CA2553833A1 - Nucleic acid amplification with continuous flow emulsion - Google Patents

Nucleic acid amplification with continuous flow emulsion Download PDF

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Publication number
CA2553833A1
CA2553833A1 CA002553833A CA2553833A CA2553833A1 CA 2553833 A1 CA2553833 A1 CA 2553833A1 CA 002553833 A CA002553833 A CA 002553833A CA 2553833 A CA2553833 A CA 2553833A CA 2553833 A1 CA2553833 A1 CA 2553833A1
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Prior art keywords
syringe
nucleic acid
emulsion
plunger
conduit
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Granted
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CA002553833A
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French (fr)
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CA2553833C (en
Inventor
John R. Nobile
William Lee
John H. Leamon
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454 Life Science Corp
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454 Corporation
John R. Nobile
William Lee
John H. Leamon
454 Life Sciences Corporation
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Publication of CA2553833A1 publication Critical patent/CA2553833A1/en
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Publication of CA2553833C publication Critical patent/CA2553833C/en
Expired - Fee Related legal-status Critical Current
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    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L7/00—Heating or cooling apparatus; Heat insulating devices
    • B01L7/52—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples
    • B01L7/525—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples with physical movement of samples between temperature zones
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01F—MIXING, e.g. DISSOLVING, EMULSIFYING OR DISPERSING
    • B01F23/00—Mixing according to the phases to be mixed, e.g. dispersing or emulsifying
    • B01F23/40—Mixing liquids with liquids; Emulsifying
    • B01F23/41—Emulsifying
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01F—MIXING, e.g. DISSOLVING, EMULSIFYING OR DISPERSING
    • B01F25/00—Flow mixers; Mixers for falling materials, e.g. solid particles
    • B01F25/30—Injector mixers
    • B01F25/31—Injector mixers in conduits or tubes through which the main component flows
    • B01F25/314—Injector mixers in conduits or tubes through which the main component flows wherein additional components are introduced at the circumference of the conduit
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01F—MIXING, e.g. DISSOLVING, EMULSIFYING OR DISPERSING
    • B01F33/00—Other mixers; Mixing plants; Combinations of mixers
    • B01F33/30—Micromixers
    • 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]
    • 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
    • G01N35/10—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
    • G01N35/1095—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices for supplying the samples to flow-through analysers
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01F—MIXING, e.g. DISSOLVING, EMULSIFYING OR DISPERSING
    • B01F25/00—Flow mixers; Mixers for falling materials, e.g. solid particles
    • B01F25/30—Injector mixers
    • B01F25/31—Injector mixers in conduits or tubes through which the main component flows
    • B01F25/312—Injector mixers in conduits or tubes through which the main component flows with Venturi elements; Details thereof
    • 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
    • B01J2219/00495—Means for heating or cooling the reaction vessels
    • 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
    • B01J2219/005—Beads
    • 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
    • B01J2219/00664—Three-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
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/06—Fluid handling related problems
    • B01L2200/0673—Handling of plugs of fluid surrounded by immiscible fluid
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/18—Means for temperature control
    • B01L2300/1805—Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks
    • B01L2300/1827—Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks using resistive heater
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/18—Means for temperature control
    • B01L2300/1838—Means for temperature control using fluid heat transfer medium
    • B01L2300/1844—Means for temperature control using fluid heat transfer medium using fans
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0403—Moving fluids with specific forces or mechanical means specific forces
    • B01L2400/0433—Moving fluids with specific forces or mechanical means specific forces vibrational forces
    • B01L2400/0439—Moving fluids with specific forces or mechanical means specific forces vibrational forces ultrasonic vibrations, vibrating piezo elements
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0475—Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure
    • B01L2400/0487—Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure fluid pressure, pneumatics
    • 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
    • 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

Abstract

Embodiments of the present invention are directed to methods and devices/systems for amplifying genetic material and may include providing a water-in-oil emulsion in a continuous flow. The emulsion may include a plurality of water droplets comprising microreactors. Each of the plurality of microreactors may include a single bead capable of capturing a nucleic acid template, a single species nucleic acid template and sufficient reagents to amplify the copy number of the nucleic acid template. The method also includes flowing the emulsion across a first temperature zone and a second lower temperature zone to thermally process the microreactors to amplify the nucleic acid template by polymerase chain reaction.

Claims (52)

