WO1999027135A3 - Method for identifying and inhibiting functional nucleic acid molecules in cells - Google Patents

Method for identifying and inhibiting functional nucleic acid molecules in cells Download PDF

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Publication number
WO1999027135A3
WO1999027135A3 PCT/US1998/024854 US9824854W WO9927135A3 WO 1999027135 A3 WO1999027135 A3 WO 1999027135A3 US 9824854 W US9824854 W US 9824854W WO 9927135 A3 WO9927135 A3 WO 9927135A3
Authority
WO
WIPO (PCT)
Prior art keywords
gene
genes
functional
identifying
egss
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US1998/024854
Other languages
French (fr)
Other versions
WO1999027135A2 (en
Inventor
Timothy W Nilsen
Hugh D Robertson
Thomas J Kindt
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Innovir Laboratories Inc
Original Assignee
Innovir Laboratories Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US08/976,220 external-priority patent/US6013447A/en
Application filed by Innovir Laboratories Inc filed Critical Innovir Laboratories Inc
Priority to JP2000522276A priority Critical patent/JP2001524317A/en
Priority to EP98959542A priority patent/EP1032707A2/en
Priority to AU15323/99A priority patent/AU732321B2/en
Priority to CA002310510A priority patent/CA2310510C/en
Publication of WO1999027135A2 publication Critical patent/WO1999027135A2/en
Publication of WO1999027135A3 publication Critical patent/WO1999027135A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/12—Type of nucleic acid catalytic nucleic acids, e.g. ribozymes
    • C12N2310/126—Type of nucleic acid catalytic nucleic acids, e.g. ribozymes involving RNAse P

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

Two methodologies are provided: the first provides a means for rapidly and efficiently identifying essential and functional genes; and the second provides a means for obtaining biologically active nucleic molecules (ribozymes, EGSs, and antisense) which can be used to inactivate functional genes. In the first method, a library of EGSs is prepared based on all possible known compositions. In a preferred embodiment, the EGSs are twelve or thirteen-mers for targeting bacterial RNAse to cleave a substrate. This library is added to the cells containing the genes to be screened, for example, E. coli. Those cells in which the EGS causes a loss of viability, or other phenotype, are identified. The EGS(s) responsible for the loss of viability are analyzed, and the resulting sequence information used to identify the gene within the known genomic sequences. In the second method, nucleotide molecules with optimal biological activity, for example, directing cleavage of a gene of interest by RNase P, are rapidly identified through the use of a vector including two reporter genes, the first in phase with the gene of interest, and the second as a control to verify that the vector is present in a cell or to aid in selection of cells containing the vector. Those cells where the gene of interest is cleaved by the functional oligonucleotide molecule can then be identified by reference to reporter gene 1. The responsible functional oligonucleotide molecules is then isolated and characterized. These methods provide powerful tools for identifying essential genes whose sequence is known only as part of a genome with unknown function, as well as means for identifying functional oligonucleotide molecules, useful as diagnostic reagents and therapeutics.
PCT/US1998/024854 1997-11-21 1998-11-20 Method for identifying and inhibiting functional nucleic acid molecules in cells Ceased WO1999027135A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
JP2000522276A JP2001524317A (en) 1997-11-21 1998-11-20 Methods for identifying and inhibiting functional nucleic acid molecules in cells
EP98959542A EP1032707A2 (en) 1997-11-21 1998-11-20 Method for identifying and inhibiting functional nucleic acid molecules in cells
AU15323/99A AU732321B2 (en) 1997-11-21 1998-11-20 Method for identifying and inhibiting functional nucleic acid molecules in cells
CA002310510A CA2310510C (en) 1997-11-21 1998-11-20 Method for identifying and inhibiting functional nucleic acid molecules in cells

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US08/976,220 US6013447A (en) 1997-11-21 1997-11-21 Random intracellular method for obtaining optimally active nucleic acid molecules
US08/976,220 1997-11-21
US7985198P 1998-03-30 1998-03-30
US60/079,851 1998-03-30

Publications (2)

Publication Number Publication Date
WO1999027135A2 WO1999027135A2 (en) 1999-06-03
WO1999027135A3 true WO1999027135A3 (en) 1999-07-29

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1998/024854 Ceased WO1999027135A2 (en) 1997-11-21 1998-11-20 Method for identifying and inhibiting functional nucleic acid molecules in cells

Country Status (5)

