WO2008024319A3 - Microfluidic devices for nucleic acid assembly - Google Patents

Microfluidic devices for nucleic acid assembly Download PDF

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Publication number
WO2008024319A3
WO2008024319A3 PCT/US2007/018437 US2007018437W WO2008024319A3 WO 2008024319 A3 WO2008024319 A3 WO 2008024319A3 US 2007018437 W US2007018437 W US 2007018437W WO 2008024319 A3 WO2008024319 A3 WO 2008024319A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
microfluidic devices
reagents
acid assembly
devices
Prior art date
Application number
PCT/US2007/018437
Other languages
French (fr)
Other versions
WO2008024319A2 (en
WO2008024319A8 (en
Inventor
Craig Douglas Muir
Christopher J Emig
Original Assignee
Codon Devices Inc
Craig Douglas Muir
Christopher J Emig
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 Codon Devices Inc, Craig Douglas Muir, Christopher J Emig filed Critical Codon Devices Inc
Publication of WO2008024319A2 publication Critical patent/WO2008024319A2/en
Publication of WO2008024319A3 publication Critical patent/WO2008024319A3/en
Publication of WO2008024319A8 publication Critical patent/WO2008024319A8/en

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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
    • 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
    • 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
    • B01J19/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J19/0046—Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular 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
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00281—Individual reactor vessels
    • B01J2219/00286—Reactor vessels with top and bottom openings
    • 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
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00313—Reactor vessels in a multiple arrangement the reactor vessels being formed by arrays of wells in blocks
    • B01J2219/00315—Microtiter plates
    • B01J2219/00317—Microwell devices, i.e. having large numbers of wells
    • 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
    • B01J2219/00351—Means for dispensing and evacuation of reagents
    • B01J2219/00423—Means for dispensing and evacuation of reagents using filtration, e.g. through porous frits
    • 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
    • B01J2219/00585—Parallel processes
    • 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
    • B01J2219/0059—Sequential processes
    • 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
    • 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
    • B01J2219/00781—Aspects relating to microreactors
    • B01J2219/00905—Separation
    • B01J2219/00912—Separation by electrophoresis
    • 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
    • B01L2200/10—Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept
    • 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
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0809—Geometry, shape and general structure rectangular shaped
    • B01L2300/0816—Cards, e.g. flat sample carriers usually with flow in two horizontal directions
    • 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
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0832—Geometry, shape and general structure cylindrical, tube shaped
    • B01L2300/0838—Capillaries
    • 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
    • B01L2400/0415—Moving fluids with specific forces or mechanical means specific forces electrical forces, e.g. electrokinetic
    • B01L2400/0421—Moving fluids with specific forces or mechanical means specific forces electrical forces, e.g. electrokinetic electrophoretic flow
    • 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
    • B01L3/502753—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 bulk separation arrangements on lab-on-a-chip devices, e.g. for filtration or centrifugation
    • 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

Abstract

Certain aspects of the present invention provide devices and methods for assembling nucleic acid molecules on micro fluidic devices, e.g. via extension and/or ligation reactions. The invention also provides systems comprising one or more acoustic liquid handlers, one or more microfluidic devices, and/or one or more robotic liquid handlers for automating a nucleic acid assembly procedure. The microdevice may comprise the following components: a sipper, or means for transferring reagents (310); a main channel (315); a spitter, or means for transferring reagents (320), sample wells for storage of reagents or buffers (330, 335, 340), separation or concentration channels (350, 355) and sample or reaction wells (360, 365) e.g. a thermocycler.
PCT/US2007/018437 2006-08-20 2007-08-20 Microfluidic devices for nucleic acid assembly WO2008024319A2 (en)

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US83896006P 2006-08-20 2006-08-20
US60/838,960 2006-08-20
US87833206P 2006-12-31 2006-12-31
US87833006P 2006-12-31 2006-12-31
US60/878,330 2006-12-31
US60/878,332 2006-12-31

Publications (3)

Publication Number Publication Date
WO2008024319A2 WO2008024319A2 (en) 2008-02-28
WO2008024319A3 true WO2008024319A3 (en) 2008-04-10
WO2008024319A8 WO2008024319A8 (en) 2008-05-29

