WO2003052133A3 - Oligonucleotide analogues comprising intercalator pseudonucleotides - Google Patents

Oligonucleotide analogues comprising intercalator pseudonucleotides Download PDF

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Publication number
WO2003052133A3
WO2003052133A3 PCT/DK2002/000875 DK0200875W WO03052133A3 WO 2003052133 A3 WO2003052133 A3 WO 2003052133A3 DK 0200875 W DK0200875 W DK 0200875W WO 03052133 A3 WO03052133 A3 WO 03052133A3
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
intercalator
relates
oligonucleotide
analogues
Prior art date
Application number
PCT/DK2002/000875
Other languages
French (fr)
Other versions
WO2003052133A2 (en
Inventor
Ulf Bech Christensen
Erik Bjerregaard Pedersen
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Unest As
Ulf Bech Christensen
Erik Bjerregaard Pedersen
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Application filed by Unest As, Ulf Bech Christensen, Erik Bjerregaard Pedersen filed Critical Unest As
Priority to AU2002358463A priority Critical patent/AU2002358463A1/en
Publication of WO2003052133A2 publication Critical patent/WO2003052133A2/en
Publication of WO2003052133A3 publication Critical patent/WO2003052133A3/en

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    • 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
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • 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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6832—Enhancement of hybridisation reaction
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • 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
    • C12N2310/13—Decoys
    • 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
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/318—Chemical structure of the backbone where the PO2 is completely replaced, e.g. MMI or formacetal
    • C12N2310/3181—Peptide nucleic acid, PNA
    • 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
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/321—2'-O-R Modification
    • 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
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/323—Chemical structure of the sugar modified ring structure
    • C12N2310/3231—Chemical structure of the sugar modified ring structure having an additional ring, e.g. LNA, ENA
    • 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
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3511—Conjugate intercalating or cleaving agent
    • 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
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3517—Marker; Tag

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

Abstract

The present invention relates to pairs of oligonucleotides or oligonucleotide analogue sequences capable of hybridising to one another, wherein one of or both oligonucleotides/oligonucleotide analogues comprise an intercalator pseudonucleotide. Intercalator pseudonucleotides according to the invention are capable of being incorporated into the phosphate backbone of a nucleic acid and comprise an intercalator comprising at least one essentially flat conjugated system, which is capable of co-stacking with nucleobases of a nucleic acid. Furthermore, the invention relates to oligonucleotide analogues, comprising intercalator pseudonucleotide(s). The invention also relates to methods of detecting hybridisation between a target nucleic acid and an oligonucleotide analogue comprising at least one intercalator pseudonucleotide. Furthermore, methods for amplification of nucleic acids or nucleic acid analogues, comprising using an oligonucleotide analogues comprising an intercalator pseudonucleotide capable of hybridizing with the nucleic acid sequence, which is desirable to amplify are described. In addition the invention relates to methods of modulating transcription of genes.
PCT/DK2002/000875 2001-12-18 2002-12-18 Oligonucleotide analogues comprising intercalator pseudonucleotides WO2003052133A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002358463A AU2002358463A1 (en) 2001-12-18 2002-12-18 Oligonucleotide analogues comprising intercalator pseudonucleotides

Applications Claiming Priority (18)

Application Number Priority Date Filing Date Title
DKPA200101900 2001-12-18
DKPA200101899 2001-12-18
DKPA200101900 2001-12-18
DKPA200101897 2001-12-18
DKPA200101897 2001-12-18
DKPA200101899 2001-12-18
DKPA200101898 2001-12-18
DKPA200101898 2001-12-18
US36554502P 2002-03-20 2002-03-20
US60/365,545 2002-03-20
DKPA200201575 2002-10-14
DKPA200201576 2002-10-14
DKPA200201577 2002-10-14
DKPA200201578 2002-10-14
DKPA200201577 2002-10-14
DKPA200201575 2002-10-14
DKPA200201578 2002-10-14
DKPA200201576 2002-10-14

Publications (2)

Publication Number Publication Date
WO2003052133A2 WO2003052133A2 (en) 2003-06-26
WO2003052133A3 true WO2003052133A3 (en) 2003-10-02

Family

ID=27576036

Family Applications (4)

