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WO2024059153A3 - Target recycling amplification process (trap) - Google Patents

Target recycling amplification process (trap) Download PDF

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Publication number
WO2024059153A3
WO2024059153A3 PCT/US2023/032666 US2023032666W WO2024059153A3 WO 2024059153 A3 WO2024059153 A3 WO 2024059153A3 US 2023032666 W US2023032666 W US 2023032666W WO 2024059153 A3 WO2024059153 A3 WO 2024059153A3
Authority
WO
WIPO (PCT)
Prior art keywords
trap
amplification process
assay
target recycling
nucleic acids
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/US2023/032666
Other languages
French (fr)
Other versions
WO2024059153A2 (en
Inventor
Bryan T. CUNNINGHAM
Xiaojing Wang
Skye D. SHEPHERD
Yi Lu
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.)
University of Illinois at Urbana Champaign
University of Illinois System
Original Assignee
University of Illinois at Urbana Champaign
University of Illinois System
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 University of Illinois at Urbana Champaign, University of Illinois System filed Critical University of Illinois at Urbana Champaign
Priority to CA3267802A priority Critical patent/CA3267802A1/en
Priority to JP2025515802A priority patent/JP2025532598A/en
Priority to IL319606A priority patent/IL319606A/en
Publication of WO2024059153A2 publication Critical patent/WO2024059153A2/en
Publication of WO2024059153A3 publication Critical patent/WO2024059153A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/682—Signal amplification
    • 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
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/137—Reactions characterised by the reaction format or use of a specific feature the purpose or use of a displacement step
    • C12Q2537/1373—Displacement by a nucleic acid
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/163—Reactions characterised by the reaction format or use of a specific feature the purpose or use of blocking probe
    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/137—Metal/ion, e.g. metal label
    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/155—Particles of a defined size, e.g. nanoparticles
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/519—Detection characterised by immobilisation to a surface characterised by the capture moiety being a single stranded oligonucleotide
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/601—Detection means characterised by use of a special device being a microscope, e.g. atomic force microscopy [AFM]
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/628—Detection means characterised by use of a special device being a surface plasmon resonance spectrometer

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

The current disclosure provides an improved sensitivity assay for detecting and quantifying nucleic acids in a sample. The assay utilizes target recycling amplification process (TRAP) for the digital detection of nucleic acids in tandem with photonic resonator absorption microscopy (PRAM) and utilizes toehold-mediated DNA strand displacement reactions. The disclosure also provides a system and method for use of the assay.
PCT/US2023/032666 2022-09-14 2023-09-13 Target recycling amplification process (trap) Ceased WO2024059153A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
CA3267802A CA3267802A1 (en) 2022-09-14 2023-09-13 Target recycling amplification process (trap)
JP2025515802A JP2025532598A (en) 2022-09-14 2023-09-13 Target Recycling Amplification Process (TRAP)
IL319606A IL319606A (en) 2022-09-14 2023-09-13 Target recycling amplification process (trap)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263406540P 2022-09-14 2022-09-14
US63/406,540 2022-09-14

Publications (2)

Publication Number Publication Date
WO2024059153A2 WO2024059153A2 (en) 2024-03-21
WO2024059153A3 true WO2024059153A3 (en) 2024-05-16

Family

ID=90275635

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/032666 Ceased WO2024059153A2 (en) 2022-09-14 2023-09-13 Target recycling amplification process (trap)

Country Status (4)

Country Link
JP (1) JP2025532598A (en)
CA (1) CA3267802A1 (en)
IL (1) IL319606A (en)
WO (1) WO2024059153A2 (en)

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080124810A1 (en) * 2006-05-10 2008-05-29 Dxterity Diagnostics Detection of nucleic acid targets using chemically reactive oligonucleotide probes
WO2020223153A1 (en) * 2019-04-29 2020-11-05 The Board Of Trustees Of The University Of Illinois Digital resolution detection of mirna with single base selectivity by photonic resonator absorption microscopy
WO2021202440A1 (en) * 2020-03-30 2021-10-07 Biovector, Inc. Aptamers against sars-cov-2, compositions comprising aptamers against sars-cov-2 and methods of using the same
US20210324456A1 (en) * 2017-10-26 2021-10-21 The Board Of Trustees Of The University Of Illinois Photonic Resonator Absorption Microscopy (PRAM) for Digital Resolution Biomolecular Diagnostics
WO2022147340A1 (en) * 2020-12-31 2022-07-07 The Board Of Trustees Of The University Of Illinois Specific detection of nucleic acid sequences using activate cleave & count (acc) technology

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080124810A1 (en) * 2006-05-10 2008-05-29 Dxterity Diagnostics Detection of nucleic acid targets using chemically reactive oligonucleotide probes
US20210324456A1 (en) * 2017-10-26 2021-10-21 The Board Of Trustees Of The University Of Illinois Photonic Resonator Absorption Microscopy (PRAM) for Digital Resolution Biomolecular Diagnostics
WO2020223153A1 (en) * 2019-04-29 2020-11-05 The Board Of Trustees Of The University Of Illinois Digital resolution detection of mirna with single base selectivity by photonic resonator absorption microscopy
WO2021202440A1 (en) * 2020-03-30 2021-10-07 Biovector, Inc. Aptamers against sars-cov-2, compositions comprising aptamers against sars-cov-2 and methods of using the same
WO2022147340A1 (en) * 2020-12-31 2022-07-07 The Board Of Trustees Of The University Of Illinois Specific detection of nucleic acid sequences using activate cleave & count (acc) technology

Also Published As

Publication number Publication date
WO2024059153A2 (en) 2024-03-21
JP2025532598A (en) 2025-10-01
CA3267802A1 (en) 2024-03-21
IL319606A (en) 2025-05-01

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