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WO1996029097A1 - Oligonucleotides a boucle et tige et circulaires - Google Patents

Oligonucleotides a boucle et tige et circulaires Download PDF

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Publication number
WO1996029097A1
WO1996029097A1 PCT/US1995/003602 US9503602W WO9629097A1 WO 1996029097 A1 WO1996029097 A1 WO 1996029097A1 US 9503602 W US9503602 W US 9503602W WO 9629097 A1 WO9629097 A1 WO 9629097A1
Authority
WO
WIPO (PCT)
Prior art keywords
domain
oligonucleotide
target
binding
nucleic acid
Prior art date
Application number
PCT/US1995/003602
Other languages
English (en)
Inventor
Eric T. Kool
Original Assignee
Research Corporation Technologies, 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
Application filed by Research Corporation Technologies, Inc. filed Critical Research Corporation Technologies, Inc.
Priority to PCT/US1995/003602 priority Critical patent/WO1996029097A1/fr
Publication of WO1996029097A1 publication Critical patent/WO1996029097A1/fr

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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
    • 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
    • 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
    • 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
    • C12Q1/6839—Triple helix formation or other higher order conformations in hybridisation assays
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • C12N2310/11—Antisense
    • C12N2310/111—Antisense spanning the whole gene, or a large part of it
    • 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
    • C12N2310/15—Nucleic acids forming more than 2 strands, e.g. TFOs
    • C12N2310/152—Nucleic acids forming more than 2 strands, e.g. TFOs on a single-stranded target, e.g. fold-back TFOs
    • 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
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed

Definitions

  • a portion of a target sequence is known, one skilled in the art can refer to the base pairing rules provided hereinbelow to design oligonucleotides that detectably bind to the target with higher affinity than a corresponding linear oligonucleotide.
  • the sequence of the WC domain of the subject stem-loop and circular oligonucleotides is determined by the following base pairing rules with reference to a defined nucleic acid target.
  • the circular oligonucleotides of the present invention can be made first as linear oligonucleotides and then circularized.
  • Linear oligonucleotides can be made by any of a myriad of procedures known for making DNA or RNA oligonucleotides. For example, such procedures include enzymatic synthesis and chemical synthesis.
  • RNA circularization incorporates the appropriate nucleotide sequences, preferably in a linker domain, into an RNA oligonucleotide to promote self splicing, since a circular product is formed under the appropriate conditions (Sugimoto et ajL. , 1988, Biochemistry 27:6384- 6392) .
  • the subject stem-loop oligonucleotides can be made by the procedures described hereinabove for the synthesis of linear oligonucleotides.
  • the present stem- loop oligonucleotides can be also made recombinantly by placing a nucleic acid having a sequence which is complementary to the desired stem-loop oligonucleotide into an expression vector.
  • Such an expression vector minimally encodes a segment which can effect expression of the stem-loop oligonucleotide when the segment is operably linked to the nucleic acid encoding the stem- loop oligonucleotide.
  • such an expression vector can also encode additional elements such as origins of replication, selectable markers, transcription termination signals, centromeres, autonomous replication sequences.
  • the present invention provides a kit for isolation of a template nucleic acid.
  • a kit has at least one first container providing a stem-loop or circular oligonucleotide having a WC domain that is complementary to a target contained within the template.
  • a kit for the detection of any target nucleic acid is provided which contains an oligonucleotide of the present invention linked to a reporter group. Additional containers providing reagents for detecting a linked reporter group can also be provided in the kit.
  • Free energies were determined by curve fitting as described by Petersheim et aM (1982) Biochemistry ⁇ 2:256. Values at 60°C are more accurate than those at 37°C because of smaller extrapolation from the T values.
  • a circular DNA (oligonucleotide 5) having the sequence:

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biomedical Technology (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Plant Pathology (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

L'invention concerne des oligonucléotides à tige/boucle et circulaires comprenant chacun un domaine de liaison de Watson Crick (WC) et au moins un domaine de liaison de Hoogsteen (H) correspondant, ces derniers étant séparés l'un de l'autre par des domaines de liaison. Chaque domaine WC présente une complémentarité suffisante pour se lier à un brin d'acide nucléique cible défini, par appariement de bases de Watson Crick selon une orientation antiparallèle. Chaque domaine H correspondant est capable de se lier au domaine WC par appariement de bases de Hoogsteen selon une configuration antiparallèle. L'invention concerne également des procédés de préparation et d'utilisation de ces oligonucléotides ainsi que des trousses et des compositions pharmaceutiques contenant ces derniers.
PCT/US1995/003602 1995-03-21 1995-03-21 Oligonucleotides a boucle et tige et circulaires WO1996029097A1 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
PCT/US1995/003602 WO1996029097A1 (fr) 1995-03-21 1995-03-21 Oligonucleotides a boucle et tige et circulaires

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/US1995/003602 WO1996029097A1 (fr) 1995-03-21 1995-03-21 Oligonucleotides a boucle et tige et circulaires

Publications (1)

Publication Number Publication Date
WO1996029097A1 true WO1996029097A1 (fr) 1996-09-26

Family

ID=22248854

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1995/003602 WO1996029097A1 (fr) 1995-03-21 1995-03-21 Oligonucleotides a boucle et tige et circulaires