1. A method for amplifying genetic material comprising:
providing a water-in-oil emulsion in a continuous flow wherein the emulsion comprises a plurality of water droplets comprising microreactors, wherein a plurality of the microreactors each include one or more species of nucleic acid templates, and sufficient reagents to amplify the copy number of one of the nucleic acid templates;
and thermally processing the emulsion by flowing it across stationary controlled temperature zones to amplify nucleic acid templates by polymerase chain reaction.
2. The method according to claim 1, wherein each microreactor contains one or more beads capable of capturing a nucleic acid template.
3. The method according to claim 1, wherein one or more of the beads capture amplified copies of the nucleic acid template.
4. The method according to any of claims 1 - 3, further comprising breaking the emulsion to retrieve one or more of the amplified nucleic acid templates.
5. The method according to any one of claims 1 - 3, further comprising filtering the water-in-oil emulsion to collect one or more of the amplified nucleic acid templates.
6. The method according to claim 1, wherein the microreactors have an average size of between approximately 50 to approximately 250 µm in diameter.
7. The method according to claim 1, wherein the nucleic acid templates are selected from the group consisting of genomic DNA, cDNA, episomal DNA, BAC DNA, and YAC DNA.
8. The method according to claim 2, wherein the bead has a diameter of between approximately 2 microns to approximately 100 microns.
9. The method according to claim 2, wherein the bead is selected from the group consisting of a sepharose bead, a solid bead and a monodisperse bead.
10. An apparatus for amplifying genetic material comprising:
at least one fluid delivery device;

at least one first temperature zone to cycle a plurality of microreactors each including one or more species nucleic acid templates to a first temperature;
at least one second temperature zone to cycle the plurality of microreactors to second temperature lower than the first temperature;
a first conduit for flowing at least a stream of oil therein from a first reservoir;
and a second conduit for flowing at least a water based PCR solution including nucleic acid templates and PCR reagent from a second reservoir out of an orifice and into the first conduit creating a water-in-oil emulsion, wherein the PCR solution upon entering the first conduit comprises a plurality of droplets comprising the microreactors for performing polymerase chain reactions, wherein a plurality of the microreactors each include one or more species of nucleic acid template.
11. The apparatus for amplifying genetic material according to claim 10, wherein downstream of the orifice, a length of the first conduit from a starting position to an ending position is arranged relative to at least the first and second temperature zones such that the length of the first conduit is exposed to alternating processes of heating and cooling at a temperature and time sufficient to amplify any of the nucleic acid templates by polymerase chain reaction.
12. The apparatus according to claim 10, wherein the orifice is sized between 50 µm to 300 µm.
13. The apparatus according to claim 10, wherein the orifice is sized to approximately 150 µm.
14. The apparatus according to claim 10, wherein an intersection area of the orifice and the first conduit includes a diameter of between greater than 50 µm to about 800 µm.
15. The apparatus according to claim 10, wherein an intersection area of the orifice and the first conduit includes a diameter of about 400 µm.
16. The apparatus according to claim 10, further comprising collecting means for collecting one or more of the amplified nucleic acid templates from the first conduit downstream of the heating and cooling sources.
17. The apparatus according to claim 16, wherein the collecting means comprises a filter.
18. The apparatus according to claim 10, wherein the first and second temperature zones are circumferentially arranged on opposed sides of a curved surface, wherein the length of the first conduit is helically wound around the curved surface to provide alternating portions of the length of first conduit adjacent either the first temperature zone or the second temperature zone.
19. The apparatus according to claim 18, wherein the curved surface comprises a mandrel.
20. The apparatus according to claim 10, wherein the temperature zones are arranged along opposed heating and cooling linear surfaces, respectively, wherein the length of first conduit is wound along the opposed surfaces such that portions of the length of first conduit are alternately exposed to the heating and cooling surfaces a plurality of times.
21. The apparatus according to claim 20, where the linear surfaces are substantially vertical or horizontal.
22. The apparatus according to claim 10, wherein the microreactors have an average size of between approximately 50 to approximately 250 µm in diameter.
23. The apparatus according to claim 10, wherein the nucleic acid templates are selected from the group consisting of genomic DNA, cDNA, episomal DNA, BAC DNA, and YAC DNA.
24. The apparatus according to claim 10, further the nucleic acid templates are captured onto beads, wherein the beads have a diameter of between approximately 2 microns to approximately 100 microns.
25. The apparatus according to claim 24, wherein the bead is selected from the group consisting of a sepharose bead, a solid bead and a monodisperse bead.
26. A cross-flow emulsification apparatus comprising:
a first inlet for receiving an oil flow from a first conduit;

an outlet for directing a water-in-oil emulsion out of the apparatus;
a second inlet for receiving a water based PCR amplification reaction mixture, the mixture including nucleic acid templates and PCR reaction mixture; and an orifice for delivering PCR reaction mixture from the second conduit into the first conduit, to form a plurality of water-in-oil droplets comprising microreactors, wherein a plurality of the microreactors each include one or more nucleic acid templates, and sufficient PCR amplification reaction mixture to produce a plurality of copies of nucleic acid template
27. The apparatus according to claim 26, wherein the orifice delivers the plurality of droplets into the first conduit at a narrowed region provided in the first conduit.
28. The apparatus according to claim 27, wherein the narrowed region includes a diameter between about 40 µm and 600 µm.
29. The apparatus according to claim 27, wherein the narrowed region includes a diameter of approximately 300 µm.
30. The apparatus according to claim 26, wherein the orifice includes a diameter between approximately 60 µm and about 300 µm.
31. The apparatus according to claim 26, wherein the orifice includes a diameter of approximately 120 µm.
32. The apparatus according to claim 26, wherein the microreactors have an average size of between approximately 50 to approximately 250 µm in diameter.
33. The apparatus according to claim 26, wherein the nucleic acid templates are selected from the group consisting of genomic DNA, cDNA, episomal DNA, BAC DNA, and YAC DNA.
34. The apparatus according to claim 26, wherein a plurality of the microreactors contain one of more beads, each bead having a diameter of between approximately 2 microns to approximately100 microns.
35. The apparatus according to claim 34, wherein each bead is a sepharose bead.
36. An apparatus for amplifying genetic material comprising:

