WO2003014375A3 - Nucleic acid sensor molecules and methods of using same - Google Patents

Nucleic acid sensor molecules and methods of using same Download PDF

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Publication number
WO2003014375A3
WO2003014375A3 PCT/US2002/025319 US0225319W WO03014375A3 WO 2003014375 A3 WO2003014375 A3 WO 2003014375A3 US 0225319 W US0225319 W US 0225319W WO 03014375 A3 WO03014375 A3 WO 03014375A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
acid sensor
sensor molecules
methods
molecules
Prior art date
Application number
PCT/US2002/025319
Other languages
French (fr)
Other versions
WO2003014375A2 (en
Inventor
Martin Stanton
David Epstein
Nobuko Hamaguchi
Markus Kurz
Tony Keefe
Charles Wilson
Dilara Grate
Kristin A Marshall
Thomas Mccauley
Jeffrey Kurz
Original Assignee
Archemix Corp
Martin Stanton
David Epstein
Nobuko Hamaguchi
Markus Kurz
Tony Keefe
Charles Wilson
Dilara Grate
Kristin A Marshall
Thomas Mccauley
Jeffrey Kurz
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 US09/952,680 external-priority patent/US20030087239A1/en
Application filed by Archemix Corp, Martin Stanton, David Epstein, Nobuko Hamaguchi, Markus Kurz, Tony Keefe, Charles Wilson, Dilara Grate, Kristin A Marshall, Thomas Mccauley, Jeffrey Kurz filed Critical Archemix Corp
Priority to AU2002355571A priority Critical patent/AU2002355571A1/en
Publication of WO2003014375A2 publication Critical patent/WO2003014375A2/en
Publication of WO2003014375A3 publication Critical patent/WO2003014375A3/en

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Classifications

    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y30/00—Nanotechnology for materials or surface science, e.g. nanocomposites
    • 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
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • 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
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • 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
    • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
    • C12Q1/485—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase involving kinase
    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6825—Nucleic acid detection involving sensors
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00351—Means for dispensing and evacuation of reagents
    • B01J2219/00385—Printing
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00479—Means for mixing reactants or products in the reaction vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00608—DNA chips
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/0061—The surface being organic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00612—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports the surface being inorganic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00623—Immobilisation or binding
    • B01J2219/00626—Covalent
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00623—Immobilisation or binding
    • B01J2219/0063—Other, e.g. van der Waals forces, hydrogen bonding
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00632—Introduction of reactive groups to the surface
    • B01J2219/00637—Introduction of reactive groups to the surface by coating it with another layer
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00653—Making arrays on substantially continuous surfaces the compounds being bound to electrodes embedded in or on the solid supports
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00659—Two-dimensional arrays
    • B01J2219/00662—Two-dimensional arrays within two-dimensional arrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00686—Automatic
    • B01J2219/00691—Automatic using robots
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B60/00—Apparatus specially adapted for use in combinatorial chemistry or with libraries
    • C40B60/14—Apparatus specially adapted for use in combinatorial chemistry or with libraries for creating libraries

Abstract

Methods for engineering a nucleic acid sensor molecule are provided. Biosensors comprise a plurality of nucleic acid sensor molecules labeled with a first signaling moiety and a second signaling moiety. The nucleic acid sensor molecules recognizes target molecules which do not naturally bind to DNA. Binding of a target molecule to the sensor molecules triggers a change in the proximity of the signaling moieties which leads to a change in the optical properties of the nucleic acid sensor molecules on the biosensor. Reagents and systems for performing the method are also provided. The method is useful in diagnostic applications and drug optimization.
PCT/US2002/025319 2001-08-09 2002-08-09 Nucleic acid sensor molecules and methods of using same WO2003014375A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002355571A AU2002355571A1 (en) 2001-08-09 2002-08-09 Nucleic acid sensor molecules and methods of using same

Applications Claiming Priority (20)

