Devices and methods for producing microarrays of biological samples

• US 20050106621A1
• Filed: 12/27/2004
• Published: 05/19/2005
• Est. Priority Date: 08/16/2000
• Status: Abandoned Application

• Current Assignee: University Health Network
• Original Assignee: University Health Network
• Inventors: Winegarden, Neil A., McNeil, James B.
• Application Number:
  US11/022,997
• Publication Number:
  US 20050106621A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential 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 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00691 using robots
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 13/02 for receptacle or instruments
• CPC Class Codes: B01L 2200/023 adapted for different sizes of tubes, tips or container
• CPC Class Codes: B01L 2200/143 Quality control, feedback systems
• CPC Class Codes: B01L 2300/0822 Slides
• CPC Class Codes: B01L 2400/022 droplet contacts the surface of the receptacle
• CPC Class Codes: B01L 2400/049 vacuum
• CPC Class Codes: B01L 3/0244 : using pins
• CPC Class Codes: B01L 9/523 : for multisample carriers, e.g. used for microtitration plates
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries

Abstract

The present invention is directed to systems and methods for producing microarrays of biological samples using an improved slide platform, vacuum manifold, and variable pin contact velocity. Slides onto which spotting pins produce the microarray of biological samples are secured on a flat slide platform using magnetic unit bars. The vacuum manifold effects optimal cleaning of the spotting pins by inducing increased air flow and turbulence. By reducing the velocity of the spotting pins before or after contact with the blot pad or the microarray slide, the morphology of biological samples deposited may be kept uniform. Similarly, low impact and separating velocities while acquiring biological materials prevent the pins from being overloaded with solution on the outside of the pin and causing sample wastage and non-uniform spotting.

Claims

1. A support device for holding microarray substrates in place during microarrayer operation, comprising:

a flat platform on which substrates may be placed, the flat platform including an array surface including first, second, third and fourth peripheral edges;

a first bar on the first peripheral edge;

a second bar on the second peripheral edge, the second bar perpendicular to the first bar;

a third bar on the third peripheral edge, the third bar perpendicular to the second bar and opposed to the first bar, the third bar capable of applying force to the substrates to hold them in place during microarray operation; and

a plurality of end bars perpendicular to the first and third bars and opposed to the second bar, the end bars capable of being located on the third peripheral edge or on the array surface spaced apart from the third peripheral edge, the end bars capable of applying force to the substrates to hold them in place during microarray operation.

2. The support device of claim 1, wherein the device may be loaded with the substrates for microarray operation by placing each substrate of the substrates on the flat platform and sliding it into a position suitable for microarrayer operation.

3. The support device of claim 1, wherein the end bars and second bars are moved proximate to the substrates so that the end bars and second bars apply force to the substrates to hold them in place during microarray operation.

4. The support device of claim 2, wherein the end bars and second bars are moved proximate to the substrates so that the end bars and second bars apply force to the substrates to hold them in place during microarray operation.

5. The support device of claim 1, wherein each substrate of the substrates comprise a slide.

6. The support device of claim 2, wherein each substrate of the substrates comprise a slide.

7. The support device of claim 3, wherein each substrate of the substrates comprise a slide.

8. The support device of claim 4, wherein each substrate of the substrates comprise a slide.

9. The support device of claim 1 wherein each substrate of the substrates is about a same length as an end bar.

10. The support device of claim 2, wherein each substrate of the substrates is about a same length as an end bar.

11. The support device of claim 3, wherein each substrate of the substrates is about a same length as an end bar.

12. The support device of claim 4, wherein each substrate of the substrates is about a same length as an end bar.

13. The support device of claim 9, wherein the substrate and the end bar have a length selected from the group consisting of ×

1×

3 inch, 1×

1 inch, and 2×

3 inch.

14. The support device of claim 10, wherein the substrate and the end bar have a length selected from the group consisting of 1×

3 inch, 1×

1 inch, and 2×

3 inch.

15. The support device of claim 1 wherein the substrate and the end bar have a length selected from the group consisting of 1×

3 inch, 1×

1 inch, and 2×

3 inch.

16. The support device of claim 12, wherein the substrate and the end bar have a length selected from the group consisting of 1×

3 inch, 1×

1 inch, and 2×

3 inch.

17. The support device of claim 1, wherein the flat platform comprises a magnetic material and the end bars comprise magnets capable of releasable connection to the flat platform.

18. The support device of claim 17, wherein the magnetic material comprises steel.

19. The support device of claim 1, wherein the flat platform is rectangular and includes less than 200 micrometer variation between corners.

20. The support device of claim 1, wherein the flat platform is rectangular and includes less than 200 micrometer variation between corners and the flat platform comprises a magnetic material and the end bars comprise magnets capable of releasable connection to the flat platform.

21. The support device of claim 1, wherein the flat platform is rectangular and includes less than 200 micrometer variation between corners and the magnetic material comprises steel.

22. The support device of claim 1, wherein the flat platform is about 50 cm in length×

50 cm in width.

23. The support device of claim 1, wherein the flat platform is about 50 cm in length×

50 cm in width and the flat platform comprises a magnetic material and the end bars comprise magnets capable of releasable connection to the flat platform.

24. The support device of claim 1, wherein the flat platform is about 50 cm in length×

50 cm in width and the magnetic material comprises steel.

