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WO2014060604A3 - Method and its compositions for detection of nucleic acid target from biological samples and body fluids - Google Patents

Method and its compositions for detection of nucleic acid target from biological samples and body fluids Download PDF

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Publication number
WO2014060604A3
WO2014060604A3 PCT/EP2013/071906 EP2013071906W WO2014060604A3 WO 2014060604 A3 WO2014060604 A3 WO 2014060604A3 EP 2013071906 W EP2013071906 W EP 2013071906W WO 2014060604 A3 WO2014060604 A3 WO 2014060604A3
Authority
WO
WIPO (PCT)
Prior art keywords
human
nucleic acid
amplification
genomic dna
detection
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/EP2013/071906
Other languages
French (fr)
Other versions
WO2014060604A2 (en
Inventor
Indrek Tulp
Katrin KRÕLOV
Marko Lehes
Ülo Langel
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.)
Selfdiagnostics Oue
Original Assignee
Selfdiagnostics Oue
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 Selfdiagnostics Oue filed Critical Selfdiagnostics Oue
Priority to CA2888949A priority Critical patent/CA2888949A1/en
Priority to EP13792268.8A priority patent/EP2922966A2/en
Priority to JP2015537284A priority patent/JP2015532114A/en
Priority to AU2013333763A priority patent/AU2013333763A1/en
Priority to US14/437,110 priority patent/US20150322493A1/en
Publication of WO2014060604A2 publication Critical patent/WO2014060604A2/en
Publication of WO2014060604A3 publication Critical patent/WO2014060604A3/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
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/06—Lysis of microorganisms
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Mycology (AREA)
  • Medicinal Chemistry (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Virology (AREA)
  • Biomedical Technology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Current invention is directed for rapid sample pretreatment method that allows highly sensitive and specific detection of target nucleic acid (e.g. human genomic DNA, human pathogen genomic DNA, human non-pathogen genomic DNA) by amplification directly from crude unpurified biological samples lysates (e.g. human 5 urine, saliva, blood, urethra and cervical swabs and other samples containing biological material). Invention is focused on the description of the biological sample pretreatment method that enables fast release of the genomic material from human and pathogen cells, components of what are compatible with the following nucleic acid amplification method. As an example of the application, 10 invention also discloses protocols and primer sequences for isothermal nucleic acid amplification (recombinase polymerase amplification – RPA, loop-mediated isothermal amplification - LAMP), that enable highly specific and sensitive diagnostics of the genomic material from Homo sapiens, Chlamydia trachomatis and Mycoplasma genitalium from crude biological sample lysates and/or purified 15 total DNA. The example amplification can be combined with immunochromotographic product detection using lateral-flow strips and allows rapid (under 20 min) isothermal nucleic acid amplification based C. trachomatis and M. genitalium diagnostics from human urine samples, that does not require specific laboratory equipment nor qualified personnel, and is therefore well suited 20 for point-of-care settings applications.
PCT/EP2013/071906 2012-10-20 2013-10-20 Method and its compositions for detection of nucleic acid target from biological samples and body fluids Ceased WO2014060604A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
CA2888949A CA2888949A1 (en) 2012-10-20 2013-10-20 Method and its compositions for detection of nucleic acid target from biological samples and body fluids
EP13792268.8A EP2922966A2 (en) 2012-10-20 2013-10-20 Method and its compositions for detection of nucleic acid target from biological samples and body fluids
JP2015537284A JP2015532114A (en) 2012-10-20 2013-10-20 Methods and compositions for detection of nucleic acid targets from biological samples and body fluids
AU2013333763A AU2013333763A1 (en) 2012-10-20 2013-10-20 Method and its compositions for detection of nucleic acid target from biological samples and body fluids
US14/437,110 US20150322493A1 (en) 2012-10-20 2013-10-20 Method and its compositions for detection of nucleic acid target from biological samples and body fluids

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201261716495P 2012-10-20 2012-10-20
US61/716,495 2012-10-20

Publications (2)

Publication Number Publication Date
WO2014060604A2 WO2014060604A2 (en) 2014-04-24
WO2014060604A3 true WO2014060604A3 (en) 2014-07-31

Family

ID=49596238

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2013/071906 Ceased WO2014060604A2 (en) 2012-10-20 2013-10-20 Method and its compositions for detection of nucleic acid target from biological samples and body fluids

Country Status (5)

Country Link
EP (1) EP2922966A2 (en)
JP (1) JP2015532114A (en)
AU (1) AU2013333763A1 (en)
CA (1) CA2888949A1 (en)
WO (1) WO2014060604A2 (en)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017103269A1 (en) * 2015-12-18 2017-06-22 Selfdiagnostics Deutschland Gmbh Method for the detection of a sexually transmitted infectious pathogen
US10612101B2 (en) * 2016-05-27 2020-04-07 Roche Molecular Systems, Inc. Compositions and methods for detection of Mycoplasma genitalium
WO2018089942A1 (en) * 2016-11-10 2018-05-17 Slipchip Corporation Polynucleotides for the amplification and detection of chlamydia trachomatis
CN107287320A (en) * 2017-07-12 2017-10-24 曹国君 The LAMP detections of GAPDH genes are combined and kit with primer
CN108359737A (en) * 2018-02-11 2018-08-03 苏州先达基因科技有限公司 Mycoplasma contamination detection method and application
US10450616B1 (en) * 2018-05-09 2019-10-22 Talis Biomedical Corporation Polynucleotides for the amplification and detection of Chlamydia trachomatis
CN109251963B (en) * 2018-11-12 2022-11-18 复旦大学 Method and kit for detecting mycoplasma pollution in cell culture solution at constant temperature
CN112301104B (en) * 2020-02-06 2024-03-22 广州普世利华科技有限公司 RDA method and kit for rapidly detecting chlamydia trachomatis
CN112899377A (en) * 2020-11-03 2021-06-04 南方医科大学 Kit with chlamydia trachomatis infection diagnosis and/or prognosis evaluation function
CN115873849B (en) * 2023-01-09 2024-04-05 昆明理工大学 Primer-probe combination for simultaneous detection of 16 female reproductive tract pathogens