Application Number Title Priority Date Filing Date
PCT/DK2002/000876 WO2003051901A2 (en) 2001-12-18 2002-12-18 Pseudonucleotide comprising an intercalator
PCT/DK2002/000877 WO2003052134A2 (en) 2001-12-18 2002-12-18 Oligonucleotides comprising intercalator pseudonucleotide(s) for detection of nucleic acids and mutants hereof
PCT/DK2002/000875 WO2003052133A2 (en) 2001-12-18 2002-12-18 Oligonucleotide analogues comprising intercalator pseudonucleotides
PCT/DK2002/000874 WO2003052132A2 (en) 2001-12-18 2002-12-18 Linear and hairpin oligonucleotide analogues comprising intercalator pseudonucleotides

Family Applications Before (2)

Application Number Title Priority Date Filing Date
PCT/DK2002/000876 WO2003051901A2 (en) 2001-12-18 2002-12-18 Pseudonucleotide comprising an intercalator
PCT/DK2002/000877 WO2003052134A2 (en) 2001-12-18 2002-12-18 Oligonucleotides comprising intercalator pseudonucleotide(s) for detection of nucleic acids and mutants hereof

Family Applications After (1)

Application Number Title Priority Date Filing Date
PCT/DK2002/000874 WO2003052132A2 (en) 2001-12-18 2002-12-18 Linear and hairpin oligonucleotide analogues comprising intercalator pseudonucleotides

Country Status (4)

Country Link
EP (1) EP1468007A2 (en)
CN (1) CN1653079B (en)
AU (4) AU2002358464B2 (en)
WO (4) WO2003051901A2 (en)

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WO2004101816A1 (en) * 2003-05-15 2004-11-25 Human Genetic Signatures Pty Ltd Decoys for nucleic acid-binding proteins
DE602004028478D1 (en) 2003-06-17 2010-09-16 Human Genetic Signatures Pty PROCESS FOR GENOMA PLIFICATION
EP1668148B1 (en) 2003-09-04 2008-12-31 Human Genetic Signatures PTY Ltd. Nucleic acid detection assay
JP4397659B2 (en) * 2003-09-11 2010-01-13 独立行政法人科学技術振興機構 DNA detection method using molecular beacon using switching between monomer emission and excimer emission of fluorescent molecules
US8168777B2 (en) 2004-04-29 2012-05-01 Human Genetic Signatures Pty. Ltd. Bisulphite reagent treatment of nucleic acid
DK1794173T3 (en) 2004-09-10 2010-10-25 Human Genetic Signatures Pty Amplification blocks containing intercalating nucleic acids (INA) containing intercalating pseudonucleotides (IPN)
US7671184B2 (en) 2004-09-24 2010-03-02 Universitact Bern Molecular beacons
CN101111606B (en) 2004-12-03 2012-05-16 人类遗传标记控股有限公司 Methods for simplifying microbial nucleic acids by chemical modification of cytosines
SI1888748T1 (en) * 2005-05-25 2014-02-28 Tina Holding Aps Stable and selective formation of hoogsteen-type triplexes and duplexes using twisted intercalating nucleic acids (tina) and process for the preparation of tina
CN101203618B (en) 2005-05-26 2013-03-13 人类遗传标记控股有限公司 Isothermal strand displacement amplification using primers containing a non-regular base
US8343738B2 (en) 2005-09-14 2013-01-01 Human Genetic Signatures Pty. Ltd. Assay for screening for potential cervical cancer
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US8299237B2 (en) 2007-08-30 2012-10-30 Hadasit Medical Research Services & Development Ltd. Nucleic acid sequences comprising NF-κB binding site within O(6)-methylguanine-DNA-methyltransferase (MGMT) promoter region and uses thereof for the treatment of cancer and immune-related disorders
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Publication number Publication date
WO2003052134A2 (en) 2003-06-26
AU2002358463A1 (en) 2003-06-30
AU2002358464B2 (en) 2006-04-27
AU2002358462A1 (en) 2003-06-30
AU2002358463A8 (en) 2003-06-30
AU2002361946A1 (en) 2003-06-30
AU2002358462A8 (en) 2003-06-30
WO2003051901A3 (en) 2003-11-27
WO2003052132A3 (en) 2003-10-09
WO2003051901A2 (en) 2003-06-26
CN1653079B (en) 2010-06-16
CN1653079A (en) 2005-08-10
WO2003052132A2 (en) 2003-06-26
EP1468007A2 (en) 2004-10-20
WO2003052134A3 (en) 2004-03-25
WO2003052133A2 (en) 2003-06-26
AU2002358464A1 (en) 2003-06-30
AU2002361946A8 (en) 2003-06-30

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