Molecular microarrays and methods for production and use thereof

• US 20040171053A1
• Filed: 03/05/2004
• Published: 09/02/2004
• Est. Priority Date: 11/02/1999
• Status: Abandoned Application

• Current Assignee: Celine Hu
• Original Assignee: Celine Hu
• Inventors: Hu, Celine
• Application Number:
  US10/794,305
• Publication Number:
  US 20040171053A1
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• 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 2219/00617 by chemical means
• 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 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/161 : incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• 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 provides microarrays comprising microparticles with known addresses, wherein the microparticles are coupled to chemical, biological, and/or cellular entities of interest. The invention also provided methods for producing microarrays.

Claims

1. A microarray comprising:

(a) a substrate, wherein the substrate is derivatized with either;

i) a first compound comprising a first functional group, and at least one layer of a cross-linking compound comprising multiple second functional groups, or

ii) a first compound comprising a first functional group, and a polymeric film comprising multiple second functional groups; and

(b) either;

i) a population of at least one entity of interest, wherein the population of at least one entity of interest is associated with a distinct address on the substrate through coupling of the entities and the second functional groups, or

ii) a population of microparticles, wherein the population of microparticles has at least one entity of interest coupled thereto, and wherein the population of microparticles is associated with a distinct address on the substrate through coupling of the second functional groups with the microparticles, such that the at least one entity of interest occupies a distinct address on the substrate.

2. The microarray of claim 1, wherein the microarray comprises more than one population of at least one entity of interest or population of microparticles.

3. The microarray of claim 1, wherein the at least one entity of interest is selected from the group consisting of nucleic acids, polypeptides, carbohydrates, cells, hormones, ligands, amino acids, lipids, fatty acids, small molecules, nucleosides, and nucleotides.

4. The microarray of claim 3, wherein the at least one entity of interest is a nucleic acid.

5. The microarray of claim 3, wherein the at least one entity of interest is a polypeptide.

6. The microarray of claim 3, wherein the at least one entity of interest is a cell.

7. The microarray of claim 1, wherein the at least one entity of interest is the product of a combinatorial chemistry procedure.

8. The microarray of claim 1, wherein more than one type of entity occupies a distinct address on the substrate.

9. The microarray of claim 8, wherein each address comprises at least one polypeptide and at least one nucleic acid.

10. A microarray comprising:

(a) a substrate; and

(b) a population of microparticles, wherein the population of microparticles is associated with a distinct address on the substrate, and wherein the population of microparticles has at least one entity of interest coupled thereto, the at least one entity of interest being selected from the group consisting of polypeptides, carbohydrates, cells, hormones, ligands, amino acids, lipids, fatty acids, and small molecules;

such that the at least one entity of interest occupies a distinct address on the substrate.

11. The microarray of claim 10, wherein the microarray comprises more than one population of microparticle.

12. The microarray of claim 10, wherein the at least one entity of interest is a polypeptide.

13. The microarray of claim 10, wherein the at least one entity of interest is a cell.

14. The microarray of claim 10, wherein the at least one entity of interest is the product of a combinatorial chemistry procedure.

15. A microarray comprising:

(a) a substrate; and

(b) a population of microparticles, wherein each microparticle is less than 1 μ

m in diameter, wherein the population of microparticles is associated with a distinct address on the substrate, and wherein the population of microparticles has at least one entity of interest coupled thereto,

such that the at least one entity of interest occupies a distinct address on the substrate.

16. The microarray of claim 15, wherein the microarray comprises more than one population of microparticles.

17. The microarray of claim 15, wherein the at least one entity of interest is selected from the group consisting of nucleic acids, polypeptides, carbohydrates, cells, hormones, ligands, amino acids, lipids, fatty acids, small molecules, antibiotics, nucleosides, and nucleotides.

18. The microarray of claim 17, wherein the at least one entity of interest is a nucleic acid.

19. The microarray of claim 17, wherein the at least one entity of interest is a polypeptide.

20. The microarray of claim 17, wherein the at least one entity of interest is a cell.

21. A microarray produced by a method comprising:

(a) providing a population of at least one entity of interest, wherein the entities are optionally coupled to microparticles;

(b) providing a substrate, wherein the substrate is derivatized with an activatible compound capable of coupling to the entities of interest or to the optional microparticles;

(c) contacting the population of entities with the substrate; and

(d) activating the activatible compound at the desired location(s) on the substrate,

such that the population of entities is coupled to the substrate in the desired location(s).

22. The microarray of claim 21, comprising more than one population of at least one entity of interest.

23. The microarray of claim 21, wherein the activation compound is activated by electromagnetic radiation.

24. The microarray of claim 21, wherein the desired location(s) are isolated by a mask comprising at least one orifice corresponding to the desired location(s) for the population of entities.

25. The microarray of claim 21, wherein the desired location(s) are isolated by a fiber optic beam.

26. The microarray of claim 21, wherein the desired location(s) are isolated by micromirrors.

27. The microarray of claim 21, wherein the entities are coupled to microparticles, and the substrate is derivatized with an activatible compound capable of coupling to the microparticles.

