WO2001094625A2 - Capture moieties for nucleic acids and uses thereof - Google Patents

Capture moieties for nucleic acids and uses thereof Download PDF

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Publication number
WO2001094625A2
WO2001094625A2 PCT/CA2001/000820 CA0100820W WO0194625A2 WO 2001094625 A2 WO2001094625 A2 WO 2001094625A2 CA 0100820 W CA0100820 W CA 0100820W WO 0194625 A2 WO0194625 A2 WO 0194625A2
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
probe
target
acid sequence
sequence
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.)
Ceased
Application number
PCT/CA2001/000820
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English (en)
French (fr)
Other versions
WO2001094625A3 (en
Inventor
Susan Bortolin
Roman L. Zastawny
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.)
Luminex Molecular Diagnostics Inc
Original Assignee
TM Bioscience Corp
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 TM Bioscience Corp filed Critical TM Bioscience Corp
Priority to US10/297,539 priority Critical patent/US7230092B2/en
Priority to EP01944793A priority patent/EP1313881A2/en
Priority to AU2001267191A priority patent/AU2001267191A1/en
Priority to JP2002502165A priority patent/JP2003535599A/ja
Publication of WO2001094625A2 publication Critical patent/WO2001094625A2/en
Anticipated expiration legal-status Critical
Publication of WO2001094625A3 publication Critical patent/WO2001094625A3/en
Priority to US11/807,328 priority patent/US7914989B2/en
Ceased legal-status Critical Current

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Classifications

    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer

Definitions

  • temperature for hybridization needs to be controlled closely, preferably to better than +/- 1°C.
  • a and C of the molecule A-B-C-D-E-F-G are complementary to each other and covalently linked to each other by B so as to form a second intramolecular duplex under said set of conditions.
  • Figure 12A and 12B is a schematic illustrating the use of a nucleic acid capture moiety of the invention in priming synthesis in the presence of complex mixture of nucleic acid sequences.
  • the target nucleic acid sequence may be so labelled, or , alternatively, labelled secondary probes may be employed.
  • a "secondary probe" includes a nucleic acid sequence which is complementary to either a region of the target nucleic acid sequence or to a region of the capture moiety. Region G of a probe (which will most often not be complementary to the target, might be useful in capturing a secondary labelled nucleic acid probe.
  • “Substantially complementary” means capable of forming a hybrid stable enough to allow for propagation of duplex formation between target and probe under the conditions employed.
  • the nucleation site of a probe of the invention should be long enough to allow a matching target to bind.
  • the nucleation site should be at least 3 bases, more preferably 5 bases, but fewer than 8 bases in length.
  • the orientation of the nucleic acid capture moiety and hence the target binding region can be in either the 5 ' -3 ' or 3 ' -5 ' direction.
  • Probes having SEQ ID NOs: 1 and 2 were tested to determine their relative abilities in discriminating between molecules having SEQ ID NOs:3 to 13 (Table 1).
  • Example 1 The protocol outlined in Example 1 was followed with probes having SEQ ID NOs: 1 and 14 with targets having SEQ ID NOs:3 and 6 to 11. The results are shown in Figure 4. In this case, net RLUs (relative light units) are plotted for each target and probe combination tested. It can be seen that the intensity of the results obtained with the probe lacking the first hai ⁇ in ( Figure 4B) are generally much lower than the intensity of the results obtained with the double-hai ⁇ in probe ( Figure 4A). This indicates that the sensitivity of a system using the double hai ⁇ in probe should be substantially greater than the sensitivity of an assay using a comparable probe lacking the 5 '-hai ⁇ in.
  • White, opaque, flat-bottom microtitre wells (Costar) were first coated using 100 ⁇ L of 0.2 ⁇ mol/L avidin in carbonate buffer (0.05 M carbonate/bicarbonate pH 9.6). Following a one hour incubation at room temperature, the wells were washed 6x in assay buffer (IM NaCl, 0. IM Tris, 0.08% Triton X-100, pH 8.0) using a Dynex 96-pin automated washer. All probes were diluted in assay buffer to a final concentration of 0.05 ⁇ mol/L. One hundred microlitres of each probe (5 pmol/well) were then added to the avidin-coated wells, incubated for 30 minutes at room temperature while shaking and washed 6x using assay buffer.
  • assay buffer IM NaCl, 0. IM Tris, 0.08% Triton X-100, pH 8.0
  • Probes of this invention will find application as members of a universal family of probes.
  • a particular application includes the use of a family of HP 2 probes or a family of linear looped probes for discriminating between several closely related sequences present in multiplexed systems.
  • Such a family could be included as part of a microarray or as part of a bead-based universal array.
  • An example of one such system involves the Luminex 100 LabMAP technology which uses 100 spectrally distinct bead populations to simultaneously measure up to 100 different analytes in a single reaction. Each of the 100 different carboxylated bead populations could be coupled to a unique amino-modified probe of the present invention.
  • a family of probes of the present invention comprises a family of "tags", as they are often referred to in the art.
  • An example for covalently linking such a tag to a solid carboxylated bead support involves the use of l-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) as a cross-linking reagent in a buffer consisting of 0.1 M MES (2-(N-mo ⁇ holino) ethane sulfonic acid) pH 4.5 or similar linking chemistry.
  • EDC l-ethyl-3-(3-dimethylaminopropyl)-carbodiimide

