Methods of making arrays

• US 7,901,897 B2
• Filed: 03/16/2009
• Issued: 03/08/2011
• Est. Priority Date: 12/28/1998
• Status: Expired due to Fees

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Casas, Laura S, Auger, Steven R, Stuelpnagel, John R, Baker, Shawn Christopher, Chee, Mark S, Kain, Robert C, Wang, Gan G
• Primary Examiner(s): Calamita; Heather
• Application Number:
  US12/405,163
• Publication Number:
  US 20090221450A1
• Time in Patent Office: 722 Days
• Field of Search: None
• US Class Current: 435/7.1
• 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 2219/00315 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 method of detecting one or more target DNA molecules, comprising:

(a) providing a tray having multiple wells, each of the wells containing a solution of different DNA molecules;

(b) providing multiple projections extending from a substrate, wherein each projection has a surface that is furthest from the substrate, and wherein an array of DNA probes is arranged on the surface such that the surface comprises a plurality of individual positions on each projection;

(c) simultaneously placing the projections that extend from the substrate into the wells of the tray, wherein the arrays of DNA probes on the surfaces of the projections contact the solution in the wells of the tray, and wherein the arrays of DNA probes bind to one or more target DNA molecules in the solution if the one or more target DNA molecules are present in the wells; and

(d) removing from the wells of the tray the projections that extend from the substrate and then detecting the arrays, thereby detecting one or more target DNA molecules that bound to the arrays prior to removing the projections.

2. The method of claim 1, wherein the projections and the substrate form a molded unit.

3. The method of claim 1, wherein the substrate comprises a block and the projections comprise fiber optic bundles.

4. The method of claim 1, wherein different positions in the array of DNA probes comprise different DNA sequences.

5. The method of claim 4, wherein the different positions are contiguous with each other.

6. The method of claim 4, wherein the different positions are non-contiguous with each other.

7. The method of claim 1, wherein the array of DNA probes comprises from 10,000,000 to 2,000,000,000 individual positions per square centimeter.

8. The method of claim 1, wherein the array of DNA probes comprises from 100,000 to about 10,000,000 individual positions per square centimeter.

9. The method of claim 1, wherein the array of DNA probes comprises from 10,000 to about 100,000 individual positions per square centimeter.

10. The method of claim 1, wherein the projections provide 96 arrays of DNA probes.

11. The method of claim 1, wherein the tray comprises 96 wells.

12. The method of claim 1, wherein surfaces of the projections are flat and perpendicular to the direction in which the projections extend.

13. The method of claim 1, wherein the DNA probes are coupled to the positions by a photolithographic technique.

14. The method of claim 1, further comprising labeling DNA probes in the arrays of DNA probes that bind to one or more target DNA molecules in the solution.

15. The method of claim 14, wherein the labeling uses an enzyme.

16. The method of claim 14, wherein the labeling uses a fluorochrome.

17. The method of claim 14, wherein detecting the one or more target DNA molecules that bound to the arrays prior to removing the projections comprises detecting the labeled DNA probes.

18. The method of claim 1, wherein the one or more target DNA molecules comprises labels.

19. The method of claim 18, wherein the labels are fluorochromes.

20. The method of claim 1, wherein the detecting the one or more target DNA molecules further comprises identifying a single nucleotide polymorphism.

21. The method of claim 1, wherein the detecting the one or more target DNA molecules further comprises detecting one or more cDNA molecules.

22. The method of claim 1, wherein the arrays of DNA probes on the surfaces of the projections are washed after the removing step and prior to the detecting step.

23. The method of claim 1, wherein the projections are aligned in rows and columns.

24. The method of claim 1, wherein all of the DNA probes on an array are detected.

25. A method of detecting one or more target DNA molecules, comprising:

(a) providing a tray having multiple wells, each of the wells containing a solution of different DNA molecules;

(b) providing multiple projections extending from a substrate, wherein each projection has a surface that is furthest from the substrate, the surface being flat and perpendicular to the direction in which the projections extend, and wherein an array of DNA probes is arranged on the surface such that the surface comprises a plurality of individual positions on each projection, the array of DNA probes comprising from 100,000 to about 10,000,000 individual positions per square centimeter;

(c) simultaneously placing the projections that extend from the substrate into the wells of the tray, wherein the arrays of DNA probes on the surfaces of the projections contact the solution in the wells of the tray, and wherein the arrays of DNA probes bind to one or more target DNA molecules in the solution if the one or more target DNA molecules are present in the wells; and

(d) removing from the wells of the tray the projections that extend from the substrate and then detecting the arrays, thereby detecting one or more target DNA molecules that bound to the arrays prior to removing the projections.

26. The method of claim 25, wherein different positions in the array of DNA probes comprise different DNA sequences.

27. The method of claim 25, wherein the different positions are contiguous with each other.

28. The method of claim 25, wherein the different positions are non-contiguous with each other.

29. The method of claim 25, wherein the tray comprises 96 wells.

30. The method of claim 25, wherein the DNA probes are coupled to the positions by a photolithographic technique.

31. The method of claim 25, further comprising labeling DNA probes in the arrays of DNA probes that bind to one or more target DNA molecules in the solution.

32. The method of claim 25, wherein the one or more target DNA molecules comprises labels.

33. The method of claim 25, wherein the arrays of DNA probes on the surfaces of the projections are washed after the removing step and prior to the detecting step.

34. The method of claim 25, wherein the projections are aligned in rows and columns.