a water-in-oil emulsion in a continuous flow wherein the emulsion comprises a plurality of water droplets comprising microreactors, wherein a plurality of the microreactors include a single bead capable of capturing one or more nucleic acid templates, and sufficient reagents to amplify the copy number of the one or more nucleic acid templates; and thermal processing means for thermally processing the emulsion to amplify nucleic acid templates by polymerase chain reaction.
37. An emulsion generator comprising:
an emulsion oil supply;
at least one syringe including a body and a plunger for dispensing a mixture for emulsifying into the emulsion oil;
a cross-flow emulsification device for emulsifying the mixture, the device including an input attached to the output of the syringe; and a syringe pump including an actuator capable of oscillating the plunger of the at least one syringe micrometer distances at a predetermined frequency along a length of travel of the plunger within the syringe body of the at least one syringe.
38. The emulsion generator according to claim 37, wherein the actuator is capable of moving the plunger between about 5µm and about 50µm.
39. The emulsion generator according to claim 37, wherein the desired frequency is between about 1Hz and 500 Hz.
40. A method for substantially reducing clogging of a nozzle in syringe pump, comprising:
providing a syringe pump having at least one syringe including a body, a plunger having a plunger axis and an exit nozzle, the body for dispensing a mixture of micron or less sized particles suspended in a medium; and oscillating the plunger of the syringe along the axis of the plunger for micrometer distances at a predetermined frequency along a length of travel of the plunger within the syringe body.
41. The method according to claim 40, wherein the actuator is capable of moving the plunger between about 5 µm and about 50 µm.
42. The method according to claim 40, wherein the desired frequency is between about 1Hz and 500 Hz.
43. An emulsion generator comprising:
an emulsion oil supply;
at least one syringe including a body and a plunger for dispensing a mixture for emulsifying into the emulsion oil;
a magnetically-attractive mixing element disposed in the body of the syringe;
a cross-flow emulsification device for emulsifying the mixture, the device including an input attached to the output of the syringe; and a device capable of moving an external magnetic force axially along body of the syringe while in close proximity to the syringe body.
44. An emulsion generator comprising:
an emulsion oil supply;
at least one syringe including a body and a plunger for dispensing a mixture for emulsifying into the emulsion oil;
a magnetically-attractive mixing element disposed in the body of the syringe;
a cross-flow emulsification device for emulsifying the mixture, the device including an input attached to the output of the syringe; and a rotating drum having a magnet helically wound along the surface of the drum, wherein the surface of the drum is positioned adjacent the body of the syringe.
45. The emulsion generator according to claim 44, wherein the magnet comprises a plurality of individual magnets helically spaced along the surface of the drum.
46. The emulsion generator according to claim 44, wherein the mixing element comprises a plastic coated metallic ball.
47. A syringe pump comprising:
an area for receiving at least one syringe, wherein the syringe includes a body and a plunger having a plunger axis, the syringe for dispensing a mixture for emulsification into an emulsion oil; and an actuator capable of oscillating the plunger of the at least one syringe along the plunger axis micrometer distances at a predetermined frequency along a length of travel of the plunger within body of the at least one syringe.
48. The syringe pump according to claim 47, wherein the actuator is capable of moving the plunger between about 5 µm and about 50 µm.
49. The syringe pump according to claim 47, wherein the desired frequency is between about 1 Hz and 500 Hz.
50. A syringe pump comprising:
an area for receiving at least one syringe, wherein the syringe includes a body and a plunger having a plunger axis, the syringe for dispensing a mixture for emulsification into emulsion oil;
a magnetically attractive mixing element disposed in the body of the syringe;
and a rotating drum having a magnet helically wound along the surface of the drum, wherein the surface of the drum is positioned adjacent the body of the syringe.
51. The syringe pump according to claim 50, wherein the magnet comprises a plurality of individual magnets helically spaced along the surface of the drum.
52. The syringe pump according to claim 50, wherein the mixing element comprises a plastic coated metallic ball.
CA2553833A 2004-01-28 2005-01-28 Nucleic acid amplification with continuous flow emulsion Expired - Fee Related CA2553833C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US54001604P 2004-01-28 2004-01-28
US60/540,016 2004-01-28
PCT/US2005/003488 WO2005073410A2 (en) 2004-01-28 2005-01-28 Nucleic acid amplification with continuous flow emulsion

Publications (2)

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CA2553833A1 true CA2553833A1 (en) 2005-08-11
CA2553833C CA2553833C (en) 2012-10-02

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US (2) US7927797B2 (en)
EP (1) EP1735458B1 (en)
CA (1) CA2553833C (en)
ES (1) ES2432040T3 (en)
WO (1) WO2005073410A2 (en)

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