Methods and reagents for oligonucleotide synthesis

• US 7,205,399 B1
• Filed: 07/03/2002
• Issued: 04/17/2007
• Est. Priority Date: 07/06/2001
• Status: Expired due to Term

• Current Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Original Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Inventors: Wang, Weimin, Vargeese, Chandra
• Primary Examiner(s): LEWIS, PATRICK T
• Application Number:
  US10/190,359
• Time in Patent Office: 1,749 Days
• Field of Search: 536/22.1, 536/25.3, 536/25.31, 536/25.32, 536/25.33
• US Class Current: 536/25.3
• 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 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical

Abstract

The present invention features novel compositions, linkers, derivatized solid supports, and methods for the efficient solid phase synthesis of oligonucleotides, including RNA, DNA, RNA-DNA chimeras, and analogs thereof.

Claims

1. A method for the preparation of oligonucleotides having Formula I:

5. The method of claim 1, wherein the scaffold SP is selected from the group consisting of controlled pore glass;

nylon, polystyrene;

silica gel;

cellulose paper;

polyamide/kieselgur; and

polacryloylmorpholide.

9. The method of claim 1, wherein said Formula V is a 5′

-O-dimethoxytrityl-2′

-O-tert-butyldimethylsilyl, 5′

-O-dimethoxytrityl-2′

-O-methyl, 5′

-O-dimethoxytrityl-2′

-N-phthaloyl, 5′

-O-dimethoxytrityl-2′

-deoxy, or 5′

-O-dimethoxytrityl-2′

-deoxy-2′

-C-allyl nucleoside with or without exocyclic amine protection.

13. The method of claim 9, wherein the exocyclic amine protection is N-acetyl, N-benzoyl, or N-isobutyryl amine protection.

14. The method of claim 1, wherein the nucleoside component of Formula II is loaded onto the scaffold SP at a concentration greater than or equal to 40 umol/gram of solid support and less than 100 umol/gram of solid support.

2. A method for the preparation of oligonucleotides having Formula I:

6. The method of claim 2, wherein the scaffold SP is selected from the group consisting of controlled pore glass;

nylon, polystyrene;

silica gel;

cellulose paper;

polyamide/kieselgur; and

polacryloylmorpholide.

10. The method of claim 2, wherein said Formula V is a 5′

-O-dimethoxytrityl-2′

-O-tert-butyldimethylsilyl, 5′

-O-dimethoxytrityl-2′

-O-methyl, 5′

-O-dimethoxytrityl-2′

-N-phthaloyl, 5′

-O-dimethoxytrityl-2′

-deoxy, or 5′

-O-dimethoxytrityl-2′

-deoxy-2′

-C-allyl nucleoside with or without exocyclic amine protection.

15. The method of claim 2, wherein the nucleoside component of Formula II is loaded onto the scaffold SP at a concentration greater than or equal to 40 umol/gram of solid support and less than 100 umol/gram of solid support.

18. The method of claim 10, wherein the exocyclic amine protection is N-acetyl, N-benzoyl, or N-isobutyryl amine protection.

3. A method for the preparation of oligonucleotides having Formula IX:

7. The method of claim 3, wherein the scaffold SP is selected from the group consisting of controlled pore glass;

nylon, polystyrene;

silica gel;

cellulose paper;

polyamide/kieselgur; and

polacryloylmorpholide.

11. The method of claim 3, wherein said Formula V is a 5′

-O-dimethoxytrityl-2′

-O-tert-butyldimethylsilyl, 5′

-O-dimethoxytrityl-2′

-O-methyl, 5′

-O-dimethoxytrityl-2′

-N-phthaloyl, 5′

-O-dimethoxytrityl-2′

-deoxy, or 5′

-O-dimethoxytrityl-2′

-deoxy-2′

-C-allyl nucleoside with or without exocyclic amine protection.

16. The method of claim 3, wherein the nucleoside component of Formula X is loaded onto the scaffold SP at a concentration greater than or equal to 40 umol/gram of solid support and less than 100 umol/gram of solid support.

19. The method of claim 11, wherein the exocyclic amine protection is N-acetyl, N-benzoyl, or N-isobutyryl amine protection.

4. A method for the preparation of oligonucleotides having Formula IX:

8. The method of claim 4, wherein the scaffold SP is selected from the group consisting of controlled pore glass;

nylon, polystyrene;

silica gel;

cellulose paper;

polyamide/kieselgur; and

polacryloylmorpholide.

12. The method of claim 4, wherein said Formula V is a 5′

-O-dimethoxytrityl-2′

-O-tert-butyldimethylsilyl, 5′

-O-dimethoxytrityl-2′

-O-methyl, 5′

-O-dimethoxytrityl-2′

-N-phthaloyl, 5′

-O-dimethoxytrityl-2′

-deoxy, or 5′

-O-dimethoxytrityl-2′

-deoxy-2′

-C-allyl nucleoside with or without exocyclic amine protection.

17. The method of claim 4, wherein the nucleoside component of Formula X is loaded onto the scaffold SP at a concentration greater than or equal to 40 umol/gram of solid support and less than 100 umol/gram of solid support.

20. The method of claim 12, wherein the exocyclic amine protection is N-acetyl, N-benzoyl, or N-isobutyryl amine protection.