Method and system for microfluidic interfacing to arrays

• US 20040037739A1
• Filed: 08/26/2002
• Published: 02/26/2004
• Est. Priority Date: 03/09/2001
• Status: Active Grant

• Current Assignee: Roche NimbleGen, Inc. (Roche Holding AG)
• Original Assignee: BioMicro Systems, Inc. (Danaher Corporation)
• Inventors: Moyer, Thomas, Howard, Michael, Jensen, John, Adey, Nils, Ayliffe, Edward, Coffin, Stephen, McNeely, Michael, Beutel, Darin, Spute, Mark
• Granted Patent: US 7,223,363 B2
• Time in Patent Office: Days
• US Class Current: 422/58
• CPC Class Codes: B01F 25/50 Circulation mixers, e.g. wherein at least part of the mixture is discharged from and reintroduced into a receptacle
• CPC Class Codes: B01F 31/31 using receptacles with deformable parts, e.g. membranes, to which a motion is imparted
• CPC Class Codes: B01F 31/86 with vibration of the receptacle or part of it
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01J 19/0093 Microreactors, e.g. miniaturised or microfabricated reactors laboratory containers with capillary fluid transport in microfabricated channels or chambers B01L3/5027
• CPC Class Codes: B01J 2219/00351 Means for dispensing and evacuation of reagents
• CPC Class Codes: B01J 2219/0043 for direct application of reagents, e.g. through openings in a shutter
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01L 2200/025 Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/026 Fluid interfacing between devices or objects, e.g. connectors, inlet details
• CPC Class Codes: B01L 2200/0689 Sealing
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2300/0822 Slides
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2300/0883 : Serpentine channels
• CPC Class Codes: B01L 2300/0887 : Laminated structure
• CPC Class Codes: B01L 3/0293 : for liquids
• CPC Class Codes: B01L 3/502715 : characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/50273 : characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502746 : characterised by the means for controlling flow resistance, e.g. flow controllers, baffles B01L3/502738 takes precedence
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B01L 9/52 : Supports specially adapted for flat sample carriers, e.g. for plates, slides, chips
• CPC Class Codes: B01L 9/527 : for microfluidic devices, e.g. used for lab-on-a-chip
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2035/00158 : Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 2035/00237 : Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: G01N 2035/00544 : using fluid flow
• CPC Class Codes: G01N 33/543 : with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 35/00 : Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
• CPC Class Codes: G01N 35/025 : having a carousel or turntable for reaction cells or cuvettes
• CPC Class Codes: G01N 35/028 : having reaction cells in the form of microtitration plates

Abstract

A method and system for providing a fluidic interface to slides bearing microarrays of biomolecules or other samples immobilized thereon to perform a variety of chemical reactions or processing steps on the slide. An interface device seals against the slide to form a chamber or chambers containing all or a portion of the microarray, providing selective access to portions of the slide. The interface device includes inlet and outlet ports permitting liquid sample and reagents to be introduced to and removed from the chamber accessing the slide surface. Pre-and post-array microfluidic circuitry may be included in the interface device or in attachable modules. The system may include one or more compartments for collecting and storing waste fluids.

Claims

1. An interface device for interfacing to a surface of a substrate bearing a biological sample immobilized on a first surface thereof, comprising:

a. a main interface layer having an interface surface adapted to conform to the first surface of the substrate;

b. a gasket positioned at said interface surface and having at least one opening formed therethrough, said opening defining an interface channel;

c. an inlet channel formed in said main interface layer and opening into said at least one opening;

d. an outlet channel formed in said main interface layer and opening into said at least one opening; and

e. at least one air bladder formed in said main interface layer adjacent said interface surface, wherein said at least one air bladder has a flexible lower surface capable of being deflected outward as said air bladder is inflated or inward as said air bladder is deflated, and wherein said air bladder communicates with at least one air channel that passes through said main interface layer and is adapted for connection with a pressure source.

2. The interface device of claim 1, wherein said gasket defines an interface channel having a height of between about 20 μ

m and about 30 μ

m.

3. The interface device of claim 1, wherein said gasket defines an interface channel having a height of between about 23 μ

m and about 27 μ

m.