Country Status (1)

Country Link
WO (1) WO1996029097A1 (fr)

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002004667A3 (fr) * 2000-07-07 2002-12-27 Helen Lee Signal de detection et capture ameliores dans des analyses sur bandelettes
WO2003020931A3 (fr) * 2001-09-01 2003-11-20 Galapagos Genomics Nv Dosage biologique de choc a interference arn de courte duree et constructions
WO2004072294A3 (fr) * 2003-02-12 2005-03-10 Global Genomics Ab Procedes et moyen de sequençage de sequences nucleotidiques
EP1578761A4 (fr) * 2002-11-05 2008-03-26 Isis Pharmaceuticals Inc Motifs structurels, composes oligomeriques et utilisation de ceux-ci dans la modulation de gene
US7893036B2 (en) 2001-07-12 2011-02-22 University Of Massachusetts In vivo production of small interfering RNAs that mediate gene silencing
EP1900815B1 (fr) * 2001-07-12 2016-09-07 University of Massachusetts Production in vivo de petits ARN interférents qui modèrent le silençage génique

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5208149A (en) * 1983-10-20 1993-05-04 The Research Foundation Of State University Of New York Nucleic acid constructs containing stable stem and loop structures

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5208149A (en) * 1983-10-20 1993-05-04 The Research Foundation Of State University Of New York Nucleic acid constructs containing stable stem and loop structures

Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
ADVANCES IN VIRUS RESEARCH, Volume 44, Published 1994, MARAMOROSCH et al., by ACADEMIC PRESS (SAN DIEGO), pages 267-303. *
ANTISENSE RESEARCH AND DEVELOPMENT, Volume 4, issued 05 May 1994, C.H. HOBBS et al., "Differential Regulation of Gene Expression In Vivo by Triple Helix Forming Oligonucleotides as Detected by a Reporter Enzyme", pages 1-8. *
ANTISENSE RESEARCH AND DEVELOPMENT, Volume 4, issued 09 August 1994, B. PODDEVIN, "Improved Anti-Herpes Simplex Virus Type I Activity of a Phosphodiester Antisense Oligonucleotide Containing a 3'-Terminal Hairpin-Like Structure", pages 147-154. *
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Volume 113, No. 16, issued 31 July 1991, S.T. CLOAD et al., "Polyether Tethered Oligonucleotide Probes", pages 6324-6326. *
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Volume 114, issued 22 April 1992, G. PRAKASH et al., "Structural Effects in the Recognition of DNA by Circular Oligonucleotides", pages 3523-3527. *
PROC. NATL. ACAD. SCI. U.S.A., Volume 85, issued August 1988, J. GOODCHILD et al., "Inhibition of Human Immunodeficiency Virus Replication by Antisense Oligodeoxynucleotides", pages 5507-5511. *
PROC. NATL. ACAD. SCI. U.S.A., Volume 91, issued September 1994, D.S. PILCH et al., "Ligand Induced Formation of Nucleic Acid Triple Helices", pages 9332-9336. *
SCIENCE, Volume 241, issued 22 July 1988, M. COONEY et al., "Site-Specific Oligonucleotide Binding Represses Transcription of the Human C-myc Gene In Vitro", pages 456-459. *

Cited By (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002004667A3 (fr) * 2000-07-07 2002-12-27 Helen Lee Signal de detection et capture ameliores dans des analyses sur bandelettes
EP1900815B1 (fr) * 2001-07-12 2016-09-07 University of Massachusetts Production in vivo de petits ARN interférents qui modèrent le silençage génique
US7893036B2 (en) 2001-07-12 2011-02-22 University Of Massachusetts In vivo production of small interfering RNAs that mediate gene silencing
US8232260B2 (en) 2001-07-12 2012-07-31 University Of Massachusetts In vivo production of small interfering RNAs that mediate gene silencing
US8530438B2 (en) 2001-07-12 2013-09-10 University Of Massachusetts Vivo production of small interfering RNAs that mediate gene silencing
US8557785B2 (en) 2001-07-12 2013-10-15 University Of Massachusetts In vivo production of small interfering RNAS that mediate gene silencing
US9175287B2 (en) 2001-07-12 2015-11-03 University Of Massachusetts In vivo production of small interfering RNAs that mediate gene silencing
EP2360251B1 (fr) * 2001-07-12 2016-09-28 University of Massachusetts Production in vivo de petits ARN interférents qui modèrent le silençage génique
US9850487B2 (en) 2001-07-12 2017-12-26 University Of Massachusetts In vivo production of small interfering RNAs that mediate gene silencing
US10731155B2 (en) 2001-07-12 2020-08-04 University Of Massachusetts In vivo production of small interfering RNAs that mediate gene silencing
WO2003020931A3 (fr) * 2001-09-01 2003-11-20 Galapagos Genomics Nv Dosage biologique de choc a interference arn de courte duree et constructions
EP1578761A4 (fr) * 2002-11-05 2008-03-26 Isis Pharmaceuticals Inc Motifs structurels, composes oligomeriques et utilisation de ceux-ci dans la modulation de gene
WO2004072294A3 (fr) * 2003-02-12 2005-03-10 Global Genomics Ab Procedes et moyen de sequençage de sequences nucleotidiques

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