Methods for assembling protein microarrays

• US 20060003381A1
• Filed: 05/03/2002
• Published: 01/05/2006
• Est. Priority Date: 05/03/2001
• Status: Abandoned Application

• Current Assignee: High Throughput Genomics, Inc.
• Original Assignee: High Throughput Genomics, Inc.
• Inventors: Gilmore, James, Daniel, Steven, Hogan, Mike, Tam, Sunny, Wiese, Rick
• Application Number:
  US10/476,739
• Publication Number:
  US 20060003381A1
• Time in Patent Office: Days
• US Class Current: 435/7.100
• 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 2219/00369 in multiple or parallel arrangements
• CPC Class Codes: B01J 2219/00373 Hollow needles
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00574 radioactive
• 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 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00628 Ionic
• CPC Class Codes: B01J 2219/00639 the compounds being trapped in or bound to a porous medium
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00691 : using robots
• CPC Class Codes: B01J 2219/00704 : integrated with the reactor apparatus
• CPC Class Codes: B01J 2219/00707 : separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 33/54353 : with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: G01N 33/545 : Synthetic resin

Abstract

The invention provides methods for assembling protein arrays. In one aspect, the methods comprise use of charged or polar array surfaces in the construction of the array. The methods also comprise use of viscous solutions for the deposition of the polypeptides on the array surface in the construction of the array.

Claims

1. A method for assembling protein arrays comprising the following steps:

(a) providing an array comprising a surface having a net positive or a net negative charge;

(b) providing a solution comprising a polypeptide having a net positive (cationic) charge density or a net positive charge polarity or a net negative (anionic) charge density or a net negative charge polarity at an amino terminal end or a carboxy terminal end; and

(c) adding the solution to the array under conditions allowing the positive or negative end of the polypeptide to align with the negative or positive charge of the array surface.

2. The method of claim 1, wherein the array surface comprises a net negative (anionic) charge density or a net negative charge polarity and the polypeptide comprises the net positive (cationic) charge density or the net positive charge polarity.

3. The method of claim 2, wherein hydroxyl groups on the array surface provide the net negative (anionic) charge density or the net negative charge polarity.

4. The method of claim 2, wherein sulfhydryl groups on the array surface provide the net negative (anionic) charge density or the net negative charge polarity.

5. The method of claim 1, wherein the array surface comprises a net positive (cationic) charge density or a net positive charge polarity and the polypeptide comprises a negative (anionic) charge density or a net negative charge polarity.

6. The method of claim 5, wherein the array surface comprises a net positive (cationic) charge density or a net positive charge polarity due to a plurality of charged amino groups on the array surface.

7. A method for assembling protein arrays comprising the following steps:

(a) providing an array;

(b) providing a solution comprising a polypeptide, wherein the solution comprises a viscosity sufficient to produce a surface tension such that the polypeptide-containing solution does not spread over an array surface area larger than about 200 nm in diameter; and

(c) adding the solution to the array.

9. The method of claim 7 or claim 8, wherein the solution comprises an organic polymer.

10. The method of claim 7 or claim 8, wherein the solution comprises glycerol.

11. The method of claim 7 or claim 8, wherein the solution comprises polyethylene glycol.

12. The method of claim 7 or claim 8, wherein the solution comprises sodium azide or sodium iodide.

13. The method of claim 12, wherein the sodium azide concentration is between about 0.2% and about 0.5%.

8. A method for assembling protein arrays comprising the following steps:

(a) providing an array;

(b) providing a solution comprising a polypeptide, wherein the solution comprises a viscosity of between about 1 mN*s/m² to about 30 mN*s/m²; and

(c) adding the solution to the array.

14. A method for assembling polypeptide arrays comprising the following steps:

(a) providing a substrate having a surface with a first net charge;

(b) providing a solution, wherein the solution includes a polypeptide having a net charge density or a net charge polarity for at least one of an amino terminal end or a carboxy terminal end; and

,

(c) contacting the solution to the substrate.

15. The method of claim 14, wherein the first net charge comprises a negative (anionic) charge density or a negative charge polarity, and the net charge density of the polypeptide comprises a positive (cationic) charge density or the net charge polarity of the polypeptide comprises a positive charge polarity.

16. The method of claim 15, wherein at least one of hydroxyl groups or sulfhydryl groups on the substrate surface provide the first net charge with a negative (anionic) charge density or a negative charge polarity.

17. The method of claim 14, wherein the first net charge comprises a positive (cationic) charge density or a positive charge polarity, and the net charge density of the polypeptide comprises a negative (anionic) charge density or the net charge polarity of the polypeptide comprises a net negative charge polarity.

18. The method of claim 17, wherein amino groups on the substrate surface provide the first net charge with a positive (cationic) charge density or a positive charge polarity.

