Nucleic acid catalysts with endonuclease activity

• US 6,127,173 A
• Filed: 09/22/1998
• Issued: 10/03/2000
• Est. Priority Date: 09/22/1997
• Status: Expired due to Fees

• Current Assignee: Max-Planck-Gesellschaft Zur Foerderung Der Wissenschaften e.V. (Max-Planck-Gesellschaft zur Frderung der Wissenschaften e)
• Original Assignee: Ribozyme Pharmaceuticals, Inc. (Alnylam Pharmaceuticals Incorporated)
• Inventors: Vaish, Narendra K., Heaton, Paul A., Eckstein, Fritz
• Primary Examiner(s): Schwartzman, Robert A.
• Assistant Examiner(s): EPPS -SMITH, JANET L
• Application Number:
  US09/159,274
• Time in Patent Office: 742 Days
• Field of Search: 536/23.1, 536/23.2, 536/24.5, 435/320.1, 435/91.1, 435/91.31
• US Class Current: 435/320.1
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/111 spanning the whole gene, or a large part of it
• CPC Class Codes: C12N 2310/121 Hammerhead
• CPC Class Codes: C12N 2310/18 acting by a non-sequence specific mechanism other than C12N2310/16 or C12N2310/17

Abstract

Nucleic acid molecules with new motifs having catalytic activity, methods of synthesis, and use thereof are also described.

Claims

1. A nucleic acid molecule with an endonuclease activity having the formula I:

##STR2## wherein, each N represents independently a nucleotide or an abasic moiety, which may be same or different;

X and Y are independent oligonucleotides of length sufficient to stably interact with a target nucleic acid molecule;

m and n are integers greater than or equal to 1, wherein if (N)_m and (N)_n are nucleotides, (N)m and (N)n may interact by hydrogen bond interaction;

J is an oligonucleotide having a sequence selected from the group consisting of 5'"'"'-GGCAUCC-3'"'"', 5'"'"'-AGCAUU-3'"'"', 5'"'"'-GCAUCA-3'"'"', 5'"'"'-AGCAUC-3'"'"', and, 5'"'"'-AGCGUC-3'"'"';

L is a linker which may be present or absent, wherein said linker, when present, is a nucleotide linker or a non-nucleotide linker, or a combination of nucleotide and a non-nucleotide linker, wherein said nucleotide linker comprises a single-stranded region, or double-stranded region, or a combination of single-stranded and a double-stranded region;

represents a chemical linkage; and

C and G represent cytidine and guanosine nucleotides, respectively.

4. The nucleic acid molecules of any of claims 1-3, wherein said L in said nucleic acid molecule is nucleotide linker.

5. The nucleic acid molecule of claim 4, wherein said nucleotide linker is a nucleic acid aptamer.

6. The nucleic acid molecule of claim 5, wherein said aptamer is an ATP aptamer.

7. The nucleic acid molecule of any of claims 1-3, wherein said L is non-nucleotide linker.

8. The nucleic acid molecule of any of claims 1-3, wherein said (N)m and (N)n each have a nucleotide sequence.

9. The nucleic acid molecule of claim 8, wherein said nucleotide sequence of said (N)m is complementary to the nucleotide sequence of said (N)n.

10. The nucleic acid molecule of any of claims 1-3, wherein said nucleic acid cleaves a separate nucleic acid molecule.

11. The nucleic acid molecule of claim 10, wherein said separate nucleic acid molecule is RNA.

12. The nucleic acid molecule of claim 10, wherein said nucleic acid comprises between 12 and 100 bases complementary to said separate nucleic acid molecule.

13. The nucleic acid molecule of claim 10, wherein said nucleic acid comprises between 14 and 24 bases complementary to said separate nucleic acid molecule.

14. A cell including the nucleic acid molecule of any of claims 1-3, wherein said cell is not a living human.

15. The cell of claim 14, wherein said cell is a mammalian cell.

16. The cell of claim 15, wherein said cell is a human cell.

17. An expression vector comprising nucleic acid sequence encoding at least one of the nucleic acid molecule of any of claims 1-3, in a manner which allows expression of that nucleic acid molecule.

