Array kits and processing systems

• US 8,628,952 B2
• Filed: 03/16/2009
• Issued: 01/14/2014
• Est. Priority Date: 12/28/1998
• Status: Expired due to Fees

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Stuelpnagel, John R., Chee, Mark S., Auger, Steven R., Wang, Gan G., Casas, Laura S., Baker, Shawn Christopher, Kain, Robert C.
• Primary Examiner(s): Bhat, Narayan
• Application Number:
  US12/405,162
• Publication Number:
  US 20090215649A1
• Time in Patent Office: 1,765 Days
• Field of Search: 435/6.1, 435/283.1, 435/287.2, 435/288.3, 435/288.4, 435/288.7, 422/68.1, 422/82.05, 436/518, 536/23.1, 536/24.3
• US Class Current: 435/287.2
• 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 2219/00382 Stamping
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/00524 in the shape of fiber bundles
• 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 2219/00612 the surface being inorganic
• 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 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00704 integrated with the reactor apparatus
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: G01N 33/54393 : Improving reaction conditions or stability, e.g. by coating or irradiation of surface, by reduction of non-specific binding, by promotion of specific binding

Abstract

The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.

Claims

1. A robotic system for manipulating arrays, said system comprising:

a multiwell plate;

a base plate having at least one array component associated therewith, said at least one array component comprising a plurality of projections, each projection having an end comprising a surface, said surface having an array of different nucleic acids distributed thereon, wherein said array of different nucleic acids comprises nucleic acids having different nucleotide sequences, and wherein the projections are configured to be dipped into wells of said multiwell plate; and

a plate handler for dipping the projections of said at least one array component into wells of said multiwell plate.

2. The robotic system of claim 1 further comprising a fluidics system.

3. The robotic system of claim 2, wherein said fluidics system and said plate handler are integrated.

4. The robotic system of claim 2, wherein said fluidics system and said plate handler are separated.

5. The robotic system of claim 2 further comprising a controller for programming processes performed by said plate handler or fluidics system.

6. The robotic system of claim 5, wherein said controller is programmed with a script that instructs said plate handler to dip said projections of said at least one array component into wells of said multiwell plate.

7. The robotic system of claim 1, wherein manipulation of said arrays is partially automated.

8. The robotic system of claim 1, wherein manipulation of said arrays is fully automated.

9. The robotic system of claim 1, wherein said base plate is a holder comprising at least one depression into which said array component is inserted.

10. The robotic system of claim 1, wherein said base plate comprises a plate to which said array component is attached.

11. The robotic system of claim 1, wherein said at least one array component comprises a plurality of array components each comprising a plurality of projections.

12. The robotic system of claim 1, wherein said base plate and said multiwell plate each further comprises one or more alignment moieties.

13. The robotic system of claim 12, wherein said one or more alignment moieties on said multiwell plate are female fittings and said one or more alignment moieties on said base plate are male fittings.

14. The robotic system of claim 13, wherein said one or more male fittings are inserted into said one or more female fittings.

15. The robotic system of claim 14, wherein each array comprises at least 1000 different nucleic acids per square centimeter.

16. The robotic system of claim 15, wherein said surface is a glass surface.

17. The robotic system of claim 15, wherein said surface is planar.

18. The robotic system of claim 17, wherein said nucleic acids are attached to planar surface in an ordered arrangement.

19. The robotic system of claim 18, wherein said arrays are substantially identical to each other.

20. The robotic system of claim 19, wherein said multiwell plate comprises 96 wells.

21. The robotic system of claim 20, wherein said at least one array component comprises 96 projections.

22. The robotic system of claim 20, wherein said at least one array component comprises less than 96 projections.

23. The robotic system of claim 20, wherein said array is made by a spotting, printing or photolithographic technique.

24. The robotic system of claim 20, wherein said projections are made of a material that resists the transmission of light.

25. The robotic system of claim 1, wherein said projections are not fiber optic bundles.

26. The robotic system of claim 25, wherein the configuration orients the surface having the nucleic acids distributed thereon such that said surface faces a bottom of a well in the multiwell plate.

27. The robotic system of claim 26, wherein said nucleic acids are present at sites.

28. The robotic system of claim 27, wherein the sites are contiguous.

29. A robotic system for manipulating arrays, said system comprising:

a multiwell plate;

a base plate having at least one array component associated therewith, said at least one array component comprising a plurality of projections, each projection having an end comprising a surface, said surface having an array of different nucleic acids distributed thereon, wherein said array of different nucleic acids comprises nucleic acids having different nucleotide sequences, and wherein the projections are configured to be dipped into wells of said multiwell plate;

a plate handler for dipping the projections of said at least one array component into wells of said multiwell plate; and

a controller programmed for controlling processes performed by said robotic system, wherein said processes comprise hybridization of the nucleic acids to target nucleic acids, washing the array of different nucleic acids and acquiring an image of the array of different nucleic acids.

