PROTECTED MONOMERS AND METHODS OF DEPROTECTION FOR RNA SYNTHESIS

• US 20120184724A1
• Filed: 12/28/2011
• Published: 07/19/2012
• Est. Priority Date: 09/22/2009
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Sierzchala, Agnieszka B., Dellinger, Douglas J., Dellinger, Geraldine, Myerson, Joel, Smart, Brian Phillip, Timar, Zoltan
• Application Number:
  US13/339,082
• Publication Number:
  US 20120184724A1
• Time in Patent Office: Days
• US Class Current: 536/23.1
• CPC Class Codes: C07B 59/005 Sugars; Derivatives thereof; Nucleosides; Nucleotides; Nucleic acids
• CPC Class Codes: C07H 19/067 with ribosyl as the saccharide radical
• CPC Class Codes: C07H 19/167 with ribosyl as the saccharide radical
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C07H 23/00 Compounds containing boron, silicon, or a metal, e.g. chelates, vitamin B12 esters with inorganic acids C07H11/00; metal salts, see parent compounds
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

A nucleoside monomer that is protected by a thionocarbamate protecting group and contains one or more ²H, ¹³C, or ¹⁵N isotopes in the ribose and/or base part is provided, as well as a method for making a polynucleotide that uses the same. Also provided is a polynucleotide synthesis method that employs a diamine to deprotect a protected polynucleotide.

Claims

1. A compound of the structure:

2. The compound of claim 1 wherein:

one of R¹ and R² is selected from a phosphoramidite group and a H-phosphonate group; and

one of R¹ and R² is a protecting group.

3. The compound of claim 1, wherein said thionocarbamate protecting group (PG) is selected from one of the structures:

4. The compound of claim 1, wherein said thionocarbamate protecting group (PG) is selected from one of the structures:

5. The compound of claim 1, wherein said thionocarbamate protecting group (PG) is of the

6. The compound of claim 5 wherein, R¹ is DMT, R² is beta-cyanoethyl-N,N-diisopropylphosphoramidite and BP is selected from the group consisting of U, N⁶-benzoyl-A, N⁶-isobutyryl-A, N⁶—

(N,N)-dimethylacetamidine-A, N⁶—

(N,N)-dibutylformamidine-A, N⁶-phenoxyacetyl-A, N⁶-4-tert-butylphenoxyacetyl-A, N⁴-acetyl-C, N⁴-isobutyryl-C, N⁴-phenoxyacetyl-C, N⁴-4-tert-butylphenoxyacetyl-C, N²-isobutyryl-G, N²—

(N,N)-dibutylformamidine-G, N²—

(N,N)-dimethylformamidine-G, N²-phenoxyacetyl-G and N²-4-tert-butylphenoxyacetyl-G.

7. A method of synthesizing a polynucleotide comprising at least one ribonucleotide residue, said method comprising:

contacting a nucleotide residue or a nucleoside monomer having an unprotected hydroxyl group with;

a compound of claim 2 under conditions sufficient to covalently bond said compound to said nucleotide residue or said nucleoside monomer and produce said polynucleotide.

8. The method of claim 7 further comprising:

contacting said polynucleotide with a composition comprising a sulfurization agent to produce an oxidized polynucleotide.

9. The method of claim 7 wherein said nucleotide residue or said nucleoside monomer is bound directly or indirectly to a solid support.

10. The method according to claim 7, further comprising:

cleaving said polynucleotide from a solid support to produce a free polynucleotide.

11. A polynucleotide product produced by the method of claim 7.

12. A polynucleotide comprising:

a ribonucleotide residue comprising the structure;

13. The polynucleotide of claim 12 wherein said thionocarbamate protecting group (PG) is selected from one of the structures:

14. The polynucleotide of claim 12, wherein said thionocarbamate protecting group (PG) is selected from one of the structures:

15. The polynucleotide of claim 12, wherein said thionocarbamate protecting group (PG) is of the structure:

16. A method of deprotecting a solid support bound polynucleotide comprising at least one 2′

-protected ribonucleotide residue, wherein said residue is not a 2′

-ester protected ribonucleotide, said method comprising;

contacting said polynucleotide with a composition comprising a diamine under conditions sufficient to deprotect said 2′

-protected ribonucleotide residue.

17. The method of claim 16 wherein said 2′

-protected ribonucleotide residue comprises the structure;

18. The method of claim 17 wherein said thionocarbamate protecting group (PG) is selected from one of the structures:

19. The method of claim 17 wherein said thionocarbamate protecting group (PG) is selected from one of the structures:

20. The method of claim 17, wherein said thionocarbamate protecting group (PG) is of the structure: