Method of making and decoding of array sensors with microspheres

• US 7,060,431 B2
• Filed: 06/24/1999
• Issued: 06/13/2006
• Est. Priority Date: 06/24/1998
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Czarnik, Anthony W., Chee, Mark S., Stuelpnagel, John R.
• Primary Examiner(s): Marschel, Ardin H.
• Assistant Examiner(s): Skibinsky, Anna
• Application Number:
  US09/344,526
• Publication Number:
  US 20020132221A1
• Time in Patent Office: 2,546 Days
• Field of Search: 435/6, 435/4, 435/7.1, 435/7.5, 435/7.7, 435/7.42, 435/7.74, 536/24.3, 536/23.1, 422/50, 422/52, 702/19
• US Class Current: 435/6.1
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00576 fluorophore
• 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 2219/00619 using hydrophilic or hydrophobic regions
• 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 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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 2219/00677 : Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00702 : Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6825 : Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2521/313 : Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2527/137 : Concentration of a component of medium
• CPC Class Codes: C12Q 2537/143 : Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/107 : fluorescence
• CPC Class Codes: C12Q 2563/155 : Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2563/179 : the label being a nucleic acid
• 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: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 33/54313 : the carrier being characterised by its particulate form
• CPC Class Codes: Y10S 977/924 : using nanostructure as support of dna analysis

Abstract

The invention relates to compositions and methods for decoding microsphere array sensors.

Claims

1. A method of making a bead array comprising:

a) contacting a substrate with a surface comprising discrete sites at a density of at least 100 sites per 1 mm², with a solution comprising a population of different beads, wherein said beads do not comprise an optical signature; and

b) applying energy to said substrate or said solution, or both, such that at least a subpopulation of said different beads randomly associate onto sites.

2. A method according to claim 1 wherein said discrete sites comprise wells.

3. A method according to claim 1 wherein said energy is in the form of agitation.

4. A method according to claim 1, wherein said energy is dipping said substrate into said beads.

5. A method according to claim 4, wherein said substrate is a fiber optic bundle.

13. The method according to claim 1, wherein said population of different beads comprises at least a first and second subpopulation.

14. The method according to claim 13, wherein said first and second subpopulations each comprise a different bioactive agent.

15. The method according to claim 14, wherein said bioactive agent comprises a protein.

16. The method according to claim 14, wherein said bioactive agent comprises a nucleic acid.

17. The method according to claim 16, wherein said nucleic acid comprises DNA.

18. The method according to claim 14, wherein said first and second subpopulations of beads each comprise a different identifier binding ligand.

19. The method according to claim 18, wherein said identifier binding ligand comprises a protein.

20. The method according to claim 18, wherein said identifier binding ligand comprises a nucleic acid.

21. The method according to claim 20, wherein said bioactive agent and said identifier binding ligand within the same subpopulation each comprise an identical nucleic acid sequence for binding a decoder binding ligand.

22. The method according to claim 18 further comprising decoding a location of said bioactive agent on said array by correlating said bioactive agent with said location, whereby said decoding comprises contacting said array with at least first and second different decoder binding ligands, whereby said first and second decoder binding ligands bind to first and second identifier binding ligands, whereby said first and second identifier binding ligands identify said first and second bioactive agents, respectively, to thereby identify a location of said first and second bioactive agents to thereby decode said array.

23. The method according to claim 22, wherein said decoder binding ligands comprise proteins.

24. The method according to claim 22, wherein said decoder binding ligands comprise nucleic acids.

25. The method according to claim 1, wherein said substrate comprises a flat planar substrate.

6. A method of determining the presence of a target analyte in a sample comprising:

a) contacting said sample with an array comprising;

i) substrate with a surface comprising discrete sites at a density of at least 100 sites per 1 mm², wherein said sites are wells; and

ii) a population of microspheres randomly distributed on said sites, wherein said population comprises at least a first and a second subpopulation each comprising;

(a) a different bioactive agent; and

(b) a different identifier binding ligand;

b) determining the presence or absence of said target analyte; and

c) decoding a location of said bioactive agent by correlating said bioactive agent with said location, whereby said decoding comprises contacting said array with at least first and second different decoder binding ligands, whereby said first and second decoder binding ligands bind to a first and second identifier binding ligands, whereby said first and second identifier binding ligands identify said first and second bioactive agents, respectively, to thereby identify a location of said first and second bioactive agents to thereby decode said array.

7. The method according to claim 6, wherein said first and second bioactive agents comprise nucleic acids.

8. The method according to claim 7, wherein said nucleic acids comprise DNA.

9. The method according to claim 7, wherein said nucleic acids comprise single stranded nucleic acids.

10. The method according to claim 7, wherein said nucleic acids comprise double stranded nucleic acids.

11. The method according to claim 6, wherein said first and second bioactive agents comprise proteins.

12. The method according to claim 6, wherein said substrate comprises a fiber optic bundle.

26. The method according to claim 6, wherein said identifier binding ligands comprise proteins.

27. The method according to claim 6, wherein said identifier binding ligands comprise nucleic acids.

28. The method according to claim 6, wherein comprise decoder binding ligands are proteins.

29. The method according to claim 6, wherein comprise decoder binding ligands are nucleic acids.

30. The method according to claim 6, wherein said substrate comprises a flat planar substrate.

31. A method of determining the presence of a target analyte in a sample comprising:

a) contacting said sample with an array comprising;

i) a substrate with a surface comprising sites at a density of at least 100 sites per 1 mm², wherein said sites are present in a depression; and

ii) a population of particles randomly distributed on said sites, wherein said population comprises at least a first and a second subpopulation each comprising;

(a) a different bioactive agent; and

(b) a different identifier binding ligand;

b) decoding a location of said bioactive agent by correlating said bioactive agent with said location, whereby said decoding comprises contacting said array with at least first and second different decoder binding ligands, whereby said first and second decoder binding ligands bind to a first and second identifier binding ligands, whereby said first and second identifier binding ligands identify said first and second bioactive agents, respectively, to thereby identify a location of said first and second bioactive agents to thereby decode said array; and

c) determining the presence or absence of said target analyte.

32. The method according to claim 31, wherein said bioactive agents comprise nucleic acids.

33. The method according to claim 32, wherein said nucleic acids comprise DNA.

34. The method according to claim 32, wherein said nucleic acids comprise single stranded nucleic acids.

35. The method according to claim 32, wherein said nucleic acids comprise double stranded nucleic acids.

36. The method according to claim 31, wherein said bioactive agents comprise proteins.

37. The method according to claim 31, wherein said identifier binding ligands comprise proteins.

38. The method according to claim 31, wherein said identifier binding ligands comprise nucleic acids.

39. The method according to claim 31, wherein said decoder binding ligands comprise proteins.

40. The method according to claim 31, wherein said decoder binding ligands comprise nucleic acids.

41. The method according to claim 31, wherein said substrate comprises a fiber optic bundle.

42. The method according to claim 31, wherein said substrate comprises a flat planar substrate.

43. The method according to claim 31, wherein said particles are beads.

44. The method according to claim 31, wherein said sites are contiguous.

45. A method of determining the presence of a target analyte in a sample comprising:

a) contacting said sample with an array comprising;

i) a substrate with a surface comprising sites at a density of at least 100 sites per 1 mm², wherein said sites comprise wells; and

ii) a population of particles randomly distributed on said sites, wherein said population comprises at least a first and a second subpopulation each comprising;

(a) a different bioactive agent; and

(b) a different identifier binding ligand;

b) decoding a location of said bioactive agent by correlating said bioactive agent with said location, whereby said decoding comprises contacting said array with at least first and second different decoder binding ligands, whereby said first and second decoder binding ligands bind to a first and second identifier binding ligands, whereby said first and second identifier binding ligands identify said first and second bioactive agents, respectively, to thereby identify a location of said first and second bioactive agents to thereby decode said array; and

c) determining the presence or absence of said target analyte.

46. The method according to claim 45, wherein said sites are discrete sites.

47. The method according to claim 45, wherein said bioactive agents comprise nucleic acids.

48. The method according to claim 47, wherein said nucleic acids comprise DNA.

49. The method according to claim 47, wherein said nucleic acids comprise single stranded nucleic acids.

50. The method according to claim 47, wherein said nucleic acids comprise double stranded nucleic acids.

51. The method according to claim 45, wherein said bioactive agents comprise proteins.

52. The method according to claim 45, wherein said identifier binding ligands comprise proteins.

53. The method according to claim 45, wherein said identifier binding ligands comprise nucleic acids.

54. The method according to claim 45, wherein said decoder binding ligands comprise proteins.

55. The method according to claim 45, wherein said decoder binding ligands comprise nucleic acids.

56. The method according to claim 45, wherein said substrate comprises a fiber optic bundle.

57. The method according to claim 45, wherein said substrate comprises a flat planar substrate.

58. The method according to claim 45, wherein said particles are beads.

59. A method of making a particle array comprising:

a) contacting a substrate with a surface comprising sites at a density of at least 100 sites per 1 mm², with a solution comprising a population of different particles, wherein said particles do not comprise an optical signature, and wherein said sites comprise wells; and

b) applying energy to said substrate or said solution, or both, such that at least a subpopulation of said different particles randomly associate onto sites.

60. The method according to claim 59, wherein said sites are discrete sites.

61. The method according to claim 59, wherein said energy is in the form of agitation.

62. The method according to claim 59, wherein said energy is dipping said substrate into said particles.

63. The method according to claim 59, wherein said substrate is a fiber optic bundle.

64. The method according to claim 59, wherein said population of different particles comprises at least a first and second subpopulation.

65. The method according to claim 64, wherein said first and second subpopulations each comprise a different bioactive agent.

66. The method according to claim 65, wherein said bioactive agent comprises a protein.

67. The method according to claim 65, wherein said bioactive agent comprises a nucleic acid.

68. The method according to claim 67, wherein said nucleic acid comprises DNA.

69. The method according to claim 65, wherein said first and second subpopulations of particles each comprise a different identifier binding ligand.

70. The method according to claim 69, wherein said identifier binding ligand comprises a protein.

71. The method according to claim 69, wherein said identifier binding ligand comprises a nucleic acid.

72. The method according to claim 71, wherein said bioactive agent and said identifier binding ligand within the same subpopulation each comprise an identical nucleic acid sequence for binding a decoder binding ligand.

73. The method according to claim 69 further comprising decoding a location of said bioactive agent on said array by correlating said bioactive agent with said location, whereby said decoding comprises contacting said array with at least first and second different decoder binding ligands, whereby said first and second decoder binding ligands bind to first and second identifier binding ligands, whereby said first and second identifier binding ligands identify said first and second bioactive agents, respectively, to thereby identify a location of said first and second bioactive agents to thereby decode said array.

74. The method according to claim 73, wherein said decoder binding ligands comprise proteins.

75. The method according to claim 73, wherein said decoder binding ligands comprise nucleic acids.

76. The method according to claim 59, wherein said substrate comprises a flat planar substrate.