Citations (3)

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Publication number Priority date Publication date Assignee Title
WO2008135196A1 (en) * 2007-05-03 2008-11-13 Roche Diagnostics Gmbh SINGLE-CELL mRNA QUANTIFICATION WITH REAL-TIME RT-PCR
US20090035748A1 (en) * 2007-08-01 2009-02-05 Lizzi Tiffiny Marie Bromelain as a clinical sample pre-treatment, lysis agent and nuclease inhibitor
US20110091873A1 (en) * 2009-10-21 2011-04-21 Microfluidic Systems, Inc. Integrated sample preparation and amplification for nucleic acid detection from biological samples

Family Cites Families (5)

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Publication number Priority date Publication date Assignee Title
IL114697A0 (en) * 1994-07-22 1995-11-27 Demeter Biotech Ltd Polypeptides comprising ubiquitin-lytic peptide fusion protein products deriving therefrom their preparation and use
US20020127587A1 (en) * 2001-02-13 2002-09-12 Domenica Simms Methods and compositions for isolation of biological macromolecules
US8497353B2 (en) * 2008-02-14 2013-07-30 3M Innovative Properties Company Polypeptides for microbial detection
CN102770208B (en) * 2009-12-30 2016-02-03 3M创新有限公司 Live Bioburden Detection Using Microparticles
JP2011188855A (en) * 2010-03-11 2011-09-29 Samsung Techwin Co Ltd Method for real-time detection of salmonella using cleavable chimeric probe

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008135196A1 (en) * 2007-05-03 2008-11-13 Roche Diagnostics Gmbh SINGLE-CELL mRNA QUANTIFICATION WITH REAL-TIME RT-PCR
US20090035748A1 (en) * 2007-08-01 2009-02-05 Lizzi Tiffiny Marie Bromelain as a clinical sample pre-treatment, lysis agent and nuclease inhibitor
US20110091873A1 (en) * 2009-10-21 2011-04-21 Microfluidic Systems, Inc. Integrated sample preparation and amplification for nucleic acid detection from biological samples

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
BOMAN J ET AL: "Molecular diagnosis of Chlamydia pneumoniae infection", JOURNAL OF CLINICAL MICROBIOLOGY, AMERICAN SOCIETY FOR MICROBIOLOGY, US, vol. 37, no. 12, 1 December 1999 (1999-12-01), pages 3791 - 3799, XP002276123, ISSN: 0095-1137 *
HENKE WOLFGANG ET AL: "Betaine improves the PCR amplification of GC-rich DNA sequences", NUCLEIC ACIDS RESEARCH, OXFORD : OXFORD UNIV. PRESS, 1974-ANFANGS: LONDON : INFORMATION RETRIEVAL LTD, GB, vol. 25, no. 19, 1 January 1997 (1997-01-01), pages 3957 - 3958, XP002171292, ISSN: 0305-1048, DOI: 10.1093/NAR/25.19.3957 *
KIM A. BROGDEN: "Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?", NATURE REVIEWS MICROBIOLOGY, vol. 3, no. 3, 1 March 2005 (2005-03-01), pages 238 - 250, XP055110431, ISSN: 1740-1526, DOI: 10.1038/nrmicro1098 *
LOESSNER M J ET AL: "A NEW PROCEDURE FOR EFFICIENT RECOVERY OF DNA, RNA, AND PROTEINS FROM LISTERIA CELL BY RAPID LYSIS WITH A RECOMBINANT BACTERIOPHAGE ENDOLYSIN", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, AMERICAN SOCIETY FOR MICROBIOLOGY, US, vol. 61, no. 3, 1 March 1995 (1995-03-01), pages 1150 - 1152, XP008060594, ISSN: 0099-2240 *
SHAI Y: "Mechanism of the binding, insertion and destabilization of phospholipid bilayer membranes by alpha-helical antimicrobial and cell non-selective membrane-lytic peptides", BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOMEMBRANES, ELSEVIER, AMSTERDAM, NL, vol. 1462, no. 1-2, 15 December 1999 (1999-12-15), pages 55 - 70, XP004273110, ISSN: 0005-2736, DOI: 10.1016/S0005-2736(99)00200-X *
TREHIN R ET AL: "Chances and pitfalls of cell penetrating peptides for cellular drug delivery", EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS, ELSEVIER SCIENCE PUBLISHERS B.V., AMSTERDAM, NL, vol. 58, no. 2, 1 September 2004 (2004-09-01), pages 209 - 223, XP004526307, ISSN: 0939-6411, DOI: 10.1016/J.EJPB.2004.02.018 *

Also Published As

Publication number Publication date
JP2015532114A (en) 2015-11-09
EP2922966A2 (en) 2015-09-30
CA2888949A1 (en) 2014-04-24
WO2014060604A2 (en) 2014-04-24
AU2013333763A1 (en) 2015-05-14

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