30. The robotic system of claim 29, wherein said processes controlled by the controller further comprise signal amplification using an antibody.

31. The robotic system of claim 29 further comprising a fluidics system adapted to provide fluids to wells of said multiwell plate.

32. The robotic system of claim 29, wherein said controller is programmed with a script that instructs said plate handler to dip said projections of said at least one array component into wells of said multiwell plate.

33. The robotic system of claim 29, wherein said base plate is a holder comprising at least one depression into which said array component is inserted.

34. The robotic system of claim 29, wherein each array comprises at least 1000 different nucleic acids per square centimeter.

35. The robotic system of claim 29, wherein said base plate and said multiwell plate each further comprises one or more alignment moieties.

36. The robotic system of claim 29, wherein said multiwell plate comprises 96 wells.

37. The robotic system of claim 36, wherein said at least one array component comprises less than 96 projections.

38. The robotic system of claim 29 further comprising a thermoregulating system.

39. The robotic system of claim 29, wherein the vertical center axis of a projection is aligned with the center axis of a well in the multiwell plate.

40. The robotic system of claim 29 further comprising a CCD camera to acquire said image.

41. The robotic system of claim 29, wherein said plate handler fits said projections within said wells of said multiwell plate.

42. The robotic system of claim 29 further comprising a hybridization chamber that encloses said array of different nucleic acids.

43. The robotic system of claim 42, wherein the hybridization chamber encloses the array of different nucleic acids and the multiwell plate.

44. The robotic system of claim 29, wherein the robotic system is a modular system.

45. The robotic system of claim 29, wherein said projections are not fiber optic bundles.

46. The robotic system of claim 45, wherein the configuration orients the surface having the nucleic acids distributed thereon such that said surface faces a bottom of a well in the multiwell plate.

47. The robotic system of claim 46, wherein said nucleic acids are present at sites.

48. The robotic system of claim 47, wherein the sites are contiguous.

49. A robotic system for manipulating arrays, said system comprising:

a multiwell plate;

a base plate having at least one array component placed thereon, said at least one array component comprising at least one projection, each projection having an end comprising a surface, said surface having an array of different nucleic acids attached thereto, wherein said array of different nucleic acids comprises nucleic acids having different nucleotide sequences, and wherein the at least one projection is configured to be dipped into wells of said multiwell plate; and

a plate handler for dipping the projections of said at least one array component into wells of said multiwell plate.

50. The robotic system of claim 49, wherein the projections are made of a material that resists the transmission of light.

51. The robotic system of claim 49, wherein the vertical center axis of the at least one projection is aligned with the center axis of a well in the multiwell plate.

52. The robotic system of claim 49, wherein said at least one array component comprises a plurality of projections.

53. The robotic system of claim 52 further comprising a CCD camera.

54. The robotic system of claim 53 further comprising a fluidics system.

55. The robotic system of claim 54 further comprising a controller for programming processes performed by said plate handler or fluidics system.

56. The robotic system of claim 55, wherein said controller is programmed with a script that instructs said plate handler to dip said projections of said at least one array component into wells of said multiwell plate.

57. The robotic system of claim 56, wherein said base plate is a holder comprising at least one depression into which said array component is inserted.

58. The robotic system of claim 57 further comprising a thermoregulating system.

59. The robotic system of claim 58, wherein said multiwell plate comprises 96 wells.

60. The robotic system of claim 59, wherein said at least one array component comprises less than 96 projections.

61. The robotic system of claim 59, wherein said at least one array component comprises a plurality of array components each comprising a plurality of projections.

62. The robotic system of claim 59, wherein said base plate and said multiwell plate each further comprises one or more alignment moieties.

63. The robotic system of claim 49, wherein said plate handler fits said projections within said wells of said multiwell plate.

64. The robotic system of claim 49 further comprising a hybridization chamber that encloses said array of different nucleic acids.

65. The robotic system of claim 64, wherein the hybridization chamber encloses the array of different nucleic acids and the multiwell plate.

66. The robotic system of claim 49, wherein the system is a modular system.

67. The robotic system of claim 49, wherein said projections are not fiber optic bundles.

68. The robotic system of claim 67, wherein the configuration orients the surface having the nucleic acids distributed thereon such that said surface faces a bottom of a well in the multiwell plate.

69. The robotic system of claim 68, wherein said nucleic acids are present at sites.

70. The robotic system of claim 69, wherein the sites are contiguous.