CA2310510A1 - 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

Info

Publication number
CA2310510A1
CA2310510A1 CA002310510A CA2310510A CA2310510A1 CA 2310510 A1 CA2310510 A1 CA 2310510A1 CA 002310510 A CA002310510 A CA 002310510A CA 2310510 A CA2310510 A CA 2310510A CA 2310510 A1 CA2310510 A1 CA 2310510A1
Authority
CA
Canada
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.)
Granted
Application number
CA002310510A
Other languages
French (fr)
Other versions
CA2310510C (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.)
Yale University
Original Assignee
Individual
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 Individual filed Critical Individual
Publication of CA2310510A1 publication Critical patent/CA2310510A1/en
Application granted granted Critical
Publication of CA2310510C publication Critical patent/CA2310510C/en
Anticipated expiration legal-status Critical
Expired - Fee Related legal-status Critical Current

Links

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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biomedical Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Plant Pathology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (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.
CA002310510A 1997-11-21 1998-11-20 Method for identifying and inhibiting functional nucleic acid molecules in cells Expired - Fee Related CA2310510C (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US976,220 1997-11-21
US08/976,220 US6013447A (en) 1997-11-21 1997-11-21 Random intracellular method for obtaining optimally active nucleic acid molecules
US7985198P 1998-03-30 1998-03-30
US60/079,851 1998-03-30
PCT/US1998/024854 WO1999027135A2 (en) 1997-11-21 1998-11-20 Method for identifying and inhibiting functional nucleic acid molecules in cells

Publications (2)

Publication Number Publication Date
CA2310510A1 true CA2310510A1 (en) 1999-06-03
CA2310510C CA2310510C (en) 2007-04-17

Family

ID=26762503

Family Applications (1)

Application Number Title Priority Date Filing Date
CA002310510A Expired - Fee Related CA2310510C (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
EP1034308A4 (en) * 1997-12-04 2002-04-03 Smithkline Beecham Corp Method of generating conditionally expressed mutant cells using expressible antisense sequences
WO2000058457A2 (en) * 1999-03-31 2000-10-05 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
US20030134265A1 (en) * 1999-12-23 2003-07-17 Peter Buckel 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

Family Cites Families (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
EP0707638A4 (en) * 1992-12-04 1998-05-20 Innovir Lab Inc Regulatable nucleic acid therapeutic and methods of use thereof
AU4961996A (en) * 1994-12-14 1996-07-03 Innovir Laboratories, Inc. Ribozyme-mediated inactivation of leukemia-associated rna
AU6904596A (en) * 1995-09-13 1997-04-01 Chiron Corporation Method and construct for screening for inhibitors of transcriptional activation
US5877162A (en) * 1996-03-14 1999-03-02 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
CA2278734A1 (en) * 1997-01-23 1998-07-30 Immusol Incorporated Gene functional analysis and discovery using randomized or target-specific ribozyme gene vector libraries

Also Published As

Publication number Publication date
EP1032707A2 (en) 2000-09-06
AU732321B2 (en) 2001-04-12
AU1532399A (en) 1999-06-15
WO1999027135A3 (en) 1999-07-29
JP2001524317A (en) 2001-12-04
CA2310510C (en) 2007-04-17
WO1999027135A2 (en) 1999-06-03

Similar Documents

Publication Publication Date Title
Tao et al. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing
Oeltjen et al. Large-scale comparative sequence analysis of the human and murine Bruton’s tyrosine kinase loci reveals conserved regulatory domains
Verdine et al. How do DNA repair proteins locate damaged bases in the genome?
Strobel et al. Double strand cleavage of genomic DNA at a single site by triple helix formation
US10465187B2 (en) Integrated system for programmable DNA methylation
Boerrigter et al. Plasmid-based transgenic mouse model for studying in vivo mutations.
Ouellette et al. Toxic cyanobacteria: the evolving molecular toolbox
US20020106673A1 (en) Method of sequencing by hybridization of oligonucleotide probes
EP2264165B1 (en) Selection and isolation of living cells using mRNA-binding probes
KR20080083179A (en) Improved targeted nucleotide exchange with lna modified oligonucleotides
US20040235013A1 (en) Method of sequencing by hybridization of oligonucleotide probes
Rizzo et al. Chimeric RNA–DNA molecular beacon assay for ribonuclease H activity
Lengerova et al. Multicolor FISH mapping of the dioecious model plant, Silene latifolia
CA2076750A1 (en) Nucleic acid amplification with dna-dependent rna polymerase activity of rna replicases
Chen et al. Sequence-specific scission of DNA by the chemical nuclease activity of 1, 10-phenanthroline-copper (I) targeted by RNA.
US20230257799A1 (en) Methods of identifying and characterizing gene editing variations in nucleic acids
CA2310510A1 (en) Method for identifying and inhibiting functional nucleic acid molecules in cells
WO1995011971A1 (en) Nucleic acid marker ladder for estimating mass
Herdewijn Oligonucleotide synthesis: methods and applications
CN116751764B (en) Cas9 protein, type II CRISPR/Cas9 gene editing system and application
Joshi et al. MutS recognition: multiple mismatches and sequence context effects
Shimoda et al. Mermaid, a family of short interspersed repetitive elements, is useful for zebrafish genome mapping
Konrad et al. Initial nucleotide frequencies of bacterial RNA synthesized during amino-acid starvation or changes of carbon source
AU4255899A (en) Method for non-radioactive detection of membrane-bonded nucleic acids and test kit
JPH09154581A (en) Substantially pure microorganism capable of producing uricase

Legal Events

Date Code Title Description
EEER Examination request
MKLA Lapsed

Effective date: 20141120