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
PCT/CA2001/000820 2000-06-06 2001-06-06 Capture moieties for nucleic acids and uses thereof Ceased WO2001094625A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
US10/297,539 US7230092B2 (en) 2000-06-06 2001-06-06 Capture moieties for nucleic acids and uses thereof
EP01944793A EP1313881A2 (en) 2000-06-06 2001-06-06 Capture moieties for nucleic acids and uses thereof
AU2001267191A AU2001267191A1 (en) 2000-06-06 2001-06-06 Capture moieties for nucleic acids and uses thereof
JP2002502165A JP2003535599A (ja) 2000-06-06 2001-06-06 核酸の捕捉部とその使用
US11/807,328 US7914989B2 (en) 2000-06-06 2007-05-25 Capture moieties for nucleic acids and uses thereof

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US20959500P 2000-06-06 2000-06-06
US60/209,595 2000-06-06

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US10297539 A-371-Of-International 2001-06-06
US11/807,328 Continuation US7914989B2 (en) 2000-06-06 2007-05-25 Capture moieties for nucleic acids and uses thereof

Publications (2)

Publication Number Publication Date
WO2001094625A2 true WO2001094625A2 (en) 2001-12-13
WO2001094625A3 WO2001094625A3 (en) 2003-03-13

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/CA2001/000820 Ceased WO2001094625A2 (en) 2000-06-06 2001-06-06 Capture moieties for nucleic acids and uses thereof

Country Status (5)

Country Link
US (2) US7230092B2 (enExample)
EP (1) EP1313881A2 (enExample)
JP (1) JP2003535599A (enExample)
AU (1) AU2001267191A1 (enExample)
WO (1) WO2001094625A2 (enExample)

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JP2006520206A (ja) * 2003-03-13 2006-09-07 ヴァラ，クリストフ プローブ、バイオチップおよびそれらの使用方法
US7208295B2 (en) 2001-11-19 2007-04-24 Affymetrix, Inc. Multiplex oligonucleotide addition and target amplification
US7291459B2 (en) * 2002-12-10 2007-11-06 University Of Alabama At Huntsville Nucleic acid detector and method of detecting targets within a sample
EP1876246A1 (en) * 2006-07-03 2008-01-09 FUJIFILM Corporation Self-complementary primers used in LAMP gene amplification method
WO2007114986A3 (en) * 2006-04-04 2008-01-31 Arcxis Biotechnologies Inc Cooperative probes and methods of using them
AU2005262357B2 (en) * 2004-07-01 2009-10-29 Gen-Probe Incorporated Methods and compositions to detect nucleic acids in a biological sample
EP2343383A1 (fr) * 2006-04-25 2011-07-13 Biomérieux Nouvelle sonde de détection agissant par reconnaissance moléculaire
US8399222B2 (en) 2008-11-25 2013-03-19 Gen-Probe Incorporated Compositions and methods for detecting small RNAs, and uses thereof
WO2013116774A1 (en) * 2012-02-01 2013-08-08 Gen-Probe Incorporated Asymmetric hairpin target capture oligomers
US8628924B2 (en) 2009-07-21 2014-01-14 Gen-Probe Incorporated Methods and compositions for quantitative amplification and detection over a wide dynamic range
WO2015083001A3 (en) * 2013-12-02 2015-11-26 Vanadis Diagnostics Nucleic acid probe and method of detecting genomic fragments
US9297036B2 (en) * 2005-07-01 2016-03-29 Agilent Technologies, Inc Nucleic acid probes for analysis of small RNAs and other polynucleotides
US9938641B2 (en) 2006-12-18 2018-04-10 Fluidigm Corporation Selection of aptamers based on geometry
EP3250716A4 (en) * 2015-01-30 2018-10-24 President and Fellows of Harvard College Microscope-free imaging
US10190151B2 (en) 2014-03-11 2019-01-29 President And Fellows Of Harvard College High-throughput and highly multiplexed imaging with programmable nucleic acid probes
US10316352B2 (en) 2008-05-13 2019-06-11 Gen-Probe Incorporated Methods of capturing a target nucleic acid for amplification and detection using an inactivatable target capture oligomer
US10407717B2 (en) 2001-11-19 2019-09-10 Affymetrix, Inc. Methods of analysis of methylation
US10508300B2 (en) 2015-09-18 2019-12-17 Vanadis Diagnostics Probe set for analyzing a DNA sample and method for using the same
US10526643B2 (en) 2013-12-02 2020-01-07 Vanadis Diagnostics Multiplex detection of nucleic acids
US10577647B2 (en) 2009-06-29 2020-03-03 Luminex Corporation Chimeric primers with hairpin conformations and methods of using same
US11359229B2 (en) 2016-09-20 2022-06-14 President And Fellows Of Harvard College Molecular verification systems
US12142104B2 (en) 2018-03-22 2024-11-12 President And Fellows Of Harvard College Methods and compositions for molecular authentication

