CA2339163A1 - Thermal and fluidic cycling device for nucleic acid hybridization - Google Patents

Thermal and fluidic cycling device for nucleic acid hybridization Download PDF

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Publication number
CA2339163A1
CA2339163A1 CA002339163A CA2339163A CA2339163A1 CA 2339163 A1 CA2339163 A1 CA 2339163A1 CA 002339163 A CA002339163 A CA 002339163A CA 2339163 A CA2339163 A CA 2339163A CA 2339163 A1 CA2339163 A1 CA 2339163A1
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CA
Canada
Prior art keywords
solid substrate
thermal management
fluid
cavity
management module
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.)
Granted
Application number
CA002339163A
Other languages
French (fr)
Other versions
CA2339163C (en
Inventor
Aaron Custance
Jonathan Iam Parker
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.)
DIGILAB Inc
Original Assignee
Genomic Solutions, Inc.
Aaron Custance
Jonathan Iam Parker
Digilab, 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
Application filed by Genomic Solutions, Inc., Aaron Custance, Jonathan Iam Parker, Digilab, Inc. filed Critical Genomic Solutions, Inc.
Publication of CA2339163A1 publication Critical patent/CA2339163A1/en
Application granted granted Critical
Publication of CA2339163C publication Critical patent/CA2339163C/en
Anticipated expiration legal-status Critical
Expired - Fee Related legal-status Critical Current

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Classifications

    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00Sampling; Preparing specimens for investigation
    • G01N1/28Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/30Staining; Impregnating ; Fixation; Dehydration; Multistep processes for preparing samples of tissue, cell or nucleic acid material and the like for analysis
    • G01N1/31Apparatus therefor
    • G01N1/312Apparatus therefor for samples mounted on planar substrates
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L7/00Heating or cooling apparatus; Heat insulating devices
    • B01L7/52Heating 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
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/00029Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor provided with flat sample substrates, e.g. slides
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/04Closures and closing means
    • B01L2300/041Connecting closures to device or container
    • B01L2300/045Connecting closures to device or container whereby the whole cover is slidable
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/06Auxiliary integrated devices, integrated components
    • B01L2300/0627Sensor or part of a sensor is integrated
    • B01L2300/0636Integrated biosensor, microarrays
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/08Geometry, shape and general structure
    • B01L2300/0809Geometry, shape and general structure rectangular shaped
    • B01L2300/0822Slides
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/08Geometry, shape and general structure
    • B01L2300/0861Configuration of multiple channels and/or chambers in a single devices
    • B01L2300/0877Flow chambers
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/18Means for temperature control
    • B01L2300/1805Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks
    • B01L2300/1822Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks using Peltier elements
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00Moving or stopping fluids
    • B01L2400/04Moving fluids with specific forces or mechanical means
    • B01L2400/0475Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure
    • B01L2400/0487Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure fluid pressure, pneumatics
    • B01L2400/049Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure fluid pressure, pneumatics vacuum
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/00029Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor provided with flat sample substrates, e.g. slides
    • G01N2035/00099Characterised by type of test elements
    • G01N2035/00158Elements containing microarrays, i.e. "biochip"
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N2035/00346Heating or cooling arrangements
    • G01N2035/00356Holding samples at elevated temperature (incubation)
    • G01N2035/00366Several different temperatures used

Abstract

An apparatus (100) for automatically hybridizing nucleic acid samples is disclosed. The apparatus includes a fluid control module (108) and a temperature control (104) for precisely controlling fluid contacting and temperature of a plurality of DNA samples. The DNA samples are typically arrayed on solid substrates (glass microscope slides) (106), and the disclos ed apparatus can process up to twelve slides at one time on a master unit; satellite units can be added to increase the number of slides. All slides ca n be processed in parallel, or may be addressed individually to undergo different hybridization protocols. Thermal control is typically by slide pairs, such that slide pair undergoes the same temperature profile. Processe s are carried out under software control by an embedded PC (personal computer) (122). User input is by touchscreen (124) or floppy disk drive (126).</SDOAB >

Claims (47)

  1. WHAT IS CLAIMED IS:
  2. 2. An apparatus for automatically hybridizing a DNA microarray immobilized on a surface of a solid substrate, the apparatus comprising:
    at least one assembly for securing the solid substrate during hybridization, the assembly comprising a Garner and a removable cover having a surface facing the carrier, the carrier and the removable cover dimensioned to receive the solid substrate between the carrier and the surface of the removable cover so that the surfaces of the removable cover and the solid substrate define a cavity;
    a fluid control module comprising a fluid manifold, at least one liquid reservoir, at least one waste container, and a vacuum source in fluid communication with the waste container, the fluid manifold providing fluid communication between the liquid reservoir and the cavity and between the cavity and the waste container, and the vacuum source providing a pressure drop between the liquid reservoir and the waste container, wherein the pressure drop drives fluid flow throughout the fluid control module;
    at least one thermal management module for controlling temperature of the DNA
    microarray immobilized on the surface of the solid substrate, the thermal management module thermally contacting the assembly.
  3. 3. The apparatus of claim 2, wherein the apparatus includes at least two assemblies for securing solid substrates during hybridization.
  4. 4. The apparatus of claim 3, wherein the apparatus includes at least two thermal management modules.
  5. 5. The apparatus of claim 4, wherein each of the thermal management modules thermally contact different assemblies.
  6. 6. The apparatus of claim 2, wherein the apparatus includes at least six assemblies for securing solid substrates during hybridization.
  7. 7. The apparatus of claim 6, wherein the apparatus includes at least six thermal management modules.
  8. 8. The apparatus of claim 7, wherein each of the thermal management modules thermally contact different assemblies.
  9. 9. The apparatus of claim 2, further comprising a shim removably disposed between the surface of the solid substrate and the removable cower, the shim defining a standoff between the surface of the removable cover and the surface of the solid substrate.
  10. 10. The apparatus of claim 9, wherein the shim has a cut-out demarcating an inner periphery, the inner periphery of the shim encompassing a smaller area than the surface of the solid substrate.
  11. 11. The apparatus of claim 10, further comprising an o-ring contained in a groove on the surface of the removable cover, the grove located adjacent the inner periphery of the shim.
  12. 12. The apparatus of claim 11, wherein the o-ring is fabricated from a perfluoroelastomer.
  13. 13. The apparatus of claim 2, wherein the removable cover is fabricated from a high-temperature plastic.
  14. 14. The apparatus of claim 13, wherein the high temperature plastic is polysulfone.
  15. 15. The apparatus of claim 2, wherein the removable cover has first and second diffusion channels opening into the cavity, the first and second diffusion channels in fluid communication with the fluid manifold.
  16. 16. The apparatus of claim 15, wherein the fluid control module includes a pulse valve in fluid communication with the first diffusion channel for agitating fluid within the cavity.
  17. 17. The apparatus of claim 15, wherein the first and second diffusion channels provide for fluid flow into and out of the cavity.
  18. 18. The apparatus of claim 17, wherein the first and second diffusion channels are spaced apart so that fluid entering and exiting the cavity via the first and second diffusion channels flows across the DNA microarray immobilized on the surface of the solid substrate.
  19. 19. The apparatus of claim 15, further comprising a port located in the removable cover for manually injecting liquids directly into the cavity.
  20. 20. The apparatus of claim 19, wherein the port is tapered.
  21. 21. The apparatus of claim 19, wherein the port is dimensioned to receive a pipette.
  22. 22. The apparatus of claim 19, wherein the port is in fluid communication with the second diffusion channel.
  23. 23. The apparatus of claim 22, wherein the assembly for containing the solid substrate is tilted upward from the second diffusion channel towards the first diffusion channel.
  24. 24. The apparatus of claim 2, wherein the removable. cover includes thermal breaks for reducing distortion resulting from thermal gradients in a direction parallel to the surface of the solid substrate.
  25. 25. The apparatus of claim 2, wherein the carrier includes tabs for reducing lateral movement of the solid substrate.
  26. 26. The apparatus of claim 2, wherein the Garner is fabricated from stainless steel.
  27. 27. The apparatus of claim 2, wherein the removable. cover and the carrier are adapted to secure at least two solid substrates.
  28. 28. The apparatus of claim 2, wherein the fluid manifold comprises multiple layers of acrylic.
  29. 29. The apparatus of claim 2, wherein the fluid control module includes valves providing selective fluid communication between the liquid reservoir and the cavity and between the cavity and the waste container.
  30. 30. The apparatus of claim 29, wherein the valves are zero dead volume valves.
  31. 31. The apparatus of claim 2, wherein the fluid control module includes at least two waste containers.
  32. 32. The apparatus of claim 2, wherein the vacuum source is a vacuum pump.
  33. 33 The apparatus of claim 2, wherein the thermal management module includes at least one Peltier device in thermal contact with the assembly.
  34. 34. The apparatus of claim 33, wherein the thermal management module includes a thermal plate disposed between the assembly and the Peltier device.