28. The microarray of claim 21, wherein the activatible compound is a photoreactive compound.

29. The microarray of claim 21, wherein the activatible compound is a heat activatible adhesive.

30. The microarray of claim 21, wherein the at least one entity of interest is selected from the group consisting of nucleic acids, polypeptides, carbohydrates, cells, hormones, ligands, amino acids, lipids, fatty acids, small molecules, nucleosides, and nucleotides.

31. A method for constructing a microarray, wherein the method comprises:

(a) providing a substrate, wherein the substrate is derivatized with either;

i) a first compound comprising a first functional group, and at least one layer of a cross-linking compound comprising multiple second functional groups, or

ii) a first compound comprising a first functional group, and a polymeric film comprising multiple second functional groups;

(b) providing either;

i) a population of at least one entity of interest, or

ii) a population of microparticles, wherein the population of microparticles has at least one entity of interest coupled thereto;

(c) localizing the population of entities or microparticles to a distinct address on a substrate; and

(d) associating the population of localized entities or microparticles to their distinct address on the substrate through coupling of the second functional groups to the entities of interest or to the microparticles.

32. The method of claim 31, wherein the at least one entity of interest is selected from the group consisting of nucleic acids, polypeptides, carbohydrates, cells, hormones, ligands, amino acids, lipids, fatty acids, small molecules, nucleosides, and nucleotides.

33. A method for constructing a microarray, wherein the method comprises:

(a) providing a population of at least one entity of interest, wherein the entities are optionally coupled to microparticles;

(b) providing a substrate, wherein the substrate is derivatized with an activatible compound capable of coupling to the entities of interest or to the optional microparticles;

(c) contacting the population of entities with the substrate; and

(d) activating the activatible compound at the desired location(s) on the substrate,

such that the population of entities is coupled to the substrate in the desired location(s).

34. The method of claim 33, comprising more than one population of at least one entity of interest.

35. The method of claim 33, wherein the activation compound is activated by electromagnetic radiation.

36. The method of claim 33, wherein the desired location(s) are isolated by a mask comprising at least one orifice corresponding to the desired location(s) for the population of entities.

37. The method of claim 33, wherein the desired location(s) are isolated by a fiber optic beam.

38. The method of claim 33, wherein the desired location(s) are isolated by micromirrors.

39. The method of claim 33, wherein the activatible compound is a photoreactive compound.

40. The method of claim 33, wherein the activatible compound is a heat activatible adhesive.

41. The method of claim 33, wherein the at least one entity of interest is selected from the group consisting of nucleic acids, polypeptides, carbohydrates, cells, hormones, ligands, amino acids, lipids, fatty acids, small molecules, nucleosides, and nucleotides.

42. A method of producing microarrays comprising nucleic acid sequences, comprising:

(a) providing a first microarray comprising;

(i) a first substrate;

(ii) a first population of at least one nucleic acid sequence, wherein the at least one nucleic acid sequence comprises a first nucleic acid hybridization sequence at the distal end of the nucleic acid sequence, wherein the first population of nucleic acid sequence(s) is optionally coupled to microparticle(s), and wherein the population of nucleic acid sequence(s) is associated with a distinct address on the first substrate;

(b) providing a second microarray comprising;

(i) a second substrate;

(ii) a population of second hybridization sequence(s), wherein the second hybridization sequence(s) is complementary to the first hybrization sequence(s), wherein the second population of hybridization sequence(s) are optionally coupled to microparticle(s), and wherein the population of hybridization sequence(s) is associated with a distinct address on the second substrate;

(c) contacting the first and second microarrays under hybridizing conditions, such that the first and second hybridization sequences hybridize;

(d) exposing the hybridized first and second microarrays to nucleotide polymerizing conditions, such that said at least one nucleic acid sequence from the first microarray is used as a template for the production of a complementary nucleic acid sequence on the second microarray.

43. The method of claim 42, wherein the first and second hybridization sequences are at least 5 nucleotides in length.

44. The method of claim 42, wherein the at least one nucleic acid sequence is a DNA sequence.

45. The method of claim 42, wherein the at least one nucleic acid sequence is an RNA sequence.

46. A method for producing multiple copies of a microarray on a single substrate, wherein the method comprises:

(a) providing a population of microparticles, wherein the population of microparticles has at least one entity of interest coupled thereto;

(b) providing a substrate for multiple copies of a microarray;

(c) localizing the population of microparticles to the substrate at the desired location(s) for each microarray to be produced on the substrate; and

(d) associating the population of microparticles to the substrate at the desired location(s) for each microarray to be produced on the substrate.

47. The method of claim 46, wherein the microparticles are associated with to the substrate by photoactivation.

48. The method of claim 46, wherein the microparticles are associated with to the substrate by a heat activatible adhesive

49. The method of claim 46, wherein the microparticles are localized to the desired location(s) by robotic dispensing.

50. The method of claim 46, wherein the microparticles are localized to the desired location(s) by microfluidics.

51. The method of claim 46, wherein the microparticles are localized to the desired location(s) with an electrical field.

52. The method of claim 46, wherein the microparticles are localized to the desired location(s) with a magnetic field.

53. The method of claim 46, wherein the at least one entity of interest is selected from the group consisting of nucleic acids, polypeptides, carbohydrates, cells, hormones, ligands, amino acids, lipids, fatty acids, small molecules, nucleosides, and nucleotides.