Oligonucleotide analogs having modified dimers

• US 6,849,723 B2
• Filed: 07/15/2002
• Issued: 02/01/2005
• Est. Priority Date: 06/06/1995
• Status: Expired due to Fees

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Cook, Phillip Dan, Bhat, Balkrishen, Manoharan, Muthiah
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US10/195,211
• Publication Number:
  US 20030181693A1
• Time in Patent Office: 932 Days
• Field of Search: 536/23.1, 536/22.1, 536/25.3, 536/24.3
• US Class Current: 536/22.1
• 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: C12N 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/318 where the PO2 is completely replaced, e.g. MMI or formacetal
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/345 having at least two different backbone modifications
• CPC Class Codes: C12N 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: Y02P 20/582 Recycling of unreacted starting or intermediate materials

Abstract

Modified dimers having a ribose sugar moiety in the 5′ nucleoside and a 2′ modified sugar in the 3′ nucleoside are provided. The modified dimers are useful in the preparation of oligonucleotide analogs having enhanced properties compared to native oligonucleotides, including increased nuclease resistance, enhanced binding affinity and improved protein binding.

Claims

1. A compound having Formula:

wherein;

Z is a phosphodiester or phosphorothioate intersugar linkage;

each T₁ and T₂ is, independently, —

OH, —

OR₁, —

CH₂R₁, —

NH(R₁), —

SH, —

SR₁, or a blocked hydroxyl;

R₁ is C₁-C₁₂ alkyl;

B_X is a heterocyclic base; and

X is F, —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂ when Z is a phosporothioate intersugar linkage or X is —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂ when Z is a phosphodiester intersugar linkage.

2. The compound of claim 1 wherein X is —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂.

3. The compound of claim 2 wherein X is —

O—

CH₂—

CH₂—

O—

CH₃.

4. An oligonucleotide analog comprising at least one moiety having Formula:

wherein

each Z is a phosphodiester or phosphorothioate intersugar linkage;

T₃ is a nucleotide other than a ribonucleotide, a nucleoside other than a ribonucleoside, a hydroxyl, a blocked hydroxyl, or an oligonucleotide wherein the 3′

-terminal nucleotide of said oligonucleotide is not a ribonucleotide;

T₄ is a nucleotide, a nucleoside, an oligonucleotide, a hydroxyl or a blocked hydroxyl;

with the proviso that at least one of said T₃ and T₄ is not a hydroxyl, or blocked hydroxyl;

B_X is a heterocyclic base; and

each X is F, OCH₃, —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂.

8. The oligonucleotide analog of claim 4 having a length of from 1 to 200 subunits.

9. The oligonucleotide analog of claim 4 having a length of from 10 to 25 subunits.

10. The oligonucleotide analog of claim 4 having a length of from 12 to 20 subunits.

5. The oligonucleotide analog of claim wherein at least one X is OCH₃, —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂.

6. The oligonucleotide analog of claim 5 wherein X is OCH₃.

7. The oligonucleotide analog of claim 5 wherein X is —

O—

CH₂—

CH₂—

O—

CH₃.

11. A compound comprising a moiety of Formula:

wherein;

Z is a phosphodiester or phosphorothioate intersugar linkage;

B_X is a heterocyclic base; and

X is F, —

OCH₃, —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂ when Z is a phosporothioate intersugar linkage or X is OCH₃, —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂ when Z is a phosphodiester intersugar linkage; and

T₃ is a nucleotide, a nucleoside, an oligonucleotide, a hydroxyl or a blocked hydroxyl, wherein said nucleotide is not a ribonucleotide, and said nucleoside is not a ribonucleoside, and wherein the 3′

-terminal nucleotide of said oligonucleotide is not a ribonucleotide.

12. The compound of claim 11 wherein X is —

OCH₃, —

OCH₂CH₂OCH₃ or —

OCH₂CH₂CH₂NH₂.

13. The compound of claim 12 wherein X is —

OCH₃.

14. The compound of claim 12 wherein X is —

O—

CH₂—

CH₂—

O—

CH₃.