Regulatable nucleic acid therapeutic and methods of use thereof

• US 5,741,679 A
• Filed: 09/16/1994
• Issued: 04/21/1998
• Est. Priority Date: 12/04/1992
• Status: Expired due to Term

• Current Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Original Assignee: Innovir Laboratories, Inc. (Baxter International Inc.)
• Inventors: Shih, Andy, Bockman, Jeffrey Michael, George, Shaji T.
• Primary Examiner(s): Elliott, George C.
• Assistant Examiner(s): SCHWARTZMAN, ROBERT A
• Application Number:
  US08/307,401
• Time in Patent Office: 1,313 Days
• Field of Search: 435/91.31, 435/172.3, 435/320.1, 536/23.1, 536/24.5
• US Class Current: 435/91.31
• 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: A61P 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 31/20 for DNA viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• 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 2310/121 Hammerhead
• CPC Class Codes: C12N 2730/10122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Abstract

Regulatable RNA molecules such as regulatable ribozymes, nucleic acids encoding such regulatable ribozymes, and methods of making and using such regulatable ribozymes are disclosed. Regulatable ribozymes comprise a ligand-binding RNA sequence and a ribozyme sequence capable of cleaving a separate targeted RNA sequence, wherein upon binding of the ligand to the ligand-binding RNA sequence, the activity of the ribozyme sequence against the targeted RNA sequence is altered. The ligand may be either an inorganic or an organic molecule and may be a co-drug which can be administered to specifically regulate the ribozyme activity. Regulatable RNA molecules other than ribozymes are also disclosed, such as regulatable mRNA molecules which comprise a ligand-binding RNA sequence separate from the coding sequence, wherein upon binding of a ligand to the ligand-binding RNA sequence, translation of the regulatable mRNA is altered.

Claims

1. A regulatable ribozyme molecule comprising a ribozyme sequence which cleaves a separate targeted RNA molecule and a RNA sequence which binds to a ligand, wherein binding of the ligand alters the activity of the ribozyme against the targeted RNA,

wherein the regulatable ribozyme molecule is made by the steps of

providing a random nucleotide sequence of between 20 and 100 nucleotides in length which is to be linked to a sequence with ribozyme activity which cleaves a targeted RNA molecule,

amplifying the random sequence under conditions promoting mutation of the random sequence, wherein mutation of the random sequence results in mutated sequences,

exposing the mutated sequences to a ligand which is to be used to modify the activity of the ribozyme under conditions favorable to binding of the ribozyme to the ligand,

removing mutated sequences not binding to the ligand,

repeating the amplification and binding steps until mutated sequences are obtained which bind to the ligand,

linking each of the mutated sequences which bind to the ligand to the ribozyme sequence to form ribozyme-ligand binding sequences,

exposing the ribozyme ligand binding sequences to ligand, and

screening for alteration of the ribozyme activity when ligand is bound and when ligand is not bound to the ligand binding sequence.

2. The ribozyme molecule of claim 1 wherein the ligand is selected from the group consisting of nucleic acid molecules, proteins polysaccharides, sugars, organic molecules and inorganic molecules.

3. The ribozyme molecule of claim 1 wherein the ribozyme is derived from a ribozyme selected from the group consisting of hammerhead ribozymes, axehead ribozymes, newt satellite ribozymes, Tetrahymena ribozymes, and RNAase P.

4. The ribozyme molecule of claim 1 wherein the ribozyme is an external guide sequence for RNAase P.

5. The ribozyme molecule of claim 1 wherein the ribozyme is inactivated when the ligand is bound to the molecule.

6. The ribozyme molecule of claim 1 wherein the ribozyme is activated when the ligand is bound to the molecule.

7. The ribozyme molecule of claim 1 wherein the ligand is exogenously administered to cells containing the regulatable ribozyme molecule.

8. The ribozyme molecule of claim 2 wherein the ligand is a product found in cells and the ribozyme activity is altered by binding to the ligand within the cells.

9. The ribozyme molecule of claim 3 wherein the ribozyme is derived from a hammerhead ribozyme.

10. A nucleic acid molecule encoding a regulatable ribozyme and a gene.

11. The molecule of claim 10 further comprising nucleic acid sequence adjacent to the gene, wherein the sequence is a substrate for the ribozyme.

12. The molecule of claim 10 further comprising a promoter and a multiple cloning site, wherein expression of the regulatable ribozyme or the gene is under control of the promoter, and wherein the multiple cloning site is adjacent to the gene.

13. The molecule of claim 10 wherein the gene encodes a product which modulates the activity of the ribozyme.

14. The molecule of claim 11 wherein the sequence is 5'"'"' and 3'"'"' to the gene.

15. A method of making a regulatable ribozyme molecule comprising a ribozyme sequence which cleaves a separate targeted RNA molecule and a RNA sequence which binds to a ligand, wherein binding of the ligand alters the activity of the ribozyme against the targeted RNA, comprising the steps of

providing a random nucleotide sequence of between 20 and 100 nucleotides in length which is to be linked to a sequence with ribozyme activity which cleaves a targeted RNA molecule,

amplifying the random sequence under conditions promoting mutation of the random sequence, wherein mutation of the random sequence results in mutated sequences,

exposing the mutated sequences to a ligand which is to be used to modify the activity of the ribozyme under conditions favorable to binding of the ribozyme to the ligand,

removing mutated sequences not binding to the ligand,

repeating the amplification and binding steps until mutated sequences are obtained which bind to the ligand,

linking each of the mutated sequences which bind to the ligand to the ribozyme sequence to form ribozyme-ligand binding sequences,

exposing the ribozyme-ligand binding sequences to ligand, and

screening for alteration of the ribozyme activity when ligand is bound and when ligand is not bound to the ligand binding sequence, wherein alteration of ribozyme activity identifies a ribozyme-ligand binding sequence as a regulatable ribozyme molecule.

