WO2012145725A2 - Oscillating amplification reaction for nucleic acids - Google Patents

Oscillating amplification reaction for nucleic acids Download PDF

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Publication number
WO2012145725A2
WO2012145725A2 PCT/US2012/034589 US2012034589W WO2012145725A2 WO 2012145725 A2 WO2012145725 A2 WO 2012145725A2 US 2012034589 W US2012034589 W US 2012034589W WO 2012145725 A2 WO2012145725 A2 WO 2012145725A2
Authority
WO
WIPO (PCT)
Prior art keywords
temperature
nucleic acid
dna polymerase
primer
template
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/US2012/034589
Other languages
English (en)
French (fr)
Other versions
WO2012145725A3 (en
Inventor
Hong Cai
Nathan J. COBB
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.)
Mesa Tech International Inc
Original Assignee
Mesa Tech International 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
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=47042196&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2012145725(A2) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to JP2014506607A priority Critical patent/JP5731066B2/ja
Priority to CA2856304A priority patent/CA2856304C/en
Priority to US14/113,200 priority patent/US9428781B2/en
Priority to KR1020137030853A priority patent/KR20140044323A/ko
Priority to ES12773717T priority patent/ES2621390T5/es
Priority to EP12773717.9A priority patent/EP2699698B9/en
Priority to DK12773717.9T priority patent/DK2699698T4/da
Application filed by Mesa Tech International Inc filed Critical Mesa Tech International Inc
Priority to CN201280030581.2A priority patent/CN103608467B/zh
Priority to KR1020167005417A priority patent/KR101878889B1/ko
Publication of WO2012145725A2 publication Critical patent/WO2012145725A2/en
Publication of WO2012145725A3 publication Critical patent/WO2012145725A3/en
Anticipated expiration legal-status Critical
Priority to US15/247,728 priority patent/US10316358B2/en
Priority to US16/377,749 priority patent/US11293058B2/en
Priority to US17/696,027 priority patent/US20220205019A1/en
Priority to US18/656,534 priority patent/US12421543B2/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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502723—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by venting arrangements
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/26—Preparation of nitrogen-containing carbohydrates
    • C12P19/28—N-glycosides
    • C12P19/30—Nucleotides
    • C12P19/34—Polynucleotides, e.g. nucleic acids, oligoribonucleotides
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • 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
    • C12Q2522/00—Reaction characterised by the use of non-enzymatic proteins
    • C12Q2522/10—Nucleic acid binding proteins
    • C12Q2522/101—Single or double stranded nucleic acid binding proteins
    • 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
    • C12Q2527/00—Reactions demanding special reaction conditions
    • C12Q2527/101—Temperature

Definitions

  • Yet another embodiment of the present invention provides a method for amplifying a template of nucleic acid target sequence contained in a sample.
  • the method includes contacting the sample with an amplification reaction mixture comprising a primer or a primer pair having a length of between 35-70 base pairs and complementary to the template of the nucleic acid target sequence and wherein the melting temperature of each primer of the primer pair is between 70- 80°C.
  • the amplification reaction mixture also includes DMSO, monovalent cation, divalent cation, dNTPs, and DNA Polymerase.
  • Another embodiment of the present invention provides an amplification reaction mixture buffer comprising one or more of the following: single strand or double strand nucleic acid destabilizer; monovalent cation; divalent cation; dNTPs ;and DNA Polymerase buffered at a pH to support activity.
  • the DNA polymerase may be a thermostable DNA polymerase.
  • the DNA polymerase may be selected from the group consisting of TAQ DNA polymerase, VentR DNA polymerase, and DeepVentR DNA polymerase but not limited thereto.
  • the DNA polymerase may have a strand displacing activity.
  • the DNA polymerase may be selected which does not have 3'-> 5' exonuclease activity.
  • Nucleic acid samples may be isolated from cells or viruses and may include chromosomal DNA, extra-chromosomal DNA including plasmid DNA, recombinant DNA, DNA fragments, messenger RNA, ribosomal RNA, transfer RNA, double stranded RNA or other RNAs that occur in cells or viruses.
  • Nucleic acid may be isolated from any number of sources such as agriculture, food, environmental, fermentations, or biological fluids such as saliva, blood, nasal or lung aspirates, cerebrospinal fluid, sputum, stool, milk, swabs of mucosal tissues, tissue samples, or cells.
  • Nucleic acid may be isolated, cloned or synthesized in vitro. Within the described nucleic acids above, individual nucleotides may be subject to modification or chemical alterations such as methylation. These modifications or alterations may arise naturally or by in vitro synthesis.
  • a method for exponentially amplifying a specific nucleic acid target by thermal cycling where temperature variation is preferably less than 20 °C, more preferably less than 15 °C, and even more preferably less than 10 °C. This includes the steps of providing a single-stranded template of the nucleic acid to be amplified,
  • oligonucleotide primer pair may be used to simultaneously amplify multiple nucleic acid targets in the same reaction mixture.
  • the oligonucleotide primers may have a length and GC content so that the melting temperature is greater than 65 °C under universally accepted PCR buffer conditions, preferably greater than 70 °C.
  • the DNA polymerase used is preferably selected from Taq DNA polymerase, VentR DNA polymerase, DeepVentR DNA polymerase, and similar thermostable DNA polymerases.
  • the DNA polymerase possesses a strand- displacing activity and does not contain a 3' ⁇ 5' exonuclease activity (see figure 1 B).
  • Platinum Taq is a commercially available hot-start enzyme (Invitrogen, Carlsbad, CA) that is conjugated to an antibody which dissociates upon heating the reaction solution to 94 °C under normal PCR conditions. In the presence of template nucleic acid, this primer pair will produce a product of 153 bp. It is clear that this hot-start preparation is no better than conventional Taq in reducing the formation of ⁇ 1 10 bp primer dimmers during OPCRar. One complication of long primers used in the OPCRar reaction is that they are more prone to result in non-specific and unwanted amplification products known as primer dimmers.
  • OPCRar according to one embodiment of the present invention was performed in the presence or absence of thermostable SSB under the following conditions: / ' ) 1 5% DMSO; / ' / ' ) 1 5% DMSO, 5% Glycerol; Hi) 15% DMSO, 0.25 M Betaine.
  • the cycling parameters used for all reactions were 75 °C for 1 5 sec and 65 °C for 15 sec, repeated 45 times.
  • PCR cyclers and methods have controlled heating design where ramping up is about > 3 deg/second, and ramping down rate is about >1 deg/second.
  • Ramping time is not included in the typical cycling profiles, the instrument does not start counting time duration during denaturation, annealing and extension stage until the desired temperature is reached. For instance, denaturation time is 10 second at 90 deg, the instrument will not starting counting the 10 second time until 90 deg is reached.
  • a system and method of the present invention provides for a low cost heater device which is designed for example the 80 deg for 10 second means the time starts counting when the heating process starts (rather than waiting until the desired denaturing temperature is reached).
  • TYPE Bacterial DNA

