WO2003020985B1 - Detection of genetic sequences using a bipartite probe - Google Patents

Detection of genetic sequences using a bipartite probe

Info

Publication number
WO2003020985B1
WO2003020985B1 PCT/US2002/027865 US0227865W WO03020985B1 WO 2003020985 B1 WO2003020985 B1 WO 2003020985B1 US 0227865 W US0227865 W US 0227865W WO 03020985 B1 WO03020985 B1 WO 03020985B1
Authority
WO
WIPO (PCT)
Prior art keywords
sequence
nucleic acid
hybridizing
detectable amplification
amplification molecule
Prior art date
Application number
PCT/US2002/027865
Other languages
French (fr)
Other versions
WO2003020985A1 (en
Inventor
Timothy A Hodge
Shawn O'malley
Original Assignee
Transnetyx 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 Transnetyx Inc filed Critical Transnetyx Inc
Publication of WO2003020985A1 publication Critical patent/WO2003020985A1/en
Publication of WO2003020985B1 publication Critical patent/WO2003020985B1/en

Links

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/00584—Control arrangements for automatic analysers
    • G01N35/00722—Communications; Identification
    • G01N35/00871—Communications between instruments or with remote terminals
    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/30—Staining; Impregnating ; Fixation; Dehydration; Multistep processes for preparing samples of tissue, cell or nucleic acid material and the like for analysis
    • G01N1/31—Apparatus therefor
    • G01N1/312—Apparatus therefor for samples mounted on planar substrates
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/02—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
    • G01N35/025—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations having a carousel or turntable for reaction cells or cuvettes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H40/00—ICT specially adapted for the management or administration of healthcare resources or facilities; ICT specially adapted for the management or operation of medical equipment or devices
    • G16H40/60—ICT specially adapted for the management or administration of healthcare resources or facilities; ICT specially adapted for the management or operation of medical equipment or devices for the operation of medical equipment or devices
    • G16H40/67—ICT specially adapted for the management or administration of healthcare resources or facilities; ICT specially adapted for the management or operation of medical equipment or devices for the operation of medical equipment or devices for remote operation
    • 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
    • B01J2219/00387—Applications using probes
    • 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
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/00527—Sheets
    • B01J2219/00533—Sheets essentially rectangular
    • 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
    • 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
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S436/00—Chemistry: analytical and immunological testing
    • Y10S436/80—Fluorescent dyes, e.g. rhodamine
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S436/00—Chemistry: analytical and immunological testing
    • Y10S436/805—Optical property
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Abstract

The present invention concerns a method to improve detection or quantification of a genetic sequence in a genetic sample using a bipartite probe. A bipartite probe is made of a nucleic acid binding sequence capable of hybridizing a target genetic sequence and a binding probe sequence capable of hybridizing to a detectable amplification molecule through a nucleic acid sequence capable of hybridizing to the binding probe sequence of the bipartite probe. The amplification molecule (6) can be a dendriver that includes a label in its core and/or on any of its arms. Moreover, a secondary signal generation molecule (11) may also be added to the mixture to further increase signal. Similarly, tertiary (20) and quaternary (30), etc. amplification molecules may successively be added to yield increase signal.