19. A method for assembling protein arrays comprising the following steps:

(a) providing a substrate;

(b) providing a solution comprising a polypeptide, wherein the solution has a viscosity sufficient to produce a surface tension such that the polypeptide-containing solution does not spread over a surface area larger than about 200 nm in diameter; and

(c) adding the solution to the substrate.

20. The method of claim 19, wherein the solution comprises an organic polymer.

21. The method of claim 19, wherein the solution comprises glycerol.

22. The method of claim 19, wherein the solution comprises polyethylene glycol.

23. The method of claim 19, wherein the solution comprises sodium azide or sodium iodide.

24. The method of claim 23, wherein the sodium azide concentration is between about 0.2% and about 0.5%.

25. A method for assembling protein arrays comprising the following steps:

(a) providing a substrate;

(b) providing a solution, wherein the solution includes a peptide and a viscosity of between about 1 mN*s/m² to about 30 mN*s/m²; and

(c) contacting the solution to the substrate.

26. The method of claim 25 wherein the solution comprises an organic polymer.

27. The method of claim 25, wherein the solution comprises glycerol.

28. The method of claim 25, wherein the solution comprises polyethylene glycol.

29. The method of claim 25, wherein the solution comprises sodium azide or sodium iodide.

30. The method of claim 29, wherein the sodium azide concentration is between about 0.2% and about 0.5%.

31. A method for assembling protein arrays comprising the following steps:

(a) providing a substrate having a surface with a net positive charge;

(b) providing a solution, wherein the solution includes a polypeptide having a net negative charge density or a net negative charge polarity for at least one of an amino terminal end or a carboxy terminal end; and

,

(c) contacting the solution to the array.

32. The method of claim 31, wherein the solution comprises a viscosity sufficient to produce a surface tension such that the polypeptide-containing solution does not spread over an array surface area larger than about 200 nm in diameter.

33. The method of claim 31, wherein the solution comprises a viscosity of between about 1 mN*s/m² to about 30 mN*s/m².

34. The method of claim 31, wherein amino groups on the substrate surface produce the net positive charge by way of a net positive charge density or a net positive charge polarity.

35. A method for assembling protein arrays comprising the following steps:

(a) providing a substrate having a surface with a net negative charge;

(b) providing a solution, wherein the solution includes a polypeptide having a net positive (cationic) charge density or a net positive charge polarity for at least one of an amino terminal end or a carboxy terminal end; and

,

(c) contacting the solution to the substrate.

36. The method of claim 35, wherein at least one of hydroxyl groups or sulfhydryl groups on the substrate surface produce the net negative charge by way of a net negative charge density or a net negative charge polarity.

37. The method of claim 36, wherein the solution comprises an organic polymer.

38. The method of claim 36, wherein the solution comprises glycerol.

39. The method of claim 36, wherein the solution comprises polyethylene glycol.

40. The method of claim 36, wherein the solution comprises sodium azide or sodium iodide.

41. The method of claim 40, wherein the sodium azide concentration is between about 0.2% and about 0.5%.

42. A method of claim 35, wherein the solution comprises a viscosity of between about 1 mN*s/m² to about 30 mN*s/m².

43. The method of claim 42, wherein the solution comprises an organic polymer.

44. The method of claim 42, wherein the solution comprises glycerol.

45. The method of claim 42, wherein the solution comprises polyethylene glycol.

46. The method of claim 42, wherein the solution comprises sodium azide or sodium iodide.

47. The method of claim 46, wherein the sodium azide concentration is between about 0.2% and about 0.5%.

48. The method of claim 35, wherein amino groups on the substrate surface provide a net positive charge density or a net positive charge polarity.

49. A method of making a polypeptide array on a substrate having a surface with a net charge, the method comprising contacting the surface with a liquid comprising a polypeptide selected or modified to have an opposite net charge at an end thereof.

50. A method of making an oriented polypeptide array, the method comprising

(a) selecting or modifying a plurality of polypeptides to have a net charge at an end thereof;

(b) selecting or modifying a substrate to have an opposite net charge on a surface thereof, and

(c) separately contacting aqueous liquids comprising one or more of the polypeptides with discrete regions of the surface.

51. A method of making an array comprising a substrate having a surface with a plurality of different polypeptides immobilized at discrete regions thereof, the method comprising contacting each region of the surface with a separate aqueous liquid comprising one of the polypeptides, wherein each polypeptide has an end having a net charge opposite the net charge of the surface.

52. A method for assembling polypeptide arrays, the method comprising:

(a) providing an array substrate having a surface with a net positive charge or a net negative charge;

(b) providing a solution comprising a polypeptide wherein at least one of an amino or carboxy terminal end of the polypeptide has one of i) a net positive (cationic) charge density, ii) a net positive charge polarity, iii) a net negative (anionic) charge density, or iv) a net negative charge polarity; and

(c) contacting the solution and the substrate under conditions allowing the end of the polypeptide to align with the charge of the surface.