Methods for fabricating an array for use in multiplexed biochemical analysis

• US 6,312,960 B1
• Filed: 12/22/1998
• Issued: 11/06/2001
• Est. Priority Date: 12/31/1996
• Status: Expired due to Fees

• Current Assignee: High Throughput Genomics, Inc.
• Original Assignee: Genometrix Genomics Inc.
• Inventors: Hogan, Michael E., Balch, William J.
• Primary Examiner(s): Chin, Christopher L.
• Assistant Examiner(s): PHAM, MINH QUAN K
• Application Number:
  US09/218,979
• Time in Patent Office: 1,050 Days
• Field of Search: 436/164, 436/172, 436/501, 436/518, 436/800, 436/804, 436/805, 436/43, 436/50, 436/524, 436/525, 436/527, 436/531, 435/4, 435/174, 435/6, 435/286.1, 435/286.6, 435/286.5, 422/62, 422/63, 422/67, 422/68.1, 422/81, 422/105, 422/112
• US Class Current: 506/32
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00369 in multiple or parallel arrangements
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• 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 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2300/0893 having a very large number of wells, microfabricated wells
• CPC Class Codes: B01L 3/0262 using touch-off at substrate or container
• CPC Class Codes: B01L 3/0268 : using pulse dispensing or spraying, eg. inkjet type, piezo actuated ejection of droplets from capillaries
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2035/00237 : Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: G01N 2035/1034 : Transferring microquantities of liquid
• CPC Class Codes: G01N 2035/1039 : Micropipettes, e.g. microcapillary tubes
• CPC Class Codes: G01N 2035/1041 : Ink-jet like dispensers
• CPC Class Codes: G01N 33/54366 : Apparatus specially adapted for solid-phase testing
• CPC Class Codes: G01N 35/0099 : comprising robots or similar manipulators robots per se B25J
• CPC Class Codes: G01N 35/028 : having reaction cells in the form of microtitration plates
• CPC Class Codes: G01N 35/1065 : Multiple transfer devices
• CPC Class Codes: G01N 35/1074 : arranged in a two-dimensional array
• CPC Class Codes: Y10S 435/808 : Optical sensing apparatus
• CPC Class Codes: Y10S 436/80 : Fluorescent dyes, e.g. rhodamine
• CPC Class Codes: Y10S 436/804 : Radioisotope, e.g. radioimmunoassay
• CPC Class Codes: Y10S 436/805 : Optical property
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 436/11 : Automated chemical analysis
• CPC Class Codes: Y10T 436/115831 : Condition or time responsive

Abstract

The invention provides methods for preparing a reaction substrate for use as assay devices comprising parallel printing of arrays of biosites on reaction substrates, wherein each biosite comprises a single type of capture probe bound to the reaction substrate and the array of biosites is deposited on the reaction substrate by a capillary bundle printer device.

Claims

1. A method for preparing a reaction substrate for use as an assay device, comprising a step of parallel printing an array of biosites on said reaction substrate, wherein each biosite comprises a single type of capture probe bound to said reaction substrate, and wherein the array of biosites is deposited on the reaction substrate by a capillary bundle printer device, wherein the capillary bundle device comprises:

a plurality of bundled capillary tubes, each tube having a proximal end and a distal end;

an attachment site for holding the bundled capillary tubes at a point spaced from the distal ends of the capillary tubes;

an array template for slidably holding each capillary tube near its distal end, and for allowing the distal end of each capillary tube to move with respect to the attachment site;

at least one manifold for positioning the proximal end of each capillary tube within a corresponding supply chamber, wherein each supply chamber is capable of supplying a liquid reagent to at least one corresponding capillary tube; and

a positioning device for precisely positioning the array template and the bundled capillary tubes with respect to the reaction substrate and depositing liquid reagents from the distal end of the capillary tubes onto the reaction substrates as biosites.

2. The method of claim 1, wherein the plurality of bundled capillary tubes comprises about 2 to about 10,000 tubes, having a center-to center spacing of about 80 μ

m to about 5 mm.

3. The method of claim 1, wherein each supply chamber supplies only one capillary tube.

4. The method of claim 1, wherein a supply chamber supplies the plurality of bundled capillary tubes.

5. The method of claim 1, wherein the bundled capillary tubes comprise a stainless steel, a plastic, a rubber, a glass, a TEFLON™

, a flexible metal, or a fused silica coated with polyimide.

