Method for in situ, on-chip chemical synthesis

• US 20040175710A1
• Filed: 11/06/2003
• Published: 09/09/2004
• Est. Priority Date: 05/22/2001
• Status: Abandoned Application

• Current Assignee: Parallel Synthesis Technologies, Inc.
• Original Assignee: Parallel Synthesis Technologies, Inc.
• Inventors: Haushalter, Robert C.
• Application Number:
  US10/477,085
• Publication Number:
  US 20040175710A1
• 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 2219/00416 Vacuum
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• 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 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• 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
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

Apparatus and methods for the synthesis of arrays of molecules bound to a substrate, and in particular oligomeric molecules such as DNA oligonucleotides and peptides. The methods of the invention comprise providing a substrate having first and second surfaces and a plurality of isolated porous regions extending through the substrate and communicating with the first and second surfaces, contacting selected ones of the porous regions with a reagent, allowing the reagent to bind to or otherwise interact with the selected porous regions, and withdrawing unreacted first reagent from the substrate through the selected porous regions by introducing a pressure differential across the substrate. The events may be repeated as required to form oligomeric molecules.

Claims

1. A method for the synthesis of an array of molecules, comprising:

(a) providing a substrate having first and second surfaces, and a plurality of isolated porous regions extending through said substrate and communicating with said first and second surfaces;

(b) contacting selected ones of said porous regions with a first reagent;

(c) allowing said first reagent to bind to said selected porous regions; and

(d) withdrawing unreacted said first reagent from said substrate through said selected porous regions by introducing a pressure differential across said substrate.

2. The method of claim 1, further comprising

(a) contacting said selected ones of said porous regions with a wash solution;

and

(b) withdrawing said wash solution through said selected porous regions by introducing a pressure differential across said substrate.

3. The method of claim 1, further comprising:

(a) contacting said selected ones of said porous regions with a second reagent;

(b) allowing said second reagent to bind to first reagent at said selected porous regions; and

(c) withdrawing unreacted said second reagent from said substrate through said selected porous regions by introducing a pressure differential across said substrate;

4. The method of claim 3, further comprising

(a) contacting said selected ones of said porous regions with an nth reagent;

(b) allowing said nth reagent to bind to a previously bound said reagent at said selected porous regions; and

(c) withdrawing unreacted said nth reagent from said substrate through said selected porous regions by introducing a pressure differential across said substrate.

5. The method of claim 1, wherein said substrate includes at least 96 of said isolated porous regions.

6. The method of claim 5, wherein said substrate includes at least 384 of said isolated porous regions.

7. The method of claim 1, wherein said isolated porous regions comprise mesh regions etched into said substrate.

8. The method of claim 1, wherein said isolated porous regions comprise controlled porous glass regions associated with said substrate.

21. The method of claim 6, wherein said surface modifier comprises a cleavable linker group.

22. A method for producing oligomers from the array of claim 21, comprising cleaving said cleavable linker group to release said oligomers from said substrate and form a plurality of free oligomers.

47. The method of claim 8, wherein each of said porous regions includes a plurality of pores with an average pore size of between about 0.1 millimeter in diameter and about 1 millimeter in diameter.

48. The method of claim 8, wherein each of said porous regions includes a plurality of pores with an average pore size of between about 0.1 millimeter in diameter and about 10 micron in diameter.

49. The method of claim 8, wherein each of said porous regions includes a plurality of pores with an average pore size of between about 1 micron in diameter and about 10 micron in diameter.

50. The method of claim 8, wherein each of said porous regions includes a plurality of pores with an average pore size of between about 1 micron in diameter and about 100 nanometers in diameter.

51. The method of claim 8, wherein each of said porous regions includes a plurality of pores with an average pore size of between about 100 nanometer in diameter and about 1 nanometer in diameter.

52. The method of claim 8, wherein said contacting said porous regions with said reagent comprises applying a liquid reagent having a volume of between about 1 milliliter and about 100 microliters.

