Methods for identifying RNA binding compounds

Drug – bio-affecting and body treating compositions – Designated organic active ingredient containing

Reexamination Certificate

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C514S04400A, C530S300000

Reexamination Certificate

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06875736

ABSTRACT:
The present invention relates to methods of screening for compounds that bind RNA molecules. In particular, the methods of the invention comprise screening a library of test compounds, each of which is attached to a solid support, with a dye-labeled RNA molecule to form a dye-labeled target RNA:support-attached test compound complex. By virtue of the dye label on the target RNA, the support becomes labeled and can be separated from unlabeled solid supports. The present invention further relates to methods of inhibiting an RNA-protein interaction, to methods of screening for compounds that increase or decrease the production of a protein, and to methods of screening for a compound that is capable of treating or preventing a disease whose progression is associated with an in vivo binding of a test compound to a target RNA.

REFERENCES:
patent: 5510240 (1996-04-01), Lam et al.
patent: 5593835 (1997-01-01), Rando et al.
patent: 5666341 (1997-09-01), Horibe et al.
patent: 5712096 (1998-01-01), Stern et al.
patent: 5866341 (1999-02-01), Spinella et al.
patent: 6004749 (1999-12-01), Giordano et al.
patent: 6090912 (2000-07-01), Lebl et al.
patent: 6107029 (2000-08-01), Giordano
patent: WO 9709342 (1997-03-01), None
Aboul-ela et al. (1995) The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by TAT protein. J. Mol. Biol. 253:313-332.
Bayer (1991) Towards The Chemical Synthesis of Protiens. Angew. Chem. 30:113-129.
Beal & Dervan (1991) Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science 1991 251(4999):1360-1363.
Chastain & Tinoco (1991) Structural elements in RNA. Prog Nucleic Acid Res Mol Biol 41:131-177.
Chow & Bogdan (1997) A structural basis for RNA-ligand interactions. Chemical Reviews 97:1489-1514.
Churcher et al. (1993) High affinity binding of TAR RNA by the human immunodeficiency virus type-1 tat protein requires base-pairs in the RNA stem and amino acid residues flanking the basic region. J. Mol. Biol. 230:90-110.
Cordingley et al. (1990) Sequence-Specific Interaction of Tat Protein and Tat Peptides with the Transactivation-Responsive Sequence Element of Human Immunodeficiency Virus Type 1 in vitro. Proc. Natl. Acad. Sci. USA 87:8985-8989.
Felber & Pavlakis (1988) A quantitative bioassay for HIV-1 based on trans-activation. Science 239:184-187.
Frankel A. D. & Pabo (1988) Cellular uptake of the tat protein from human immunodeficiency virus. Cell 55:1189-1194.
Gottesfeld et al. (1997) Regulation of gene expression by small molecules. Nature 387(6629):202-205.
Hamy et al. (1998) A new class of HIV-1 Tat antagonist acting through Tat-TAR inhibition. Biochemistry 37(15):5086-5095.
Hamy et al. (1997) An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication. Proc. Natl. Acad. Sci. USA 94:3548-3553.
Helene et al. (1992) Control of gene expression by triple helix-forming oligonucleotides. The antigene strategy. Ann N Y Acad Sci 660:27-36.
Ho et al., (1994) Specific inhibition of formation of transcription complexes by a calicheamicin oligosaccharide: a paradigm for the development of transcriptional antagonists. Proc Natl Acad Sci U S A 91(20):9203-9207.
Huq et al. (1999) Controlling human immunodeficiency virus type 1 gene expression by unnatural peptides. Biochemistry 38:5172-5177.
Hwang et al. (1999) Inhibition of gene expression in human cells through small molecule-RNA interactions . Proc. Natl. Acad. Sci. USA 96(23):12977-13002.
Jakobovits et al. (1988) A discrete element 3′ of human immunodeficiency virus 1 (HIV-1) and HIV-2 mRNA initiation sites mediates transcriptional activation by an HIV trans activator. Mol. Cell. Biol. 8:2555-2561.
Jones & Peterlin (1994) Control of RNA initiation and elongation at the HIV-1 promoter. Annu Rev Biochem 63:717-743.
Liu et al. (1996) Sequence-selective carbohydrate-DNA interaction: Dimeric and monomeric forms of the calicheamicin oligosaccharide interfere with transcription factor function. Proc Natl Acad Sci U S A 93(2):940-944.
Maher et al. (1991) Oligonucleotide-directed DNA triple-helix formation: an approach to artificial repressors? Antisense Res Dev 1(3):277-281.
Mei et al. (1998) Inhibitors of protein-RNA complexation that target the RNA: specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. Biochemistry 37(40):14240-14212.
Mei et al. (1997) Discovery of selective, small-molecule inhibitors of RNA complexes—I. The Tat protein/TAR RNA complexes required for HIV-1 transcription. Bioorg. Med. Chem. 5:1173-1184.
Miller (1996) Development of antisense and antigene oligonucleotide analogs. Prog Nucleic Acid Res Mol Biol 1996;52:261-291.
Milligan et al. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15:8783-8798.
Misiura et al. (1990) Biotinyl and phosphotyrosinyl phosphoramidite derivatives useful in the incorporation of multiple reporter groups on synthetic oligonucleotides. Nucleic Acids Res. 18:4345-4354.
Muller et al. (1991) Interaction of fluorescently labeled dideoxynucleotides with HIV-1 reverse transcriptase. Biochemistry 30:3709-3715.
Neenhold & Rana (1995) Major groove opening at the HIV-1 Tat binding site of TAR RNA evidenced by a rhodium probe. Biochemistry 34:6303-6309.
Nielsen (1999) Applications of peptide nucleic acids. Curr Opin Biotechnol 10(1):71-75.
Nordeen (1988) Luciferase reporter gene vectors for analysis of promoters and enhancers. BioTechniques 6:454-457.
Ohlmeyer et al. (1993) Complex synthetic chemical libraries indexed with molecular tags. Proc Natl Acad Sci U S A 90(23):10922-10926.
Ping et al. (1997) Dynamics of RNA-protein interactions in the HIV-1 Rev-RRE complex visualized by 6-thioguanosine-mediated photocrosslinking. RNA 3:850-860.
Puglisi et al. (1992) Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257:76-80.
Scaringe et al. (1990) Chemical synthesis of biologically active oligoribonucleotides using beta-cyanoethyl protected ribonucleoside phosphoramidites. Nucleic Acids Res. 18:5433-5441.
Shah et al. (1994) Synthesis of uridine phosphoramidite analogs: reagents for site-specific incorporation of photoreactive sites into RNA sequences. Bioconjugate Chem. 5:508-512.
Shah et al. (1996) Incorporation of an artificial protease and nuclease at the HIV-1 Tat binding site of trans-activation responsive RNA. Bioconjugate Chem. 7:283-289.
Still (1996) Discovery of sequence-selective peptide binding by synthetic receptors using encoded combinatorial libraries. Accounts of Chemical Research 29:(3) 155-163.
Wang & Rana (1996) RNA conformation in the Tat-TAR complex determined by site-specific photo-cross-linking. Biochemistry 35:6491-6499.
Weeks & Crothers (1993) Major groove accessibility of RNA. 261(5128):1574-1577.
White et al. (1998) Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 391(6666):468-471.
Needles et al. Generation and screening of an oligonucleotide-encoded synthetic peptide library. Proc Natl Acad Sci U S A. Nov. 15, 1993;90(22):10700-4.

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