Country Link
EP (1) EP1032707A2 (en)
JP (1) JP2001524317A (en)
AU (1) AU732321B2 (en)
CA (1) CA2310510C (en)
WO (1) WO1999027135A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999028508A1 (en) * 1997-12-04 1999-06-10 Smithkline Beecham Corporation Method of generating conditionally expressed mutant cells using expressible antisense sequences
AU4186600A (en) * 1999-03-31 2000-10-16 Rosetta Inpharmatics, Inc. Essential genes of yeast as targets for antifungal agents, herbicides, insecticides and anti-proliferation drugs
GB9912965D0 (en) * 1999-06-03 1999-08-04 Oxford Biomedica Ltd In vivo selection method
GB9929744D0 (en) * 1999-12-17 2000-02-09 Univ Nottingham Modifying micro-organisms
EP1248856A2 (en) * 1999-12-23 2002-10-16 Xantos Biomedicine AG Screening method for nucleic acids
AU2008202554C1 (en) * 2001-02-23 2011-07-07 Dsm Ip Assets B.V. Novel genes encoding novel proteolytic enzymes
US20130244905A1 (en) * 2010-07-06 2013-09-19 Ed Grabczyk Reporter for RNA Polymerase II Termination

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5168053A (en) * 1989-03-24 1992-12-01 Yale University Cleavage of targeted RNA by RNAase P
WO1993022434A2 (en) * 1992-04-28 1993-11-11 Yale University Targeted cleavage of rna using eukaryotic ribonuclease p and external guide sequence
WO1994013791A1 (en) * 1992-12-04 1994-06-23 Innovir Laboratories, Inc. Regulatable nucleic acid therapeutic and methods of use thereof
WO1996018733A2 (en) * 1994-12-14 1996-06-20 Innovir Laboratories, Inc. Ribozyme-mediated inactivation of leukemia-associated rna
WO1997010360A1 (en) * 1995-09-13 1997-03-20 Chiron Corporation Method and construct for screening for inhibitors of transcriptional activation
WO1997033991A1 (en) * 1996-03-14 1997-09-18 Innovir Laboratories, Inc. Short external guide sequences
WO1998006837A1 (en) * 1996-08-16 1998-02-19 Yale University Phenotypic conversion of drug-resistant bacteria to drug-sensitivity
WO1998032880A1 (en) * 1997-01-23 1998-07-30 Immusol Incorporated Gene functional analysis and discovery using randomized or target-specific ribozyme gene vector libraries

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5168053A (en) * 1989-03-24 1992-12-01 Yale University Cleavage of targeted RNA by RNAase P
WO1993022434A2 (en) * 1992-04-28 1993-11-11 Yale University Targeted cleavage of rna using eukaryotic ribonuclease p and external guide sequence
WO1994013791A1 (en) * 1992-12-04 1994-06-23 Innovir Laboratories, Inc. Regulatable nucleic acid therapeutic and methods of use thereof
WO1996018733A2 (en) * 1994-12-14 1996-06-20 Innovir Laboratories, Inc. Ribozyme-mediated inactivation of leukemia-associated rna
WO1997010360A1 (en) * 1995-09-13 1997-03-20 Chiron Corporation Method and construct for screening for inhibitors of transcriptional activation
WO1997033991A1 (en) * 1996-03-14 1997-09-18 Innovir Laboratories, Inc. Short external guide sequences
WO1998006837A1 (en) * 1996-08-16 1998-02-19 Yale University Phenotypic conversion of drug-resistant bacteria to drug-sensitivity
WO1998032880A1 (en) * 1997-01-23 1998-07-30 Immusol Incorporated Gene functional analysis and discovery using randomized or target-specific ribozyme gene vector libraries

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
GUERRIER-TAKADA C ET AL: "ARTIFICIAL REGULATION OF GENE EXPRESSION IN ESCHERICHIA COLI BY RNASE P", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, vol. 92, 1 November 1995 (1995-11-01), pages 11115 - 11119, XP002052174 *
GUERRIER-TAKADA C ET AL: "PHENOTYPIC CONVERSION OF DRUG-RESISTANT BACTERIA TO DRUG SENSITIVITY", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, vol. 94, no. 16, 5 August 1997 (1997-08-05), pages 8468 - 8472, XP002052175 *
YUAN Y AND ALTMAN S: "Selection of guide sequences that direct efficient cleavage of mRNA by human ribonuclease P", SCIENCE, vol. 263, 1994, pages 1269 - 1273, XP002104825 *
YUAN Y ET AL.: "Targeted cleavage of mRNA by human RNase P", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES USA, vol. 89, 1992, pages 8006 - 8010, XP002104826 *

Also Published As

Publication number Publication date
AU732321B2 (en) 2001-04-12
CA2310510A1 (en) 1999-06-03
JP2001524317A (en) 2001-12-04
EP1032707A2 (en) 2000-09-06
AU1532399A (en) 1999-06-15
WO1999027135A2 (en) 1999-06-03
CA2310510C (en) 2007-04-17

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