4. The interface device of claim 1, wherein said flexible lower surface of said at least one air bladder comprises a flexible diaphragm layer attached to the lower surface of said main interface layer.

5. The interface device of claim 1, wherein said flexible lower surface of said at least one air bladder comprises a thin layer of the rigid material forming the bulk of said main interface layer.

6. The interface device of claim 1, further comprising a waste reservoir in said main interface layer in fluid communication with said at least one outlet channel.

7. The interface device of claim 1, further comprising a microfluidic circuit comprising at least one of a mixing circuit, a branching structure, a reservoir, a valve, or a stop junction.

8. The interface device of claim 7, wherein said microfluidic circuit is in fluid communication between said inlet channel and said at least one interface channel.

9. The interface device of claim 7, wherein said microfluidic circuit is in fluid communication between said at least one interface channel and said outlet.

10. The interface device of claim 7, wherein said microfluidic circuit comprises at least one passive valve.

11. The interface device of claim 1, wherein said at least one interface channel is defined at least in part by an interface well or groove formed in said interface surface of said main interface layer.

12. The interface device of claim 1, wherein said gasket is formed from a resilient sheet material.

13. The interface device of claim 1, wherein said gasket is formed by application of said resilient material directly to said interface surface.

14. The interface device of claim 1, wherein said gasket is formed of an elastic material.

15. The interface device of claim 1, wherein said gasket is formed of a plastically deformable material.

16. The interface device of claim 1, wherein said gasket is formed of an adhesive material.

17. There interface device of claim 16, wherein said adhesive is adapted to adhere reversibly to said first surface of said substrate.

18. The interface device of claim of 1, wherein said interface device is constructed from multiple layers, and wherein said interface device further comprises microfluidic circuit structures formed in at least two of said multiple layers.

19. The interface device of claim 1, wherein said substrate is a microarray slide.

20. An interface device for interfacing to a surface of a substrate bearing biological samples immobilized on a first surface thereof, comprising:

a. a main interface layer having an interface surface adapted to conform to the first surface of the substrate;

b. a gasket positioned at said interface surface and having a plurality of openings formed therethrough, each said opening defining an interface channel or chamber;

c. at least one inlet channel formed in said main interface layer and opening into each said opening; and

d. at least one outlet channel formed in said main interface layer and opening into each said opening.

21. The interface device of claim 20, further comprising at least one air bladder formed in said main interface layer adjacent said interface surface, wherein said at least one air bladder has a flexible lower surface capable of being deflected outward as said air bladder is inflated or inward as said air bladder is deflated, and wherein said air bladder communicates with at least one said air channel that passes through said main interface layer and is adapted for connection with a pressure source.

22. The interface device of claim 20, further comprising a microfluidic branching structure in fluid communication between one said inlet and a plurality of said interface channels, said branching structure adapted to divide fluid entering said inlet among said plurality of interface channels.

23. The interface device of claim 20, further comprising a microfluidic circuit in fluid communication between at least two said interface channels and one said outlet, said microfluidic circuit adapted to combine fluids from said at least two interface channels into a single fluid stream flowing through said outlet.

24. The interface device of claim 20, wherein at least one said interface channel is defined at least in part by an interface well or groove formed in said interface surface of said main interface layer.

25. The interface device of claim 20, wherein said gasket is formed from a resilient sheet material.

26. The interface device of claim 20, wherein said gasket is formed by application of said resilient material directly to said interface surface.

27. The interface device of claim 20, wherein said gasket is formed of an elastic material.

28. The interface device of claim 20, wherein said gasket is formed of a plastically deformable material.

29. The interface device of claim 20, wherein said gasket is formed of an adhesive material.

30. The interface device of claim 29, wherein said adhesive is adapted to adhere reversibly to said first surface of said substrate.

31. The interface device of claim 20, wherein said interface device is formed of multiple layers, and wherein said interface device further comprises a 3D microfluidic circuit comprising microfluidic circuit components in at least two of said multiple layers.

32. The interface device of claim 31, wherein 3D microfluidic circuit comprises overlapping microfluidic circuit structures.

