Methods and compounds for making arrays

• US 20090270278A1
• Filed: 10/30/2008
• Published: 10/29/2009
• Est. Priority Date: 11/06/2007
• Status: Abandoned Application

• Current Assignee: Ambergen Inc.
• Original Assignee: Ambergen Inc.
• Inventors: Rothschild, Kenneth J., Lim, Mark J.
• Application Number:
  US12/290,429
• Publication Number:
  US 20090270278A1
• Time in Patent Office: Days
• US Class Current: 506/27
• 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 2219/00454 by chemical cleavage from the solid support
• 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 2219/00527 Sheets
• 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 2219/00648 by the use of solid beads
• 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 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/0074 Biological products
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support

Abstract

Arrays and methods of making an array are described. A plurality of beads, each bead comprising a group of compounds, each compound of said group attached to a bead through a photocleavable linker are brought in proximity (or contact) with another surface, and exposed to electromagnetic radiation. Illuminating the beads with radiation causes at least a portion of the compounds to be photocleaved from the beads and transferred to the surface to form a plurality of transferred groups of compounds on said surface, at least a portion of which is positioned in different locations on said surface.

Claims

1. A method of making an array, comprising:

a) providing i) a plurality of beads, each bead comprising a group of compounds, each compound of said group attached to a bead through a photocleavable linker;

ii) a source of electromagnetic radiation; and

iii) a surface;

b) bringing said plurality of beads into contact with said surface; and

c) illuminating said beads with radiation from said radiation source under conditions such that at least a portion of said compounds is photocleaved from said beads and transferred to said surface to form a plurality of transferred groups of compounds on said surface, at least a portion of said plurality of transferred groups positioned in different locations on said surface.

2. The method of claim 1, wherein each compound in any one group of compounds of step a) is identical.

3. The method of claim 1, wherein each transferred group of step c) has fewer compounds than any one group of compounds of step a).

4. The method of claim 1, wherein at least a portion of said plurality of transferred groups are positioned at different predetermined locations on said surface.

5. The method of claim 1, wherein step b) comprises depositing single beads at different locations on said surface.

6. The method of claim 1, wherein step b) comprises depositing more than one bead at each location on said surface.

7. The method of claim 1, further comprising, after step c), the step d) removing at least a portion of said beads from said surface.

8. The method of claim 1, wherein said bead is selected from agarose beads, streptavidin-coated beads, NeutrAvidin-coated beads, antibody-coated beads, paramagnetic beads, magnetic beads, electrostatic beads, electrically conducting beads, fluorescently labeled beads, colloidal beads, glass beads, semiconductor beads, nanocrystalline beads and polymeric beads.

9. The method of claim 1, wherein said surface is selected from charged surfaces, hydrophobic surfaces, and hydrophilic surfaces.

10. The method of claim 1, wherein said surface is a chemically treated surface.

11. The method of claim 1, wherein said surface is an epoxy-activated surface.

12. The method of claim 1, wherein said surface is selected from surfaces coated with antibodies, surfaces coated with streptavidin, surfaces coated with cells, surfaces coated with nucleic acid, and surfaces coated with protein.

13. The method of claim 1, wherein said surface is selected from glass surfaces, hydrogel surfaces, nitrocellulose surfaces, polymeric surfaces, gold coated surfaces, surfaces suitable for surface plasmon resonance, and surfaces suitable for MALDI.

14. The method of claim 1, wherein said surface is an untreated surface.

15. The method of claim 14, wherein said untreated surface is a polymer.

16. The method of claim 15, wherein said polymer is selected from the group consisting of polystyrene and polyvinylidene fluoride.

17. The method of claim 1, wherein each compound of every transferred group is a peptide of between 6 and 50 amino acids in length.

18. The method of claim 1, wherein each compound of every transferred group is an oligonucleotide of between 18 and 150 nucleotides in length.

19. The method of claim 1, wherein said photocleavable linker comprises a 2-nitrobenzyl moiety.

20. The method of claim 1, wherein each compound of every transferred group comprises nucleic acid derived from a single nucleic acid template.

21. The method of claim 1, wherein each group consists of the amplified product from a single nucleic acid template.

22. A method of making an array, comprising:

a) providing i) a plurality of beads, each bead comprising a group of compounds and at least one coding agent, each compound of said group attached to a bead through a photocleavable linker, said coding agent attached to said bead through a photocleavable linker;

ii) a source of electromagnetic radiation; and

iii) a surface;

b) bringing said plurality of beads into contact with said surface; and

c) illuminating said beads with radiation from said radiation source under conditions such that at least a portion of said compounds is photocleaved from said beads and transferred to said surface to form a plurality of transferred groups of compounds on said surface, at least a portion of said plurality of transferred groups positioned in different locations on said surface and associated with a transferred coding agent.

