Protecting groups for RNA synthesis

• US 8,242,258 B2
• Filed: 12/03/2007
• Issued: 08/14/2012
• Est. Priority Date: 12/03/2006
• 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: Dellinger, Douglas J., Stell, Brian, Caruthers, Marvin H.
• Primary Examiner(s): OLSON, ERIC
• Application Number:
  US11/949,667
• Publication Number:
  US 20080194502A1
• Time in Patent Office: 1,716 Days
• Field of Search: None
• US Class Current: 536/26.7
• CPC Class Codes: C07H 19/00 Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Aspects of the invention include 2′ protected nucleoside monomers that are protected at the 2′ site with orthoester-type protecting groups. The 2′ protected monomers also include a second, aryl carbonate-type, protecting group. Aspects of the invention further include nucleic acids that include the protecting groups of the invention, as well as methods of synthesizing nucleic acids using the protecting groups of the invention.

Claims

1. A ribonucleoside monomer having the structure:

2. The ribonucleoside monomer according to claim 1, wherein Q² and Q³ are each a sulfur atom.

3. The ribonucleoside monomer according to claim 1, wherein Q¹ is an oxygen atom.

4. The ribonucleoside monomer according to claim 1, wherein R⁴ is a phenyl group or a substituted phenyl group.

5. The ribonucleoside monomer according to claim 4, wherein R⁴ has the structure:

6. The ribonucleoside monomer according to claim 5, wherein R⁴ has the structure:

7. The ribonucleoside monomer according to claim 1, wherein R⁵ and R⁶, together with Q², Q³ and the carbon to which Q² and Q³ are attached are cyclically linked to form a heterocyclic group.

8. The ribonucleoside monomer according to claim 7, wherein R³ has the structure:

9. The ribonucleoside monomer according to claim 8, wherein R³ has the structure:

10. A method of coupling a ribonucleoside monomer to a nucleoside residue comprising:

(a) providing a nucleoside residue having an unprotected hydroxyl group and the ribonucleoside monomer of claim 1, wherein;

one of R¹ or R² is a phosphoramidite group; and

the other of R¹ or R² is an aryl carbonate-type hydroxyl protecting group; and

(b) contacting said nucleoside residue with said ribonucleoside monomer under conditions sufficient to covalently bond said ribonucleoside monomer to said nucleoside residue via a phosphite triester linkage to produce said coupled nucleoside residue-ribonucleoside monomer.

11. The method according to claim 10, wherein said method further comprises:

contacting said coupled nucleoside residue-ribonucleoside monomer with a peroxide, thereby oxidizing said phosphite triester linkage and deprotecting said aryl carbonate-type hydroxyl protecting group to produce a polynucleotide intermediate.

12. The method according to claim 11, wherein said method further comprises reiterating said providing step and said contacting steps until a desired polynucleotide sequence is obtained.

13. The method according to claim 12, wherein said method further comprises removing said orthoester-type 2′

hydroxyl protecting group of said polynucleotide by contacting said polynucleotide with an acid.

14. The method according to claim 12, wherein said nucleoside residue is covalently bound to a solid support.

15. The method according to claim 14, wherein said method further comprises cleaving said polynucleotide from said solid support to produce a free polynucleotide.

16. The method according to claim 15, wherein said method further comprises chemically modifying said free polynucleotide to produce a modified polynucleotide.

17. The method according to claim 16, wherein said method further comprises combining said modified polynucleotide with a pharmaceutically acceptable vehicle.

18. The method according to claim 15, wherein said method further comprises combining said free polynucleotide with a pharmaceutically acceptable vehicle.

19. The method according to claim 14, wherein said method further comprises chemically modifying said polynucleotide to produce a modified polynucleotide, and then cleaving said modified polynucleotide from said solid support.

20. A polynucleotide having the structure of Formula (I):