25. The support device of claim 1, wherein the flat platform is about 50 cm in length×

50 cm in width and the flat platform is rectangular and includes less than 200 micrometer variation between corners.

26. The support device of claim 1, wherein the flat platform is impermeable to air.

27. The support device of claim 1, wherein the support device includes a microarrayer.

28. The support device of claim 17, wherein the support device includes a microarrayer.

29. The support device of claim 18, wherein the support device includes a microarrayer.

30. The support device of claim 19, wherein the support device includes a microarrayer.

31. The support device of claim 20, wherein the support device includes a microarrayer.

32. The support device of claim 21., wherein the support device includes a microarrayer.

33. The support device of claim 22, wherein the support device includes a microarrayer.

34. The support device of claim 23, wherein the support device includes a microarrayer.

35. The support device of claim 24, wherein the support device includes a microarrayer.

36. The support device of claim 25, wherein the support device includes a microarrayer.

37. The support device of claim 2.6, wherein the support device includes a microarrayer.

38. A blotting device for blotting liquid from the exterior of microarray spotting members, comprising:

a blotting surface for drawing liquid from the microarray spotting members when the microarray spotting members contact the blotting surface; and

structure for contacting the microarray spotting members with the blotting surface.

39. The blotting device of claim 38, wherein the blotting surface comprises glass.

40. The blotting device of claim 38, wherein the blotting surface comprises a fixed glass slide.

41. The blotting device of claim 38, wherein the spotting members comprise pins.

42. The blotting device of claim 39, wherein the spotting members comprise pins.

43. The blotting device of claim 40, wherein the spotting members comprise pins.

44. The blotting device of claim 41, wherein the pins comprise Telechem Chipmaker 2 pins or Telechem Chipmaker 3 pins, or a combination thereof.

45. The blotting device of claim 42, wherein the pins comprise Telechem Chipmaker 2 pins or Telechem Chipmaker 3 pins, or a combination thereof.

46. The blotting device of claim 43, wherein the pins comprise Telechem Chipmaker 2 pins or Telechem Chipmaker 3 pins, or a combination thereof.

47. The blotting device of claim 38, wherein following blotting, the blotting surface is substantially free of liquid from the interior of the microarray spotting members.

48. The blotting device of claim 38, further comprising a processing system for directing the microarray spotting members to make more than one contact with the blotting surface in a predetermined pattern so that no portion of the blotting surface is contacted by more than one microarray spotting member.

49. The blotting device of claim 38, further comprising a processing system for directing the microarray spotting members to make more than one contact with the blotting surface in a predetermined pattern so that no portion of the blotting surface is contacted by more than one microarray spotting member and wherein following blotting, the blotting surface is substantially free of liquid from the interior of the microarray spotting members.

50. The blotting device of claim 38, wherein the blotting device includes a microarrayer.

51. The blotting device of claim 47, wherein the blotting device includes a microarrayer.

52. The blotting device of claim 48, wherein the blotting device includes a microarrayer.

53. The blotting device of claim 49, wherein the blotting device includes a microarrayer.

54. A method of delivering liquid from a spotting member onto a microarray substrate for a microarray operation, comprising:

advancing the spotting member from a first position to a second position, the spotting member spaced apart from the substrate in the first position and the spotting member engaging the substrate in the second position for delivering liquid, the spotting member advancing from the first position to the second position at predetermined, variable velocity, the spotting member velocity reduced when the spotting member approaches the second position from the first position; and

permitting the spotting member to engage the substrate for a pre-determined period of time to allow the liquid to form a spot on the substrate suitable for microarray operation.

55. The method of claim 54, wherein the spot is about 200 micrometers or less.

56. The method of claim 54, further comprising forming a plurality of spots having a diameter of about 200 micrometers or less wherein the distances between spots are 400 micrometers or less.

57. The method of claim 56, capable of forming more than 9200 spots per square centimeter.

58. The method of claim 54, wherein the liquid delivered onto the solid substrate comprises DNA.

59. A method of drawing liquid from a well into a spotting member for a microarray operation, comprising:

advancing the spotting member from a first position to a second position, the spotting member spaced apart from the well in the first position and the spotting member proximate to the bottom of the well for drawing liquid in the second position, the spotting member advancing from the first position to the second position at predetermined, variable velocity, the spotting member velocity reduced when the spotting member approaches the second position from the first position; and

permitting the spotting member to remain proximate to the bottom of the well for a predetermined period of time to draw the liquid into the spotting member.

60. A method of removing liquid from a plurality of microarray spotting members, comprising:

creating turbulence in air flowing from the inlet to the outlet of an assembly in the space between a spotting member and an aperture for removing liquid from the first open end portions of the spotting members wherein turbulence is created in air by applying a source of vacuum to the spotting members of the assembly to draw air around the spotting members to flow from the inlet to the outlet;

aligning the spotting members proximate to the apertures with each spotting member body extending generally axially away from the corresponding aperture; and

repeatedly reciprocating the microarray spotting members generally axially toward and away from the apertures and limiting axially inward travel to provide clearance with the aperture in the limiting position to create turbulence in air flowing from the inlet to the outlet in the space between the spotting member and the aperture for removing liquid from the first open end portions of the spotting members.

61. A microarrayer substrate with a surface comprising 3000 or more groups of DNA molecules attached to the surface in discrete known regions, the 3000 or more groups of DNA molecules occupying a total area of less than 1 cm² on the substrate.