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US10407717B2 (en) 2001-11-19 2019-09-10 Affymetrix, Inc. Methods of analysis of methylation
US7208295B2 (en) 2001-11-19 2007-04-24 Affymetrix, Inc. Multiplex oligonucleotide addition and target amplification
US7510829B2 (en) 2001-11-19 2009-03-31 Affymetrix, Inc. Multiplex PCR
US7754451B2 (en) 2001-11-19 2010-07-13 Affymetrix, Inc. Multiplex oligonucleotide addition and target amplification
US10822642B2 (en) 2001-11-19 2020-11-03 Affymetrix, Inc. Methods of analysis of methylation
US7291459B2 (en) * 2002-12-10 2007-11-06 University Of Alabama At Huntsville Nucleic acid detector and method of detecting targets within a sample
JP2006520206A (ja) * 2003-03-13 2006-09-07 ヴァラ，クリストフ プローブ、バイオチップおよびそれらの使用方法
AU2005262357B2 (en) * 2004-07-01 2009-10-29 Gen-Probe Incorporated Methods and compositions to detect nucleic acids in a biological sample
US8551766B2 (en) 2004-07-01 2013-10-08 Gen-Probe Incorporated Methods and compositions to detect nucleic acids in a biological sample
US8034554B2 (en) * 2004-07-01 2011-10-11 Gen-Probe Incorporated Methods and compositions to detect nucleic acids in a biological sample
US9297036B2 (en) * 2005-07-01 2016-03-29 Agilent Technologies, Inc Nucleic acid probes for analysis of small RNAs and other polynucleotides
WO2007114986A3 (en) * 2006-04-04 2008-01-31 Arcxis Biotechnologies Inc Cooperative probes and methods of using them
AU2007233270B2 (en) * 2006-04-04 2013-06-20 Fluidigm Corporation Cooperative probes and methods of using them
EP2343383A1 (fr) * 2006-04-25 2011-07-13 Biomérieux Nouvelle sonde de détection agissant par reconnaissance moléculaire
EP1876246A1 (en) * 2006-07-03 2008-01-09 FUJIFILM Corporation Self-complementary primers used in LAMP gene amplification method
US9938641B2 (en) 2006-12-18 2018-04-10 Fluidigm Corporation Selection of aptamers based on geometry
US10316352B2 (en) 2008-05-13 2019-06-11 Gen-Probe Incorporated Methods of capturing a target nucleic acid for amplification and detection using an inactivatable target capture oligomer
US10829801B2 (en) 2008-05-13 2020-11-10 Gen-Probe Incorporated Inactivatable target capture oligomers for use in the selective hybridization and capture of target nucleic acid sequences
US12065693B2 (en) 2008-05-13 2024-08-20 Gen-Probe Incorporated Inactivatable target capture oligomers for use in the selective hybridization and capture of target nucleic acid sequences
US8951730B2 (en) 2008-11-25 2015-02-10 Gen-Probe Incorporated Compositions for detecting small RNAs
US8399222B2 (en) 2008-11-25 2013-03-19 Gen-Probe Incorporated Compositions and methods for detecting small RNAs, and uses thereof
US10577647B2 (en) 2009-06-29 2020-03-03 Luminex Corporation Chimeric primers with hairpin conformations and methods of using same
US12473586B2 (en) 2009-06-29 2025-11-18 Luminex Corporation Chimeric primers with hairpin conformations and methods of using same
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US9347098B2 (en) 2009-07-21 2016-05-24 Gen-Probe Incorporated Reaction mixtures for quantitative amplification and detection over a wide dynamic range
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US9856527B2 (en) 2009-07-21 2018-01-02 Gen-Probe Incorporated Methods for quantitative amplification and detection over a wide dynamic range
US11732291B2 (en) 2012-02-01 2023-08-22 Gen-Probe Incorporated Asymmetric hairpin target capture oligomers
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US10526643B2 (en) 2013-12-02 2020-01-07 Vanadis Diagnostics Multiplex detection of nucleic acids
US10294510B2 (en) 2014-03-11 2019-05-21 President And Fellows Of Harvard College High-throughput and highly multiplexed imaging with programmable nucleic acid probes
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US10822640B2 (en) 2015-09-18 2020-11-03 Vanadis Diagnostics Probe set for analyzing a DNA sample and method for using the same
US11359229B2 (en) 2016-09-20 2022-06-14 President And Fellows Of Harvard College Molecular verification systems
US12142104B2 (en) 2018-03-22 2024-11-12 President And Fellows Of Harvard College Methods and compositions for molecular authentication

Also Published As

Publication number Publication date
US7914989B2 (en) 2011-03-29
JP2003535599A (ja) 2003-12-02
US20030113781A1 (en) 2003-06-19
WO2001094625A3 (en) 2003-03-13
AU2001267191A1 (en) 2001-12-17
US20080051568A1 (en) 2008-02-28
US7230092B2 (en) 2007-06-12
EP1313881A2 (en) 2003-05-28

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