Family

ID=38996695

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2007/018437 WO2008024319A2 (en) 2006-08-20 2007-08-20 Microfluidic devices for nucleic acid assembly

Country Status (1)

Country Link
WO (1) WO2008024319A2 (en)

Cited By (11)

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US8388908B2 (en) 2009-06-02 2013-03-05 Integenx Inc. Fluidic devices with diaphragm valves
US8394642B2 (en) 2009-06-05 2013-03-12 Integenx Inc. Universal sample preparation system and use in an integrated analysis system
US8431340B2 (en) 2004-09-15 2013-04-30 Integenx Inc. Methods for processing and analyzing nucleic acid samples
US8476063B2 (en) 2004-09-15 2013-07-02 Integenx Inc. Microfluidic devices
US8512538B2 (en) 2010-05-28 2013-08-20 Integenx Inc. Capillary electrophoresis device
US8557518B2 (en) 2007-02-05 2013-10-15 Integenx Inc. Microfluidic and nanofluidic devices, systems, and applications
US8584703B2 (en) 2009-12-01 2013-11-19 Integenx Inc. Device with diaphragm valve
US8672532B2 (en) 2008-12-31 2014-03-18 Integenx Inc. Microfluidic methods
US8748165B2 (en) 2008-01-22 2014-06-10 Integenx Inc. Methods for generating short tandem repeat (STR) profiles
US8763642B2 (en) 2010-08-20 2014-07-01 Integenx Inc. Microfluidic devices with mechanically-sealed diaphragm valves
US9121058B2 (en) 2010-08-20 2015-09-01 Integenx Inc. Linear valve arrays