33. The interface device of claim 20, wherein said substrate is a microarray slide.

39. The instrument of claim 34, wherein said active element comprises a sensor, and wherein said at least one additional component receives an electrical signal from said sensor.

40. The instrument of claim 34, further comprising an adaptor for making a fluid connection to said reaction device, whereby fluid may be delivered to said interface channel or well of said reaction device from said instrument.

41. The instrument of claim 34, comprising a plurality of recesses, each recess adapted to receive one said reaction device.

42. The instrument of claim 41, further comprising a plurality of adaptors for making fluid connections to reaction devices received in said plurality of recesses, whereby fluid may be delivered to said interface channel or well of each said reaction device from said instrument.

43. An instrument for processing a substrate bearing a biological sample immobilized on a first surface thereof, Comprising:

a. a heat block adapted to fit into laboratory heater;

b. at least one recess in thermal communication with said heat block and adapted to receive a reaction device comprising;

i. a substrate bearing a biological sample immobilized on a first surface thereof; and

ii. an interface device adapted to seal to said first surface to form at least one interface channel containing said biological sample.

44. The instrument of claim 43, further comprising:

a. a mixing element located in at least one of said instrument and said interface device, said mixing element capable of producing agitation of fluid in said interface channel; and

b. a mixing controller adapted to send a mixing control signal to said mixing element.

45. The instrument of claim 44, wherein said mixing element comprises at least one air bladder located in said interface device adjacent said at least one interface channel, and wherein said mixing controller controls the generation of positive and negative air pressures used to inflate and deflate said air bladder.

46. The instrument of claim 45, wherein said mixing element comprises two air bladders located at opposite ends of said at least one interface channel, wherein said mixing controller inflates and deflates said two air bladders reciprocally to produce agitation of fluid in said at least one interface channel.

47. The instrument of claim 44, wherein said mixing element comprises a piezoelectric element, and wherein said mixing controller controls the generation of a voltage signal that causes activation of said piezoelectric element.

48. A reaction device for providing controlled delivery of fluids to the surface of a substrate bearing an immobilized biological sample, comprising:

a. a substrate bearing an immobilized biological sample on a first surface thereof;

b. an interface device adapted to seal to said first surface of said substrate to form at least one interface channel containing said biological sample, said interface device comprising

i. a main interface layer formed of a rigid material and having an interface surface adapted to conform to said first surface of the substrate;

ii. a gasket positioned at said interface surface and having at least one opening formed therethrough, said opening defining an interface channel or chamber;

iii. an inlet channel passing through said main interface layer and opening into said at least one opening; and

iv. an outlet channel passing through said main interface layer and opening into said at least one opening.

49. The reaction device of claim 48, wherein said substrate comprises a microarray slide.

50. The reaction device of claim 48, wherein said gasket defines an interface channel or chamber having a height of between about 20 μ

m and about 30 μ

m.

51. The reaction device of claim 48, wherein said gasket defines an interface channel or chamber having a height of between about 23 μ

m and about 27 μ

m.

52. The reaction device of claim 48, further comprising a base having a recess adapted to receive said substrate.

53. The reaction device of claim 52, further comprising a clamp mechanism for clamping said base, substrate, and interface device together to seal said interface device to said substrate.

54. The reaction device of claim 53, wherein said clamp mechanism comprises two c-channel clamps pivotally mounted to said base, wherein said c-channel clamps pivot laterally outward in the plane of said substrate received in said base.

55. The reaction device of claim 48, wherein said base comprises a part of an instrument adapted for processing microarray slides, and wherein said instrument further comprises a clamp mechanism adapted to press said interface device and said substrate against said base.

56. The reaction device of claim 48, further comprising an external control module.

57. The reaction device of claim 48, wherein said base further comprises an active element selected from a heating element and a piezoelectric mixing element.

58. The reaction device of claim 48, further comprising a clamp mechanism adapted to hold said interface device in sealing relationship with said substrate.

