower alkyl carbonates.

29. The method of claim 23, wherein R³ comprises a moiety that becomes fluorescent or colored upon cleavage of the carbonate —

OCOOR³.

32. The method of claim 29, wherein step (i) is conducted at neutral to mildly basic pH.

33. The method of claim 32, wherein step (b) is conducted at a pH of less than about 10.

30. A method for making an oligonucleotide array made up of array features each presenting a specified oligonucleotide sequence at an address on an array substrate, the method comprising steps of:

providing a hydroxyl-derivatized array substrate and treating the array substrate to protect hydroxyl moieties on the derivatized surface from reaction with phosphoramidites,

then iteratively carrying out the steps of (i) applying droplets of a nucleophile having a nucleophilic site and a lone electron pair on an atom adjacent to the nucleophilic site to effect deprotection of hydroxyl moieties at selected addresses and simultaneous oxidation of newly formed internucleotide phosphite triester linkage, and (ii) flooding the array substrate with a medium containing a selected monomeric nucleoside phosphoramidite having a carbonate-protected hydroxyl group, to permit covalent attachment of the selected nucleoside to the deprotected hydroxyl moieties at the selected addresses.

31. The method of claim 30, wherein steps (i) and (ii) are carried out in aqueous solution.

34. The method of claim 30, wherein the nucleophile is a peroxide.

35. The method of claim 34, wherein the peroxide is an inorganic peroxide of the formula M⁺OOH⁻

, wherein M⁺ is a counterion.

36. The method of claim 35, wherein the counterion is selected from the group consisting of H⁺, Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺.

37. The method of claim 34, wherein the peroxide is an organic peroxide of the formula ROOH, wherein R is hydrocarbyl optionally substituted with one or more nonhydrocarbyl substituents and optionally containing one or more nonhydrocarbyl linkages.

38. The method of claim 37, wherein the peroxide has the structure of formula (V), (VI) or (VII)

in which R⁴ through R¹⁰ are hydrocarbyl optionally substituted with one or more nonhydrocarbyl substituents and optionally containing one or more nonhydrocarbyl linkages.

39. The method of claim 34, wherein the peroxide is one of t-butyl hydroperoxide, m-chloroperoxybenzoic acid, and mixtures thereof.