18. A cell including the expression vector of claim 17, wherein said cell is not a living human.

19. The cell of claim 18, wherein said cell is a mammalian cell.

20. The cell of claim 18, wherein said cell is a human cell.

21. A method of cleaving a separate nucleic acid comprising, contacting the nucleic acid molecule of any of claims 1-3 with said separate nucleic acid molecule under conditions suitable for the cleavage of said separate nucleic acid molecule.

22. The method of claim 21, wherein said cleavage is carried out in the presence of a divalent cation.

23. The method of claim 22, wherein said divalent cation is Mg²⁺.

24. The nucleic acid molecule of claims 1-3, wherein said nucleic acid is chemically synthesized.

25. The expression vector of claim 17, wherein said vector comprises:

a) a transcription initiation region;

b) a transcription termination region;

c) a gene encoding at least one said nucleic acid molecule; and

wherein said gene is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

26. The expression vector of claim 17, wherein said vector comprises:

a) a transcription initiation region;

b) a transcription termination region;

c) an open reading frame;

d) a gene encoding at least one said nucleic acid molecule, wherein said gene is operably linked to the 3'"'"'-end of said open reading frame; and

wherein said gene is operably linked to said initiation region, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

27. The expression vector of claim 17, wherein said vector comprises:

a) a transcription initiation region;

b) a transcription termination region;

c) an intron;

d) a gene encoding at least one said nucleic acid molecule; and

wherein said gene is operably linked to said initiation region, said intron and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

28. The expression vector of claim 17, wherein said vector comprises:

a) a transcription initiation region;

b) a transcription termination region;

c) an intron;

d) an open reading frame;

e) a gene encoding at least one said nucleic acid molecule, wherein said gene is operably linked to the 3'"'"'-end of said open reading frame; and

wherein said gene is operably linked to said initiation region, said intron, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

2. A nucleic acid molecule with an endonuclease activity having the formula II:

##STR3## wherein, each N represents independently a nucleotide or a non-nucleotide linker, which may be same or different;

X and Y are independent oligonucleotides of length sufficient to stably interact with a target nucleic acid molecule;

m and n are integers greater than or equal to 1, wherein if (N)_m and (N)_n are nucleotides, (N)m and (N)n may interact by hydrogen bond interaction;

J is an oligonucleotide of length 6 nucleotides having a sequence 5'"'"'-GGAAUC-3'"'"';

L is a linker which may be present or absent, wherein said linker, when present, is a nucleotide linker or a non-nucleotide linker, or a combination of nucleotide and a non-nucleotide linker, wherein said nucleotide linker comprises a single-stranded region, or double-stranded region, or a combination of single-stranded and a double-stranded region;

represents a chemical linkage; and

C represents cytidine nucleotide.

3. A nucleic acid molecule with endonuclease activity having the formula III:

##STR4## wherein, each N represents independently a nucleotide or a non-nucleotide linker, which may be same or different;

X and Y are independent oligonucleotides of length sufficient to stably interact with a target nucleic acid molecule;

m and n are integers greater than or equal to 1, wherein if (N)_m and (N)_n are nucleotides, (N)m and (N)n may interact by hydrogen bond interaction;

K is an oligonucleotide of length 5 nucleotides having a sequence selected from the group consisting of 5'"'"'-UGAUG-3'"'"', 5'"'"'-UGAUC-3'"'"', and 5'"'"'-UGGGC-3'"'"';

L is a linker which may be present or absent, wherein said linker, when present, is a nucleotide linker or a non-nucleotide linker, or a combination of nucleotide and a non-nucleotide linker, wherein said nucleotide linker comprises a single-stranded region, or double-stranded region, or a combination of single-stranded and a double-stranded region;

represents a chemical linkage; and

C and G represent cytidine and guanosine nucleotides, respectively.