16. The method of claim 15 wherein the ribozyme is derived from a hammerhead ribozyme.

17. A method for controlled cleavage of a target RNA molecule in vitro or in an isolated cell comprising providing at the site where the target RNA molecule is to be cleaved

a regulatable ribozyme molecule comprising a ribozyme sequence which cleaves the target RNA molecule and a ligand binding sequence which binds to a ligand, wherein binding of the ligand alters the activity of the ribozyme against the target RNA,

wherein cleavage of the targeted RNA molecule is controlled by the presence or absence of the ligand.

18. The method of claim 17 wherein the ligand is selected from the group consisting of nucleic acid molecules, proteins, polysaccharides, sugars, organic molecules and inorganic molecules.

19. The method of claim 17 wherein the ribozyme is derived from a ribozyme selected from the group consisting of hammerhead ribozymes, axehead ribozymes, newt satellite ribozymes, Tetrahymena ribozymes, and RNAase P.

20. The method of claim 17 wherein the ribozyme is an external guide sequence for RNAase P.

21. The method of claim 17 wherein the ribozyme is inactivated when the ligand is bound to the molecule.

22. The method of claim 17 wherein the ribozyme is activated when the ligand is bound to the molecule.

23. The method of claim 17 wherein the ligand is a product found in cells and the ribozyme activity is altered by binding to the ligand within the cells.

24. The method of claim 17 wherein the ligand is a product found in virally infected cells and the ribozyme is activated by binding to the ligand.

25. The method of claim 17 wherein the regulatable ribozyme molecule is made by the steps of

providing a random nucleotide sequence of between 20 and 100 nucleotides in length which is to be linked to a sequence with ribozyme activity which cleaves a targeted RNA molecule,

amplifying the random sequence under conditions promoting mutation of the random sequence, wherein mutation of the random sequence results in mutated sequences,

exposing the mutated sequences to a ligand which is to be used to modify the activity of the ribozyme under conditions favorable to binding of the ribozyme to the ligand,

removing mutated sequences not binding to the ligand,

repeating the amplification and binding steps until mutated sequences are obtained which bind to the ligand,

linking each of the mutated sequences which bind to the ligand to the ribozyme sequence to form ribozyme-ligand binding sequences,

exposing the ribozyme-ligand binding sequences to ligand, and

screening for alteration of the ribozyme activity when ligand is bound and when ligand is not bound to the ligand binding sequence.

26. The method of claim 17 wherein the regulatable ribozyme molecule is made by the steps of

providing a random nucleotide sequence of 20 to 100 nucleotides linked to the ribozyme sequence,

amplifying the random sequence under conditions promoting mutation of the random sequence, wherein mutation of the random sequence results in mutated sequences,

exposing the mutated sequences to the ligand under conditions favorable to binding of the mutated sequences to the ligand,

removing mutated sequences not binding to the ligand,

repeating the amplifying and exposing steps until mutated sequences are obtained which bind to the ligand, wherein the mutated sequences which bind to the ligand are ligand binding sequences and wherein the ligand binding sequences and the ribozyme sequence together are ribozyme-ligand binding molecules,

exposing the ribozyme-ligand binding molecules to ligand, and

screening for alteration of the ribozyme activity when ligand is bound and when ligand is not bound to the ligand binding sequence, wherein alteration of ribozyme activity identifies a ribozyme-ligand binding sequence as a regulatable ribozyme molecule.

27. The method of claim 19 wherein the ribozyme is derived from a hammerhead ribozyme.

28. A method of making a regulatable ribozyme molecule comprising a ribozyme sequence which cleaves a separate target RNA molecule and a ligand binding sequence which binds to a ligand, wherein binding of the ligand alters the activity of the ribozyme, comprising the steps of

providing a random nucleotide sequence of 20 to 100 nucleotides linked to the ribozyme sequence,

amplifying the random sequence under conditions promoting mutation of the random sequence, wherein mutation of the random sequence results in mutated sequences,

exposing the mutated sequences to the ligand under conditions favorable to binding of the mutated sequences to the ligand,

removing mutated sequences not binding to the ligand,

repeating the amplifying and exposing steps until mutated sequences are obtained which bind to the ligand, wherein the mutated sequences which bind to the ligand are ligand binding sequences and wherein the ligand binding sequences and the ribozyme sequence together are ribozyme-ligand binding molecules,

exposing the ribozyme-ligand binding molecules to ligand, and

screening for alteration of the ribozyme activity when ligand is bound and when ligand is not bound to the ligand binding sequence, wherein alteration of ribozyme activity identifies a ribozyme-ligand binding sequence as a regulatable ribozyme molecule.