Application Number Priority Date Filing Date Title
US31137801P 2001-08-09 2001-08-09
US60/311,378 2001-08-09
US31393201P 2001-08-21 2001-08-21
US60/313,932 2001-08-21
US09/952,680 2001-09-13
US09/952,680 US20030087239A1 (en) 2000-09-13 2001-09-13 Target activated nucleic acid biosensor and methods of using same
US33818601P 2001-11-13 2001-11-13
US60/338,186 2001-11-13
US34995902P 2002-01-18 2002-01-18
US60/349,959 2002-01-18
US36448602P 2002-03-13 2002-03-13
US60/364,486 2002-03-13
US36799102P 2002-03-25 2002-03-25
US60/367,991 2002-03-25
US36988702P 2002-04-04 2002-04-04
US60/369,887 2002-04-04
US37674402P 2002-05-01 2002-05-01
US60/376,744 2002-05-01
US38509702P 2002-05-31 2002-05-31
US60/385,097 2002-05-31

Publications (2)

Publication Number Publication Date
WO2003014375A2 WO2003014375A2 (en) 2003-02-20
WO2003014375A3 true WO2003014375A3 (en) 2003-10-16

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/025319 WO2003014375A2 (en) 2001-08-09 2002-08-09 Nucleic acid sensor molecules and methods of using same

Country Status (2)

Country Link
AU (1) AU2002355571A1 (en)
WO (1) WO2003014375A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8853376B2 (en) 2002-11-21 2014-10-07 Archemix Llc Stabilized aptamers to platelet derived growth factor and their use as oncology therapeutics

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2003247576A1 (en) * 2002-06-18 2003-12-31 Archemix Corp. Aptamer-toxin molecules and methods for using same
CA2492463A1 (en) 2002-07-25 2004-02-05 Archemix Corporation Regulated aptamer therapeutics
US10100316B2 (en) 2002-11-21 2018-10-16 Archemix Llc Aptamers comprising CPG motifs
US8039443B2 (en) 2002-11-21 2011-10-18 Archemix Corporation Stabilized aptamers to platelet derived growth factor and their use as oncology therapeutics
DK2831587T3 (en) 2012-03-27 2018-07-23 Ventana Med Syst Inc Signaling conjugates and methods of use
WO2014102806A1 (en) * 2012-12-31 2014-07-03 Yeda Research And Development Co. Ltd. Protein biosensors, cross reactive sensor arrays and methods of use thereof

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WO1996027026A1 (en) * 1995-02-27 1996-09-06 Intelligene Ltd. Detection of biomolecules
US5589332A (en) * 1992-12-04 1996-12-31 Innovir Laboratories, Inc. Ribozyme amplified diagnostics
WO1999047704A1 (en) * 1998-03-17 1999-09-23 Andreas Jenne Composition containing dna coding for a ribozyme and an oligonucleotide substrate, and method for measuring transcription rates
WO1999050277A1 (en) * 1998-03-28 1999-10-07 University Of Utah Research Foundation Circular, hairpin, circular/hairpin, lariat, and hairpin-lariat hammerhead ribozymes
US6201113B1 (en) * 1998-03-05 2001-03-13 Alison V. Todd Zymogenic nucleic acid molecules

Patent Citations (5)

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Publication number Priority date Publication date Assignee Title
US5589332A (en) * 1992-12-04 1996-12-31 Innovir Laboratories, Inc. Ribozyme amplified diagnostics
WO1996027026A1 (en) * 1995-02-27 1996-09-06 Intelligene Ltd. Detection of biomolecules
US6201113B1 (en) * 1998-03-05 2001-03-13 Alison V. Todd Zymogenic nucleic acid molecules
WO1999047704A1 (en) * 1998-03-17 1999-09-23 Andreas Jenne Composition containing dna coding for a ribozyme and an oligonucleotide substrate, and method for measuring transcription rates
WO1999050277A1 (en) * 1998-03-28 1999-10-07 University Of Utah Research Foundation Circular, hairpin, circular/hairpin, lariat, and hairpin-lariat hammerhead ribozymes

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
HASELOFF ET AL.: "Simple RNA enzymes with new and highly specific endoribonuclease activities", NATURE, vol. 334, 18 August 1998 (1998-08-18), pages 585 - 591, XP002017008 *
TUSCHL ET AL.: "A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements", SCIENCE, vol. 266, 4 November 1994 (1994-11-04), pages 785 - 789, XP002965485 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8853376B2 (en) 2002-11-21 2014-10-07 Archemix Llc Stabilized aptamers to platelet derived growth factor and their use as oncology therapeutics

Also Published As

Publication number Publication date
AU2002355571A1 (en) 2003-02-24
WO2003014375A2 (en) 2003-02-20

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