6. The method of claim 1, wherein the device includes a plurality of array templates.

7. The method of claim 1, further comprising a positioning device for precisely positioning the reaction substrate.

8. The method of claim 1, wherein the capillaries have an inside diameter of about 10 μ

m to about 200 μ

m and an outside diameter of about 80 μ

m to about 500 μ

m.

9. The method of claim 1, wherein the array template comprises an array of sleeves, each sleeve having an inside diameter sufficient to permit a capillary to slide through, and a length sufficient to allow a precise pattern to be maintained while depositing fluids onto the reaction substrate.

10. The method of claim 1, wherein the array template comprises a plurality of holes formed in a rigid material.

11. The method of claim 1, wherein the array template comprises a rigidly formed or held mesh.

12. The method of claim 1, further comprising a housing for containing the supply chambers.

13. The method of claim 12, wherein the housing is capable of maintaining an inert atmosphere.

14. The method of claim 12, wherein the housing is capable of maintaining an elevated or reduced temperature.

15. The method of claim 12, wherein the housing may be pressurized to a predetermined pressure.

16. The method of claim 15, wherein the pressure is modulated to control the flow of liquid reagents through the capillary tubes.

17. The method of claim 1, wherein the supply chambers are positioned higher than the distal end of the capillary tubes to provide a pressure head.

18. The method of claim 1, wherein deposit of liquid reagent is controlled by a means for electrophoresis.

19. The method of claim 1, wherein supply of liquid reagent is controlled by a means for electro-osmosis.

20. The method of claim 1, wherein the device includes multiple sets of supply chambers, each for supplying liquid reagent to a subset of the bundled capillary tubes.

21. The method of claim 1, wherein the bundled capillary tubes are free to flex between the attachment site and the array template.

22. The method of claim 1, wherein the reaction substrate is pre-etched to define a pattern of reactive areas matching the geometry of the deposited biosites.

23. The method of claim 1, wherein the biosites are deposited substantially simultaneously.

24. The method of claim 1, wherein each biosite is fluidically isolated from each other biosite.

25. The method of claim 1, wherein the array of biosites is deposited on the reaction substrate in a single print step by the capillary bundle printer device.

26. The method of claim 1, wherein the positioning device further comprises a Z-axis motion control.

27. The method of claim 1, wherein the reaction substrate is delivered to the capillary bundle by a robotic arm.

28. The method of claim 1, wherein the capillary bundles are affixed to a robotic arm.

29. The method of claim 1, wherein the reaction substrate comprises a nylon membrane, a polypropylene, a polystyrene, a vinyl, a plastic, or a glass.

30. The method of claim 1, wherein the array template comprises a metal grid, a mesh, a rigidly-held fabric mesh, a bundle of sleeve tubes having an inner diameter sufficient to admit the fluid delivery capillaries, or a solid block having holes or channels.

31. The method of claim 1, wherein each biosite comprises a spot of about 25 to about 200 μ

m in diameter.

32. The method of claim 1, wherein said reaction substrate is optically clear and has a thickness of about 50 to about 300 μ

m.

33. A method for preparing a reaction substrate for use as an assay device, comprising a step of parallel printing an array of biosites on said reaction substrate, wherein each biosite comprises a single type of capture probe bound to said reaction substrate, and wherein the array of biosites is deposited on the reaction substrate by a capillary bundle printer device, wherein the capillary bundle device comprises:

a plurality of bundled capillary tubes, each tube having a proximal end and a distal end;

an attachment site for holding the bundled capillary tubes at a point spaced from the distal ends of the capillary tubes;

a structure for positioning the proximal end of each capillary tube within a corresponding supply chamber, each supply chamber capable of supplying a liquid reagent to at least one corresponding capillary tube;

a print head for holding the plurality of bundled capillary tubes near their distal ends and for precisely positioning the distal ends of the capillary tubes with respect to the reaction substrate to deposit liquid reagents onto the reaction substrate as biosites.

34. The method of claim 33, where the print head includes an ink-jet deposition device.

35. The method of claim 33, wherein the liquid reagent comprises at lease one capture probe.