59. The reaction device of claim 48, further comprising at least one air bladder formed in said main interface layer adjacent said interface surface, wherein said at least one air bladder has a flexible lower surface capable of being deflected outward as said air bladder is inflated or inward as said air bladder is deflated, and wherein said air bladder communicates with at least one air channel that passes through said main interface layer and is adapted for connection with a pressure source.

60. The reaction device of claim 59, wherein said flexible lower surface of said at least one air bladder comprises a flexible diaphragm layer attached to the lower surface of said main interface layer.

61. The reaction device of claim 59, wherein said flexible lower surface of said at least one air bladder comprises a thin layer of the rigid material forming the bulk of said main interface layer.

62. The reaction device of claim 48, wherein said interface device further comprises a waste reservoir in said main interface layer in fluid communication with said at least one outlet channel.

63. The reaction device of claim 48, wherein said at least one opening defines a loop channel having a loop configuration, wherein fluid is circulated through said loop channel, and wherein circulation of fluid into and around said loop is regulated by passive valves.

64. The reaction device of claim 48, wherein a first portion of said reaction device is disposable and a second portion of said reaction device is reusable.

65. The reaction device of claim 52, wherein said base is adapted to seal to said interface device to form a humidity chamber around said substrate, whereby said seal between said substrate and said interface device may be exposed to a humid environment.

66. The reaction device of claim 48, wherein the volume of said interface channel or chamber is reduced by flowing a filler material into said interface channel or chamber to fill a portion of the volume of said interface channel or chamber opposite said substrate, wherein said filler material is immiscible with fluid to be introduced to said interface channel or chamber.

67. A method of performing a chemical reaction with molecules immobilized on a substrate, comprising the steps of:

a. providing a substrate bearing immobilized molecules thereon;

b. positioning an interface device with respect to said substrate, said interface device comprising an inlet port and an outlet port;

c. clamping said interface device to said substrate, thus sealing said interface device to said substrate to form an interface channel having a first end and a second end at the interface between said interface device and said substrate, wherein said interface channel communicates with said inlet port at said first end and with said outlet port at said second end and wherein said interface channel contains at least a portion of said substrate bearing immobilized molecules;

d. introducing a fluid containing a reactant to said interface channel via an inlet port of said interface device; and

e. reacting said reactant in said fluid with said immobilized molecules in said interface channel.

68. A method of performing a binding reaction between two chemical compounds, comprising the steps of:

a. providing a substrate having a first compound immobilized thereon;

b. sealing an interface device against said substrate to form an interface channel having an inlet and an outlet and comprising a portion of said substrate having said first chemical compound immobilized thereon, said interface device comprising;

i. at least one inlet channel passing through said interface device and communicating with said interface channel via said inlet;

c. introducing a solution containing a blocking solution into interface channel via said inlet channel;

d. incubating said blocking solution on said portion of said substrate to block non-specific binding sites on said substrate;

e. introducing a first wash solution into said interface channel via said inlet channel, wherein said blocking solution exits said interface channel via said outlet as said first wash solution enters said interface channel;

f. introducing a binding solution containing a second chemical compound into said interface channel via said inlet channel, wherein said wash solution exits said interface channel via said outlet as said binding solution enters said interface channel;

g. incubating said binding solution on said portion of said substrate to produce binding of said second chemical compound to said first chemical compound; and

h. introducing a second wash solution into said interface channel via said inlet channel, wherein said binding solution exits said interface channel via said outlet as said second wash solution enters said interface channel.

69. The method of claim 68, further comprising a pre-processing step of labeling said second chemical compound in said binding solution prior to introduction of said binding solution into said inlet channel.

70. The method of claim 68, further comprising a pre-processing step of purifying impurities out of said binding solution prior to introduction of said binding solution into said inlet channel.

71. The method of claim 68, wherein said first chemical compound comprises a first polynucleotide, wherein said second chemical compound comprises a second nucleotide, wherein said blocking solution is a pre-hybridization buffer, and wherein binding of said second chemical compound to said first chemical compound comprises a hybridization reaction.

72. The method of claim 68, further comprising the step of detecting binding of said first chemical compound and said second chemical compound on said substrate.

73. The method of claim 68, wherein mixing of fluid within said interface channel is provided during at least one of said method steps.