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Hematology (AREA)
  • Clinical Laboratory Science (AREA)
  • Dispersion Chemistry (AREA)
  • General Chemical & Material Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
PCT/US2012/034589 2011-04-20 2012-04-20 Oscillating amplification reaction for nucleic acids Ceased WO2012145725A2 (en)

Priority Applications (13)

Application Number Priority Date Filing Date Title
KR1020167005417A KR101878889B1 (ko) 2011-04-20 2012-04-20 핵산의 왕복 증폭 반응
CN201280030581.2A CN103608467B (zh) 2011-04-20 2012-04-20 用于核酸的振荡扩增反应
US14/113,200 US9428781B2 (en) 2011-04-20 2012-04-20 Oscillating amplification reaction for nucleic acids
KR1020137030853A KR20140044323A (ko) 2011-04-20 2012-04-20 핵산의 왕복 증폭 반응
ES12773717T ES2621390T5 (es) 2011-04-20 2012-04-20 Reacción de amplificación oscilante para ácidos nucleicos
EP12773717.9A EP2699698B9 (en) 2011-04-20 2012-04-20 Oscillating amplification reaction for nucleic acids
DK12773717.9T DK2699698T4 (da) 2011-04-20 2012-04-20 Oscillerende amplifikations-reaktion for nukleinsyrer
JP2014506607A JP5731066B2 (ja) 2011-04-20 2012-04-20 核酸のための周期変動性増幅反応
CA2856304A CA2856304C (en) 2011-04-20 2012-04-20 Oscillating amplification reaction for nucleic acids
US15/247,728 US10316358B2 (en) 2011-04-20 2016-08-25 Oscillating amplification reaction for nucleic acids
US16/377,749 US11293058B2 (en) 2011-04-20 2019-04-08 Oscillating amplification reaction for nucleic acids
US17/696,027 US20220205019A1 (en) 2011-04-20 2022-03-16 Oscillating Amplification Reaction For Nucleic Acids
US18/656,534 US12421543B2 (en) 2011-04-20 2024-05-06 Oscillating amplification reaction for nucleic acids

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201161477437P 2011-04-20 2011-04-20
US201161477357P 2011-04-20 2011-04-20
US61/477,437 2011-04-20
US61/477,357 2011-04-20

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US14/113,200 A-371-Of-International US9428781B2 (en) 2011-04-20 2012-04-20 Oscillating amplification reaction for nucleic acids
US15/247,728 Continuation US10316358B2 (en) 2011-04-20 2016-08-25 Oscillating amplification reaction for nucleic acids

Publications (2)

Publication Number Publication Date
WO2012145725A2 true WO2012145725A2 (en) 2012-10-26
WO2012145725A3 WO2012145725A3 (en) 2013-03-14

Family

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Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2012/034589 Ceased WO2012145725A2 (en) 2011-04-20 2012-04-20 Oscillating amplification reaction for nucleic acids
PCT/US2012/034596 Ceased WO2012145730A2 (en) 2011-04-20 2012-04-20 Integrated device for nucleic acid detection and identification

Family Applications After (1)

Application Number Title Priority Date Filing Date
PCT/US2012/034596 Ceased WO2012145730A2 (en) 2011-04-20 2012-04-20 Integrated device for nucleic acid detection and identification

Country Status (10)

Country Link
US (9) US9428781B2 (enExample)
EP (2) EP2699700B8 (enExample)
JP (3) JP5879667B2 (enExample)
KR (3) KR20140044323A (enExample)
CN (2) CN103649333B (enExample)
CA (2) CA2856304C (enExample)
DK (2) DK2699698T4 (enExample)
ES (2) ES2621390T5 (enExample)
PT (1) PT2699698T (enExample)
WO (2) WO2012145725A2 (enExample)

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CN103649333A (zh) 2014-03-19
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