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US7563600B2 (en) 2002-09-12 2009-07-21 Combimatrix Corporation Microarray synthesis and assembly of gene-length polynucleotides
US8053191B2 (en) 2006-08-31 2011-11-08 Westend Asset Clearinghouse Company, Llc Iterative nucleic acid assembly using activation of vector-encoded traits
GB0815472D0 (en) * 2008-08-22 2008-10-01 Iti Scotland Ltd Microfluidic system
US8808986B2 (en) 2008-08-27 2014-08-19 Gen9, Inc. Methods and devices for high fidelity polynucleotide synthesis
WO2011056872A2 (en) 2009-11-03 2011-05-12 Gen9, Inc. Methods and microfluidic devices for the manipulation of droplets in high fidelity polynucleotide assembly
EP3085791A1 (en) 2009-11-25 2016-10-26 Gen9, Inc. Methods and apparatuses for chip-based dna error reduction
WO2011066185A1 (en) 2009-11-25 2011-06-03 Gen9, Inc. Microfluidic devices and methods for gene synthesis
US9217144B2 (en) 2010-01-07 2015-12-22 Gen9, Inc. Assembly of high fidelity polynucleotides
US8716467B2 (en) 2010-03-03 2014-05-06 Gen9, Inc. Methods and devices for nucleic acid synthesis
GB2481425A (en) * 2010-06-23 2011-12-28 Iti Scotland Ltd Method and device for assembling polynucleic acid sequences
US10457935B2 (en) 2010-11-12 2019-10-29 Gen9, Inc. Protein arrays and methods of using and making the same
US9295965B2 (en) 2010-11-12 2016-03-29 Gen9, Inc. Methods and devices for nucleic acid synthesis
US10131903B2 (en) * 2011-04-01 2018-11-20 The Regents Of The University Of California Microfluidic platform for synthetic biology applications
US9752176B2 (en) 2011-06-15 2017-09-05 Ginkgo Bioworks, Inc. Methods for preparative in vitro cloning
AU2012300401B2 (en) 2011-08-26 2018-02-08 Gen9, Inc. Compositions and methods for high fidelity assembly of nucleic acids
US20150136604A1 (en) 2011-10-21 2015-05-21 Integenx Inc. Sample preparation, processing and analysis systems
US10865440B2 (en) 2011-10-21 2020-12-15 IntegenX, Inc. Sample preparation, processing and analysis systems
US9150853B2 (en) 2012-03-21 2015-10-06 Gen9, Inc. Methods for screening proteins using DNA encoded chemical libraries as templates for enzyme catalysis
CN111876409A (en) 2012-04-24 2020-11-03 Gen9股份有限公司 Method for sorting nucleic acids and multiplex preparations in vitro cloning
CN104685116A (en) 2012-06-25 2015-06-03 Gen9股份有限公司 Methods for nucleic acid assembly and high throughput sequencing
CA2880687C (en) * 2012-08-16 2023-09-19 Synthetic Genomics, Inc. Digital to biological converter
EP3071333A4 (en) 2013-11-18 2017-11-15 IntegenX Inc. Cartridges and instruments for sample analysis
WO2015179098A1 (en) 2014-05-21 2015-11-26 Integenx Inc. Fluidic cartridge with valve mechanism
EP3552690A1 (en) 2014-10-22 2019-10-16 IntegenX Inc. Systems and methods for sample preparation, processing and analysis
EP3366370A1 (en) * 2017-02-22 2018-08-29 Briefcase Biotec GmbH Device for the synthesis of oligonucleotides
WO2019074512A1 (en) * 2017-10-12 2019-04-18 Hewlett-Packard Development Company, L.P. Embedded microfluidic devices
US11249100B2 (en) 2018-01-05 2022-02-15 Worcester Polytechnic Institute Modular robotic systems for delivering fluid to microfluidic devices
US10046322B1 (en) 2018-03-22 2018-08-14 Talis Biomedical Corporation Reaction well for assay device
WO2019209273A1 (en) 2018-04-24 2019-10-31 Hewlett-Packard Development Company, L.P. Microfluidic devices
WO2019209375A1 (en) 2018-04-24 2019-10-31 Hewlett-Packard Development Company, L.P. Droplet ejectors to draw fluids through microfluidic networks
US11325380B2 (en) 2018-07-17 2022-05-10 Hewlett-Packard Development Company, L.P. Droplet ejectors to provide fluids to droplet ejectors
US11547993B2 (en) 2018-07-17 2023-01-10 Hewlett-Packard Development Company, L.P. Droplet ejectors with target media
WO2020264260A1 (en) * 2019-06-27 2020-12-30 Zymergen Inc. Laboratory automation system implementing efficient path for material and labware transfers
US11008627B2 (en) 2019-08-15 2021-05-18 Talis Biomedical Corporation Diagnostic system

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Cited By (15)

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Publication number Priority date Publication date Assignee Title
US8551714B2 (en) 2004-09-15 2013-10-08 Integenx Inc. Microfluidic devices
US8431340B2 (en) 2004-09-15 2013-04-30 Integenx Inc. Methods for processing and analyzing nucleic acid samples
US8431390B2 (en) 2004-09-15 2013-04-30 Integenx Inc. Systems of sample processing having a macro-micro interface
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US8672532B2 (en) 2008-12-31 2014-03-18 Integenx Inc. Microfluidic methods
US8388908B2 (en) 2009-06-02 2013-03-05 Integenx Inc. Fluidic devices with diaphragm valves
US8562918B2 (en) 2009-06-05 2013-10-22 Integenx Inc. Universal sample preparation system and use in an integrated analysis system
US8394642B2 (en) 2009-06-05 2013-03-12 Integenx Inc. Universal sample preparation system and use in an integrated analysis system
US9012236B2 (en) 2009-06-05 2015-04-21 Integenx Inc. Universal sample preparation system and use in an integrated analysis system
US8584703B2 (en) 2009-12-01 2013-11-19 Integenx Inc. Device with diaphragm valve
US8512538B2 (en) 2010-05-28 2013-08-20 Integenx Inc. Capillary electrophoresis device
US8763642B2 (en) 2010-08-20 2014-07-01 Integenx Inc. Microfluidic devices with mechanically-sealed diaphragm valves
US9121058B2 (en) 2010-08-20 2015-09-01 Integenx Inc. Linear valve arrays

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Publication number Publication date
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WO2008024319A8 (en) 2008-05-29

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