Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Patent
1997-11-21
2000-01-11
Degen, Nancy
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
435 691, 435 9131, 4353201, 435455, 536 231, 536 234, 536 241, 536 245, C12Q 168, C07H 2104, C07H 2102, C12N 1563
Patent
active
06013447&
ABSTRACT:
Vectors and a method for the identification of affector RNA molecules, such as ribozymes, external guide sequences, anti-sense RNA, and triple helix-forming RNA, that inhibit expression of target RNA molecules are disclosed. The method identifies functional affector RNA molecules by screening or selecting for those RNA molecules that inhibit expression of a fusion transcript, which includes the sequence of an RNA molecule of interest, from a library of potential affector RNA molecules. The vectors include a reporter gene encoding the fusion transcript including the RNA molecule of interest and RNA encoding the reporter protein. The vectors also include a second reporter gene encoding a second reporter protein. Expression of the second reporter protein can be used both to detect transformation or transfection of the vector into cells and as a control for effects on the expression of the first reporter protein that are not due to inhibition of expression of the RNA molecule of interest. The vector also encodes an affector RNA molecule targeted to the RNA of interest. A key advantage of the disclosed method and vectors is the assessment of inhibition of expression of an RNA of interest in an in vivo setting which will be the same or similar to the setting where identified affector molecules will be used. Another advantage of the disclosed method is that all, or a substantial number of the accessible sites in the RNA of interest can be determined in one assay. Also disclosed are affector oligomers based on affector RNA molecules identified as inhibiting the expression of an RNA of interest. The disclosed method also allows direct comparison of the inhibitory activities of different affector RNA molecules directed to different target sites.
REFERENCES:
patent: 4987071 (1991-01-01), Cech et al.
patent: 5168053 (1992-12-01), Atlman et al.
patent: 5225347 (1993-07-01), Robertson
patent: 5254678 (1993-10-01), Haseloff et al.
patent: 5334711 (1994-08-01), Sproat et al.
patent: 5422251 (1995-06-01), Fresco
patent: 5496698 (1996-03-01), Draper et al.
patent: 5525468 (1996-06-01), McSwiggen
patent: 5527895 (1996-06-01), Hampel et al.
patent: 5580967 (1996-12-01), Joyce
patent: 5624824 (1997-04-01), Yuan et al.
Kawasaki et al. "Selection of the Best Target Site for Ribozyme-Mediated Cleavage within a Fusion Gene for Adenovirus E1A-Associated 300 kDa Protein (p300) and Luciferase" Nucleic Acids Research vol. 24(15): 3010-3016, 1996.
Lima et al. "Combinatorial Screening and Rational Optimization for Hybridization to Folded Hepatitis C Virus RNA of Oligonucleotides with Biological Antisense Activity" The Journal Of Biological Chemistry vol. 272(1): 626-638, Jan. 3, 1997.
Altman, "RNA Enzyme-Directed Gene Therapy," Proc. Natl. Acad. Sci. USA 90:10898-10900 (1993).
Baer, et al., "Structure And Transcription Of A Human Gene Fro(?) H1 RNA, The RNA Component Of Human RNase P," Nucleic Acids Research 18:97-103 (1989).
Beal, et al., "The Influence of Single Base Triplet Changes on the Stability of a Pur.multidot.Pur.multidot.Pyr Triple Helix Determined by Affinity Cleaving," Nuc. Acids Res. 20(11):2773-2776 (1992).
Beal, et al., "Second Structural Motif for Recognition of DNA by Oligonucleotide-Directed Triple-Helix Formation," Science 251:1360-1363 (1991).
Blume, et al., "Triple Helix Formation by Purine-Rich Oligonucleotides Targeted to the Human Dihydrofolate Reductase Promoter," Nucleic Acids Res.20:1777-1784 (1992).
Buzayan et al., Proc. Natl. Acad. Sci. USA 83:8859-8862 (1968).
Cech, "Self-Splicing Of Group I Introns," Annu. Rev. Biochem. 59:543-568 (1990).
Chalfie, et al., "Green Fluorescent Protein as a Marker for Gene Expressions" Science 263:802-805 (1994).
Cooney, et al., "Site-Specific Oligonucleotide Binding Represses Transcription of the Human c-myc Gene in Vitro," Science 241:456-459 (1988).
Cormack, et al., "FACS-optimized Mutants of the Green Fluorescent Protein (GFP)," Gene 173:33-38 (1996).
Durland, et al., "Binding of Triple Helix Forming Oligonucleotides to Sites in Gene Promoters," Biochemistry 30:9246-9255 (1991).
Duval-Valentin, et al., "Specific Inhibition of Transcription by Triple Helix-Forming Oligonucleotides," Proc. Natl. Acad. Sci. USA 89:504-508 (1992).
Forster, et al., "External Guide Sequences For An RNA Enzyme," Science 249:783-786 (1990).