Claims

AMENDED CLAIMS
[received by the International Bureau on 4 March 2003 (04.03.03); new claims 1, 16, 20, 24 and 26 replace one or more original claims; claim 7 cancelled, claims 2-6, 8-15, 17-19, 22-23 and 25 unchanged (3 pages)]
IN THE CLAIMS:
I. A method for detection or quantitation of a target genomic sequence in a genetic sample an assay which comprises using:
(a) a bipartite probe consisting essentially of a target nucleic acid binding sequence capable of hybridizing said target genomic sequence and an nucleic acid binding probe sequence capable of hybridizing with a nucleic acid sequence of a primary detectable amplification molecule; and
(b) a primary detectable amplification molecule consisting essentially of a nucleic acid sequence capable of hybridizing the binding probe sequence of said bipartite probe.
II. The method of claim 1 wherein said primary amplification molecule further consists of a nucleic acid binding sequence capable of hybridizing a labeled genetic sequence.
III. The method of claim 2 wherein said labeled genetic sequence is a single stranded oligonucleotide.
IV. The method of claim 2 wherein said primary detectable amplification molecule further consists of a nucleic acid sequence capable of hybridizing to a secondary detectable amplification molecule.
V. The method of claim 4 wherein said secondary detectable amplification molecule is a dendrimer.
VI. The method of claim 1 wherein said primary detectable amplification molecule is a dendrimer.
VII. The method of claim 2 wherein the label of said labeled genetic sequence is selected from the group consisting of enzymes, radioactive isotopes, flurogenic, chemiluminescent, electrochemical materials and members of a specific binding pair.
VIII. The method of claim 1 wherein said method further consists of sequentially hybridizing a second detectable amplification molecule.
34 IX. The method of claim 9 wherein said method further consists of sequentially hybridizing a third detectable amplification molecule.
X. The method of claim 10 wherein said method further consists of sequentially hybridizing a fourth detectable amplification molecule.
XI. The method of claim 1 wherein the said target nucleic acid binding sequence for a eukaryotic organism ranges from between 16 to 20 bases.
XII. The method of claim 1 wherein the said nucleic acid binding sequence for a prokaryotic organism ranges from between 8 to 13 bases.
XIII. The method of claim 1 wherein the said nucleic acid binding sequence is 31 bases.
XIV. The method of claim 1 wherein the said nucleic acid binding probe sequence of the secondary amplification molecule is 31 bases in length.
XV. A method to increase signal strength in an assay for a target genomic sequence in a genetic sample comprising: hybridizing at least one detectable amplification molecule with a bipartite probe in a hybridization solution, said bipartite probe consisting essentially of a target nucleic acid binding sequence capable of hybridizing said target genomic sequence and a binding probe sequence capable of hybridizing with a nucleic acid sequence of at least one detectable amplification molecule.
XVI. The method of claim 16 wherein said at least one detectable amplification molecule includes at least one capture arm.
XVII. The method of claim 17 wherein said at least one capture arm is between 16 to 90 bases.
XVIII. The method of claim 16 wherein said at least one detectable amplification molecule is a dendrimer.
XIX. A method to increase signal strength in an assay for a target genomic sequence in a genetic sample comprising: hybridizing primary and secondary detectable amplification molecules in a hybridization solution and adding a bipartite probe said bipartite probe consisting essentially of a target nucleic acid binding sequence capable of hybridizing said
35 target genomic sequence and a binding probe sequence capable of hybridizing with a nucleic acid sequence of at least one detectable amplification molecule.
XX. The method of claim 20 wherein said primary and secondary detectable amplification molecules are dendrimers.
XXI. The method of claim 20 wherein said detectable amplification molecules include at least one capture arm.
XXII. The method of claim 20 wherein said capture arms are between 16 to 90 bases.
XXIII. A method of forensic analysis for a target nucleic acid sequence comprising:
(a) isolating human genomic DNA;
(b) immobilizing said human genomic DNA on a flat substrate;
(c) hybridizing said human genomic DNA with a bipartite probe consisting essentially of a target nucleic acid binding sequence capable of hybridizing said target genomic sequence and a binding probe sequence capable of hybridizing with a nucleic acid sequence of a primary detectable amplification molecule; and a primary detectable amplification molecule consisting essentially of a nucleic acid sequence capable of hybridizing the binding probe sequence of said bipartite probe;
(d) detecting said detectable amplification molecule; and
(e) correlating said detectable amplification molecule with said target nucleic acid sequence.
XXIV. The method of claim 24 wherein said target nucleic acid sequence is polymorphism in the variable number of tandem repeats of the human genome.
XXV. The method of claim 24 wherein said target nucleic acid binding sequence capable of hybridizing said target genomic sequence comprises SEQ ID NO: 30.
PCT/US2002/027865 2001-09-04 2002-09-03 Detection of genetic sequences using a bipartite probe WO2003020985A1 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US09/945,952 US7011943B2 (en) 2000-09-06 2001-09-04 Method for detecting a designated genetic sequence in murine genomic DNA
US09/945,952 2001-09-04

Publications (2)

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WO2003020985A1 WO2003020985A1 (en) 2003-03-13
WO2003020985B1 true WO2003020985B1 (en) 2003-05-01

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US (4) US7011943B2 (en)
EP (1) EP1978110B1 (en)
TW (2) TWI313713B (en)
WO (1) WO2003020985A1 (en)

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