L-ribo-LNA analogues

• US 7,053,207 B2
• Filed: 05/04/2000
• Issued: 05/30/2006
• Est. Priority Date: 05/04/1999
• Status: Expired due to Term

• Current Assignee: Santaris Pharma A/S (Roche Holding AG)
• Original Assignee: Exiqon A/S (Qiagen NV)
• Inventors: Wengel, Jesper
• Primary Examiner(s): EPPS -SMITH, JANET L
• Application Number:
  US09/565,699
• Publication Number:
  US 20030087230A1
• Time in Patent Office: 2,217 Days
• Field of Search: 435/6, 435/91.31, 536/27.11, 536/23.1, 544/264, 544/243, 514/45
• US Class Current: 536/25.3
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• 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 9/04 Cyclic acetals

Abstract

Provided are L-ribo bicyclic nucleotide compounds as well as syntheses of such compounds. The nucleoside compounds of the invention are useful in forming oligonucleotides that can produce nucleobase specific duplexes with complementary single stranded and double stranded nucleic acids.

Claims

1. An oligomer comprising at least one unit comprising an L-ribo-LNA composition of the general formula Ia:

2. The oligomer according to claim 1, wherein P* is a 3′

-terminal group selected from the group consisting of;

hydrogen;

hydroxy;

optionally substituted C_1-6-alkoxy;

optionally substituted C_1-6-alkylcarbonyloxy;

optionally substituted aryloxy; and

—

W—

or —

W-A′

-, wherein W is selected from —

O—

, —

S—

, and —

N(R^H)—

, and wherein R^H is selected from the group consisting of hydrogen and C_1-6-alkyl; and

wherein A′

is selected from a DNA intercalator, photochemically active group, thermochemically active group, chelating group, reporter group, and ligand.

3. The oligomer according to any one of claims 1–

2, comprising 1 to 50 units.

4. The oligomer according to any one of claims 1–

2, wherein B comprises a nucleobase or a functional group protected nucleobase.

5. The oligomer according to any one of claims 1–

2, wherein the photochemically active group, the thermochemically active group, the chelating group, the reporter group, or the ligand includes a spacer (K), said spacer comprising a chemically cleavable group.

6. The oligomer according to any of claims 1–

2, wherein any P or P* is independently selected from the group consisting of;