Forster, et al., "Self-Cleavage Of Virusoid RNA Is Performed By The Proposed 55-Nucleotide Active Site," Cell 50:9-16 (1987).
Fowlkes, et al., "Transcriptional Control Regions Of The Adenovirus VAI RNA Gene," Cell 22:405-413 (1980).
Francois, et al., "Sequence-Specific Recognition and Cleavage of Duplex DNA via Triple-Helix Formation by Oligonucleotides Covalently Linked to a Phenanthroline-Copper Chelate," Proc. Natl. Acad. Sci. USA 86:9702-9706 (1989).
Graham, et al., "Characteristics of a Human Cell Line Transformed by DNA from Human Adenovirus Type 5," J. Gen Virol. 36:59-72 (1977).
Grigoriev, et al., "A Triple Helix-Forming Oligonucleotide-Intercalator Conjugate Acts As A Transcriptional Repressor Via Inhibition Of NF .kappa.B Binding To Interleukin-2 Receptor," J. Biol. Chem. 267:3389-3395 (1992).
Guerrier-takada, et al., "The RNA Moiety Of Ribonuclease P Is The Catalytic Subunit Of The Enzyme," Cell 35:849-857 (1983).
Gupta, et al., "Compliation Of Small RNA Sequences," Nucleic Acids Res. 19:2073-2075 (1990).
Hall, et al., "Transcription Initiation Of Eucaryotic Transfer RNA Genes," Cell 29:3-5 (1982).
Hannon, et al., "Multiple cis-Acting Elements Are Required for RNA Polymerase III Transcription of the Gene Encoding H1 RNA, the RNA Component of Human RNase P," J. Biol. Chem. 266:22796-22799 (1991).
Haseloff and Gerlach, "Simple RNA Enzymes with New and Highly Specific Endoribonuclease Activities," Nature 334:585-591 (1988).
Kickoefer, et al., "Vault Ribonucleoprotein Particles From Rat And Bullfrog Contain A Related Small RNA That Is Transcribed By RNA Polymerase III," J. Biol. Chem. 268:7868-7873 (1993).
Kunkel, et al., "U6 Small Nuclear RNA Is Transcribed By RNA Polymerase III," Proc. Natl. Acad. Sci. USA 83:8575-8579 (1987).
Kunkel, et al., "Transcription Of A Human U6 Small Nuclear RNA Gene In Vivo Withstands Deletion Of Intragenic Sequences But Not Of An Upstream TATATA Box," Nucleic Acids Res. 18:7371-7379 (1989).
Lieber and Strauss, "Selection of Efficient Cleavage Sites in Target RNAs by Using a Ribozyme Expression Library," Mol. Cell. Biol. 8:466-472 (1995).
Lin, et al., "Use of EDTA Derivatization To Characterize Interactions Between Oligodeoxyribonucleoside Methylphosphonates and Nucleic Acids," Biochemistry 28:1054-1061 (1989).
Liu and Altman, "Inhibition of Viral Gene Expression by the Catalytic RNA Subunit of RNase P from Escherichia coli," Genes Dev. 9:471-480 (1995).
Lomant and Fresco, "Structural and Energetic Consequences of Noncomplementary Base Oppositions in Nucleic Acid Helices" Prog. Nucl. Acid Res. Mol. Biol. 15:185 (1975).
Maher, et al., "Inhibition Of DNA Binding Proteins By Oligonucleotide-Directed Triple Helix Formation," Science 245:725-730 (1989).
Maher, et al., "Analysis of Promoter-Specific Repression by Triple-Helical DNA Complexes in a Eukaryotic Cell-Free Transcription System," Biochemistry 31:70-81 (1992).
Mather, "Establishment and Characterization of Two Distinct Mouse Testicular Epithelial Cell Lines," Biol. Reprod. 23:243-252 (1980).
Mather, et al., "Culture of Testicular Cells in Hormone-Supplemented Serum-Free Medium," Annals N. Y. Acad. Sci 383:44-68 (1982).
Mergny, et al., "Sequence Specificity in Triple-Helix Formation: Experimental and Theoretical Studies of the Effect of Mismatches on Triplex Stability," Biochemistry 30:9791-9798 (1991).
Moser and Dervan, "Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation," Science 238:645-650 (1987).
Mosinger, et al., "Cloning and Characterization of a Mouse cDNA Encoding a Cytoplasmic Protein-Tryrosine-Phosphatase," Proc. Natl. Acad. Sci. USA 89:499-503 (1992).
Nielsen, et al., "Transcription Of Human 5S rRNA Genes Is Influenced By An Upstream DNA Sequence," Nucleic Acids Res. 21:3631-3636 (1993).
Noonberg, et al.,
Kindt Thomas J.
Nilsen Timothy W.
Robertson Hugh D.
Degen Nancy
Innovir Laboratories, Inc.
McGarry Sean
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