Claims for Patent: 6,448,009

Summary for Patent: 6,448,009

Title:	Method for target site selection and discovery
Abstract:	Nucleic acid catalysts, method of screening/selection for nucleic acid catalysts, synthesis of ribozyme libraries and discovery of gene sequences involved in a biological process are described.
Inventor(s):	Thompson; James D. (Boulder, CO)
Assignee:	Ribozyme Pharmaceuticals, Inc. (Boulder, CO)
Application Number:	09/676,807
Patent Claims:	1. A method for identifying a gene that modulates a process in a biological system comprising the steps of: a) introducing a library of nucleic acid catalysts into a biological system under conditions suitable for modulating a process in the biological system, wherein each nucleic acid catalyst comprises a substrate binding domain and a catalytic domain and the substrate binding domain comprises a random sequence; b) determining the nucleotide sequence of at least a portion of the substrate binding domain of any nucleic acid catalyst in the biological system in which the process has been modulated; and c) identifying a gene that modulates a process in a biological system using the nucleotide sequence from step (b). 2. A method for identifying a gene involved in a biological process comprising the steps of: a) introducing a library of nucleic acid catalysts into a biological system under conditions suitable for altering a process in the biological system, wherein each nucleic acid catalyst comprises a substrate binding domain and a catalytic domain and the substrate binding domain comprises a random sequence; b) identifying any nucleic acid catalyst in the biological system in which the biological process has been altered; and c) determining the nucleotide sequence of at least a portion of the substrate binding domain of any nucleic acid catalyst from step (b) to identify a gene involved in said biological process. 3. A method comprising the steps of: a) providing a random binding arm nucleic acid catalyst library to a biological system under conditions suitable for a nucleic acid catalyst from the library to down-regulate the expression of a gene; b) determining the biological system in which the expression of a gene has been down-regulated; c) determining the nucleotide sequence of at least one portion of the binding arm of the nucleic acid catalyst in the biological system of step (b); and d) identifying the gene which expression is down-regulated using the nucleotide sequence from step (c). 4. The method of any of claims 1-3, wherein said nucleic acid catalyst is in a group I intron ribozyme motif, group II intron ribozyme motif hepatitis delta virus ribozyme motif, VS ribozyme motif or RNase P ribozyme motif. 5. The method of any of claims 1-3, wherein said nucleic acid catalyst is in a hammerhead ribozyme motif. 6. The method of any of claims 1-3, wherein said nucleic acid catalyst is in a hairpin ribozyme motif. 7. The method of any of claims 1-3, wherein said nucleic acid catalyst is in a catalytic DNA motif. 8. The method of any of claims 1-3, wherein said biological system is a bacterial cell. 9. The method of any of claims 1-3, wherein said biological system is of plant origin. 10. The method of any of claims 1-3, wherein said biological system is of mammalian origin. 11. The method of any of claims 1-3, wherein said biological system is of yeast origin. 12. The method of any of claims 1-3, wherein said biological system is Drosophila. 13. The method of claim 1 or claim 2, wherein said process is selected from the group consisting of growth, proliferation, apoptosis, morphology, angiogenesis, differentiation, migration, viral multiplication, drug resistance, signal transduction, cell cycle regulation, temperature sensitivity and chemical sensitivity. 14. The method of any of claims 1-3, wherein said library of nucleic acid catalysts is encoded by an expression vector in a manner which allows expression of said nucleic acid catalysts. 15. The method of claim 14, wherein said expression vector comprises: a) a transcription initiation region; b) a transcription termination region; and c) a sequence encoding at least one said nucleic acid catalyst, wherein said sequence is operably linked to said initiation region and said termination region, in a manner which allows expression or delivery or expression and delivery of said nucleic acid catalyst. 16. The method of claim 14, wherein said expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an open reading frame for a polypeptide; and d) a sequence encoding at least one said nucleic acid catalyst, wherein said sequence is operably linked to the 3'-end of said open reading frame; wherein said sequence is operably linked to said initiation region, said open reading frame and said termination region, in a manner which allows expression or delivery or expression and delivery of said nucleic acid catalyst. 17. The method of claim 14, wherein said expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; and d) a sequence encoding at least one said nucleic acid catalyst, wherein said sequence is operably linked to said initiation region, said intron and said termination region, in a manner which allows expression or delivery or expression and delivery of said nucleic acid catalyst. 18. The method of claim 14, wherein said expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading frame for a polypeptide; and e) a sequence encoding at least one said nucleic acid catalyst, wherein said sequence is operably linked to the 3'-end of said open reading frame; wherein said sequence is operably linked to said initiation region, said intron, said open reading frame and said termination region, in a manner which allows expression or delivery or expression and delivery of said nucleic acid catalyst. 19. The method of claim 14, wherein said expression vector is derived from a retrovirus. 20. The method of claim 14, wherein said expression vector is derived from an adenovirus. 21. The method of claim 14, wherein said expression vector is derived from an adenoassociated virus. 22. The method of claim 14, wherein said expression vector is derived from an alphavirus. 23. The method of claim 14, wherein said expression vector is derived from a bacterial plasmid. 24. The method of claim 14, wherein said expression vector is operably linked to a RNA polymerase II promoter element. 25. The method of claim 14, wherein said expression vector is operably linked to a RNA polymerase III promoter element. 26. The method of claim 25, wherein said RNA polymerase III promoter is derived from a transfer RNA gene. 27. The method of claim 25, wherein said RNA polymerase III promoter is derived from a U6 small nuclear RNA gene. 28. The method of claim 25, wherein the nucleic acid catalyst comprises a sequence at its 5'-end homologous to the terminal 27 nucleotides encoded by said U6 small nuclear RNA gene. 29. The method of claim 26, wherein said RNA polymerase III promoter is derived from a TRZ RNA gene. 30. The method of any of claims 1-3, wherein said biological system is of an eukaryotic origin. 31. The method of any of claims 1-3, wherein said biological system is of an prokaryotic origin. 32. The method of any of claims 1-3, wherein said biological system is of an archaebacterial origin. 33. The method of any of claims 1-3, wherein said substrate binding domain is of a length between 12 and 100 nucleotides. 34. The method any of claims 1-3, wherein said substrate binding domain is of a length between 14 and 24 nucleotides. 35. The method of any of claims 1-2, wherein said substrate binding domain comprises one substrate binding arm. 36. The method of any of claims 1-2, wherein said substrate binding domain comprises two substrate binding arms. 37. The method of claim 36, wherein said substrate binding arms are of similar length. 38. The method of claim 36, wherein said substrate binding arms are of different length. 39. The method of any of claims 1-3, wherein said library of nucleic acid catalysts is a multimer library.

Details for Patent 6,448,009

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132	06/04/1986		2017-07-03
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132			2017-07-03
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	Injection	103132			2017-07-03