  35. 35. The apparatus of claim 33, wherein the thermal management module includes a graphite-loaded pad disposed between the assembly and the Pettier device.
  36. 36. The apparatus of claim 35, wherein the thermal management module includes a thermal plate disposed between the assembly and the graphite-loaded pad.
  37. 37. The apparatus of claim 2, wherein the thermal management module includes at least four Pettier devices in thermal contact with the assembly.
  38. 38. The apparatus of claim 2, wherein the thermal management module includes at least one temperature sensor located adjacent the carrier.
  39. 39. The apparatus of claim 2, wherein the thermal management module is capable of temperature ramp rates of about one °C per second.
  40. 40. The apparatus of claim 2, wherein the thermal management module is capable of controlling the temperature of the DNA microarray between about one °C and about one hundred °C.
  41. 41. The apparatus of claim 2, further comprising an embedded personal computer communicating with the fluid control module.
  42. 42. The apparatus of claim 2, further comprising an embedded personal computer communicating with the thermal management module.
  43. 43. The apparatus of claim 42, further comprising software running on the embedded personal computer, the software controlling the thermal management module using a mathematical model that approximates thermal characteristics of the thermal management module.
  44. 44. The apparatus of claim 2, further comprising a power supply module providing electrical current to the fluid control module and thermal management module.
  45. 45. The apparatus of claim 44, wherein the power supply module uses intelligent energy scheduling.
  46. 46. An apparatus for automatically hybridizing a DNA microarray immobilized on a surface of a solid substrate, the apparatus comprising:
    at least one assembly for securing the solid substrate during hybridization, the assembly comprising a carrier and a removable cover having a surface facing the carrier, the carrier and the removable cover dimensioned to receive the solid substrate between the carrier and the surface of the removable cover so that the surfaces of the removable cover and the solid substrate define a cavity;
    a fluid control module comprising a fluid manifold, at least one liquid reservoir, at least one waste container, and a vacuum source in fluid communication with the waste container, the fluid manifold providing fluid communication between the liquid reservoir and the cavity and between the cavity and the waste container, and the vacuum source providing a pressure drop between the liquid reservoir and the waste container, wherein the pressure drop drives fluid flow throughout the fluid control module;
    at least one thermal management module for controlling temperature of the DNA
    microarray immobilized on the surface of the solid substrate, the thermal management module thermally contacting the DNA microarray through the earner and the solid substrate.
  47. 47. An apparatus for automatically hybridizing DNA microarrays, the apparatus comprising:
    a solid substrate having a DNA microarray immobilized. on a surface of the solid substrate;
    at least one assembly for securing the solid substrate doting hybridization, the assembly comprising a carrier and a removable cover having a surface facing the carrier, the carrier and the removable cover dimensioned to receive the solid substrate between the carrier and the surface of the removable cover so that the surfaces of the removable cover and the solid substrate define a cavity;
    a fluid control module comprising a fluid manifold, at least one liquid reservoir, at least one waste container, and a vacuum source in fluid communication with the waste container, the fluid manifold providing fluid communication between the liquid reservoir and the cavity and between the cavity and the waste container, and the vacuum source providing a pressure drop between the liquid reservoir and the waste container, wherein the pressure drop drives fluid flow throughout the fluid control module;
    at least one thermal management module for controlling temperature of the DNA
    microarray immobilized on the surface of the solid substrate, the thermal management module thermally contacting the assembly.
CA002339163A 1998-08-10 1999-08-10 Thermal and fluidic cycling device for nucleic acid hybridization Expired - Fee Related CA2339163C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US9610998P 1998-08-10 1998-08-10
US60/096,109 1998-08-10
PCT/US1999/018122 WO2000009650A1 (en) 1998-08-10 1999-08-10 A thermal/fluidic cycling device for the purpose of nucleic acid hybridization

Publications (2)

Publication Number Publication Date
CA2339163A1 true CA2339163A1 (en) 2000-02-24
CA2339163C CA2339163C (en) 2010-01-12

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Family Applications (1)

Application Number Title Priority Date Filing Date
CA002339163A Expired - Fee Related CA2339163C (en) 1998-08-10 1999-08-10 Thermal and fluidic cycling device for nucleic acid hybridization

Country Status (7)

Country Link
US (2) US6238910B1 (en)
EP (1) EP1105458B1 (en)
JP (1) JP2002522065A (en)
AU (2) AU772769B2 (en)
CA (1) CA2339163C (en)
DE (1) DE69935230T2 (en)
WO (1) WO2000009650A1 (en)

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US6238910B1 (en) 2001-05-29
US6432696B2 (en) 2002-08-13
EP1105458A1 (en) 2001-06-13
AU772769B2 (en) 2004-05-06
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JP2002522065A (en) 2002-07-23
DE69935230T2 (en) 2007-12-20

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