23. The method of claim 22, wherein each compound in any one group of compounds of step a) is identical.

24. The method of claim 22, wherein each transferred group of step c) has fewer compounds than any one group of compounds of step a).

25. The method of claim 22, wherein at least a portion of said plurality of transferred groups are positioned at different predetermined locations on said surface.

26. The method of claim 22, wherein step b) comprises depositing single beads at different locations on said surface.

27. The method of claim 22, wherein step b) comprises depositing more than one bead at each location on said surface.

28. The method of claim 22, further comprising, after step c), the step d) removing at least a portion of said beads from said surface.

29. The method of claim 22, wherein said bead is selected from agarose beads, streptavidin-coated beads, NeutrAvidin-coated beads, antibody-coated beads, paramagnetic beads, magnetic beads, electrostatic beads, electrically conducting beads, fluorescently labeled beads, colloidal beads, glass beads, semiconductor beads, nanocrystalline beads, and polymeric beads.

30. The method of claim 22, wherein said surface is selected from charged surfaces, hydrophobic surfaces, and hydrophilic surfaces.

31. The method of claim 22, wherein said surface is a chemically treated surface.

32. The method of claim 22, wherein said surface is an epoxy-activated surface.

33. The method of claim 22, wherein said surface is selected from surfaces coated with antibodies, surfaces coated with streptavidin, surfaces coated with cells, surfaces coated with nucleic acid, and surfaces coated with protein.

34. The method of claim 22, wherein said surface is selected from glass surfaces, hydrogel surfaces, nitrocellulose surfaces, polymeric surfaces, gold coated surfaces, surfaces suitable for surface plasmon resonance, and surfaces suitable for MALDI.

35. The method of claim 22, wherein said surface is an untreated surface.

36. The method of claim 35, wherein said untreated surface is a polymer.

37. The method of claim 36, wherein said polymer is selected from the group consisting of polystyrene and polyvinylidene fluoride.

38. The method of claim 22, wherein each compound of every transferred group is a peptide of between 6 and 50 amino acids in length.

39. The method of claim 22, wherein each compound of every transferred group is an oligonucleotide of between 18 and 150 nucleotides in length.

40. The method of claim 22, wherein said photocleavable linker comprises a 2-nitrobenzyl moiety.

41. The method of claim 22, wherein each compound of every transferred group comprises nucleic acid derived from a single nucleic acid template.

42. The method of claim 22, wherein each group consists of the amplified product from a single nucleic acid template.

43. The method of claim 22, further comprising, after step d), the step e) using said coding agent to determine the identity of said compounds in said portion of said transferred groups.

44. The method of claim 22, wherein said coding agent is selected from the group consisting of nanoparticles, quantum dots, and fluorescent molecules.

45. The method of claim 22, wherein the coding agent has identifiable spectral properties.

46. The method of claim 45, wherein the identifiable spectral property is detecting using a method selected from fluorescence spectroscopy, absorption spectroscopy, infrared spectroscopy, Raman spectroscopy, nuclear magnetic resonance, mass spectrometry.

47. A method of making an array, comprising:

a) providing i) a plurality of avidin-coated beads, each bead comprising a group of photocleavable biotin-labeled compounds attached to said bead through a biotin-avidin attachment;

ii) a source of electromagnetic radiation; and

iii) a surface;

b) bringing said plurality of beads into contact with said surface; and

c) illuminating said beads with radiation from said radiation source under conditions such that at least a portion of said compounds is photocleaved from said beads and transferred to said surface to form a plurality of transferred groups of compounds on said surface, at least a portion of said plurality of transferred groups positioned in different locations on said surface.

48. The method of claim 47, wherein each compound in any one group of compounds of step a) is identical.

49. The method of claim 47, wherein each transferred group of step c) has fewer compounds than any one group of compounds of step a).

50. The method of claim 47, wherein at least a portion of said plurality of transferred groups are positioned at different predetermined locations on said surface.

51. The method of claim 47, wherein step b) comprises depositing single beads at different locations on said surface.

52. The method of claim 47, wherein step b) comprises depositing more than one bead at each location on said surface.

53. The method of claim 47, further comprising, after step c), the step d) removing at least a portion of said beads from said surface.

54. The method of claim 47, wherein said avidin-coated bead is selected from agarose beads, paramagnetic beads, magnetic beads, electrostatic beads, electrically conducting beads, fluorescently labeled beads, colloidal beads, glass beads, semiconductor beads, nanocrystalline beads and polymeric beads.

55. The method of claim 47, wherein each compound of every transferred group is a peptide of between 6 and 50 amino acids in length.

56. The method of claim 47, wherein each compound of every transferred group is a oligonucleotide of between 18 and 150 nucleotides in length.

57. The method of claim 47, wherein said photocleavable biotin comprises a 2-nitrobenzyl moiety.

58. The method of claim 47, wherein each compound of every transferred group is a nascent protein labeled with photocleavable biotin during translation.