—

CH₂—

CH₂—

CH₂—

, —

CH₂—

CO—

CH₂—

, —

CH₂—

CHOH—

CH₂—

, —

O—

CH₂—

O—

, —

O—

CH₂—

CH₂—

, —

O—

CH₂—

CH═

, —

CH₂—

CH₂—

O—

, —

NR^H—

CH₂—

CH₂—

, —

CH₂—

CH₂—

NR^H—

, —

CH₂—

NR^H—

CH₂—

, —

O—

CH₂—

CH₂—

NR^H—

, —

NR^H—

CO—

O—

, —

NR^H—

CO—

NR^H—

, —

NR^H—

CS—

NR^H—

, —

NR^H—

C(═

NR^H)—

NR^H—

, —

NR^H—

CO—

CH₂—

NR^H—

, —

O—

CO—

O—

, —

O—

CO—

CH₂—

O—

, —

O—

CH₂—

CO—

O—

, —

CH₂CO—

NR^H—

, —

O—

CO—

NR^H—

, —

NR^H—

CO—

CH₂—

, —

O—

CH₂—

CO—

NR^H—

, —

O—

CH₂—

CH₂—

NR^H—

, CH═

N—

O—

, —

CH₂—

NR^H—

O—

, —

CH₂—

O—

N═

, —

CH₂—

O—

NR_H—

, —

CO—

NR^H—

CH₂—

, —

CH₂—

NR^H—

O—

, —

CH₂—

NR^H—

CO—

, —

O—

NR^H—

CH₂—

, —

O—

NR^H—

, —

O—

CH₂—

S—

, —

S—

CH₂—

O—

, —

CH₂—

CH₂—

S—

, —

O—

CH₂—

CH₂—

S—

, —

S—

CH₂—

CH═

, —

S—

CH₂—

CH₂—

, —

S—

CH₂—

CH₂—

O—

, —

S—

CH₂—

CH₂—

S—

, —

CH₂—

S—

CH₂—

, —

CH₂—

SO—

CH₂—

, —

CH₂—

SO₂—

CH₂—

, —

O—

SO—

O—

, —

O—

S(—

O—

)₂—

O—

, —

O—

S(—

O—

)₂—

CH₂—

, —

O—

S(O)₂—

NR^H—

, —

NR^H—

S(O)₂—

CH₂—

, —

O—

S(O)₂—

CH₂—

, —

O—

P(O)₂—

O—

, —

O—

P(O,S)—

O—

, —

O—

P(S)₂—

O—

, —

S—

P(O)₂—

O—

, —

S—

P(O,S)—

O—

, —

S—

P(S)₂—

O—

, —

O—

P(O)₂—

S—

, —

O—

P(O,S)—

S—

, —

O—

P(S)₂—

S—

, —

S—

P(O)₂—

S—

, —

S—

P(O,S)—

S—

, —

S—

P(S)₂—

S—

, —

O—

PO(R^H)—

O—

, —

O—

PO(OCH₃)—

O—

, —

O—

PO(BH₃)—

O—

, —

O—

PO(NHR^N)—

O—

, —

O—

P(O)₂—

NH^H—

, —

NR^H—

P(O)₂—

O—

, —

O—

P(ONR^H)—

O—

, and —

O—

Si(R^H)₂—

O—

.

7. A kit comprising a solid support and an oligomer according to any of claims 1–

2.

8. A kit comprising an oligomer according to any of claims 1–

2 and a label.

9. The kit according to claim 8, wherein the oligomer comprises a fluorophor and a quencher molecule.

10. A kit comprising an affinity pair comprising an oligomer according to any of claims 1–

2 and its complementary sequence.

11. An assay, comprising:

a. contacting one or more naturally occurring or synthetic double-stranded or single-stranded nucleic acids, with an oligomer according to any one of claims 1–

2 and

b. detecting binding of the oligomer to the oligonucleotide.

12. The assay according to claim 11, wherein the oligomer comprises a fluorophor and a quencher, the fluorophor providing a fluorescent signal and the quencher being positioned such that the hybridized state of the oligonucleotide can be distinguished from the unbound state of the oligonucleotide by a change in the fluorescent signal.

13. A method for making an oligomer comprising:

providing an L-Ribo LNA composition according to any of claims 1–

2 and incorporating the same into an oligomer using a phosphoramidite method, a phosphortriester method, an H-phosphonate method or an enzymatic synthesis method.

14. The method according to claim 13, wherein the L-Ribo-LNA nucleoside is included at the 3′

-end or 5-end of the oligomer.

15. The method according to claim 13, wherein the oligomer comprises one or more units according to any of claims 1–

2.

16. The method according to claim 14, wherein the method is performed in solution or on a solid phase.

17. The method according to claim 13, wherein the oligomers are linear, branched or circular.

18. The oligomer of claim 1, wherein the biradical is independently selected from

—

(CH₂)_0-1—

O—

(CH₂)_1-3—

, —

(CH₂)_0-1—

S—

(CH₂)_1-3—

, and —

(CH₂)_0-1—

N(R^N)—

(CH₂)_1-3—

.

19. The oligomer of claim 18, wherein the biradical is independently selected from —

O—

CH₂, —

S—

CH₂, and —

N(R^N)—

CH₂—

.

20. A method of using the oligomer of claim 1 or 2 as a nucleic acid binding agent, the method comprising the steps of contacting the oligomer with the nucleic acid and forming a complex to bind the nucleic acid.

21. The method of claim 20, wherein the nucleic acid is RNA.

22. The method of claim 21, wherein the RNA is selected from tRNA, rRNA, snRNA, and scRNA.

23. The oligomer of claim 1, wherein the succeeding monomer is a naturally occuring nucleoside, peptide nucleic acid (PNA), or a locked nucleic acid (LNA).

24. The oligomer of claim 1, wherein the succeeding oligomer comprises a naturally occuring nucleoside, peptide nucleic acid (PNA), or a locked nucleic acid (LNA).

25. The oligomer of claim 1, wherein the proceeding monomer is a naturally occuring nucleoside, peptide nucleic acid (PNA), or a locked nucleic acid (LNA).

26. The oligomer of claim 1, wherein the proceeding oligomer comprises a naturally occuring nucleoside, peptide nucleic acid (PNA), or a locked nucleic acid (LNA).

27. A composition having the following formula IIa:

28. The composition of claim 27, wherein the biradical is independently selected from

—

(CH₂)_0-1—

O—

(CH₂)_1-3—

, —

(CH₂)_0-1—

S—

(CH₂)_1-3—

, and —

(CH₂)_0-1—

N(R^N)—

(CH₂)_1-3—

.

29. The composition of claim 28, wherein the biradical is independently selected from O—

CH₂, S—

CH₂, and —

N(R^N)—

CH₂—

.