53. The method of claim 8, wherein said contacting said porous regions with said reagent comprises applying a liquid reagent having a volume of between about 100 microliters and about 1 microliter.

54. The method of claim 8, wherein said contacting said porous regions with said reagent comprises applying a liquid reagent having a volume of between about 1 microliter and 100 nanoliters.

55. The method of claim 8, wherein said contacting said porous regions with said reagent comprises applying a liquid reagent having a volume of between about 100 nanoliters and 1 nanoliter.

56. The method of claim 8, wherein said contacting said porous regions with said reagent comprises applying a liquid reagent having a volume of between about 1 nanoliter and about 1 picoliter.

57. The method of claim 8, wherein said contacting said porous regions with said reagent comprises applying a liquid reagent having a volume of between about 1 picoliter and about 1 femtoliter.

58. The method of claim 8, further comprising cleaving said nucleic acids from said substrate.

59. The method of claim 49, further comprising carrying out a polymerase chain reaction using said nucleic acids cleaved from said substrate to make copies of said nucleic acids.

60. The method of claim 49, further comprising coupling said nucleic acids together.

61. The method of claim 49, further comprising inserting said cleaved nucleic acids into a DNA molecule to provide a mutation therein.

9. A method for the synthesis of an array of oligomeric molecules, comprising:

(a) providing a substrate having first and second surfaces, and a plurality of isolated porous regions extending through said substrate and communicating with said first and second surfaces;

(b) contacting selected ones of said porous regions with a first reagent including a first monomer;

(c) allowing said first monomer to bind to said selected porous regions;

(d) withdrawing excess said first reagent from said substrate through said selected porous regions;

(e) contacting said selected ones of said porous regions with a second reagent including a second monomer;

(f) allowing said second monomer to couple to said first monomer;

(g) withdrawing excess said second reagent from said substrate through said selected porous regions;

(ii) repeating events (e), (f) and (g) n times using n reagents with n monomers respectively, wherein n equals zero or an integer number, to form said array of oligomeric molecules.

10. The method of claim 9, further comprising contacting said porous regions with a surface modifier capable of allowing said first monomer to bind to said porous regions.

11. The method of claim 9, further comprising

(a) contacting said selected ones of said porous regions with a wash solution;

and

(b) withdrawing said wash solution through said selected porous regions by introducing a pressure differential across said substrate.

12. The method of claim 9, wherein said oligomeric molecules comprise nucleic acids.

13. The method of claim 12, wherein said nucleic acids are selected from the group consisting of DNA and RNA.

14. The method of claim 9, wherein said oligomeric molecules comprise peptides.

15. The method of claim 12, further comprising applying a target nucleic acid molecule to said array of nucleic acids and allowing said target nucleic acid molecule to hybridize with said nucleic acids.

16. A method for hybridizing nucleic acids using the array of claim 12, comprising:

(a) applying a target nucleic acid molecule to said array of nucleic acids;

(b) allowing said labeled target nucleic acid molecule to hybridize with said nucleic acids; and

(c) washing said array to remove unhybridized labeled target nucleic acid molecule therefrom.

17. The method of claim 15, wherein said target nucleic acid is labeled.

18. The method of claim 17, further comprising detecting said labeled target nucleic acid molecule on said array.

19. The method of claim 18, wherein said labeled target nucleic acid includes a fluorescent label, and said detecting comprises fluorescence detecting.

20. The method of claim 18, wherein said labeled target nucleic acid includes a magnetic label, and said detecting comprises magnetic detecting.

23. The method of claim 9, wherein said isolated porous regions each comprise a plurality of holes extending through said substrate, said holes plurality of holes formed by a microfabrication technique.

24. The method of claim 23 wherein said microfabrication comprises a technique selected from the group consisting of wet chemical etching, ion bombardment, reactive ion etching, water jet, mechanical cutting, abrasion, ion beam lithography, electron beam lithography, and drilling.

25. The method of claim 9, wherein said substrate material is selected from the group consisting of silicon, glass, ceramic, ferrous metal alloy, and non-ferrous metal alloy.

26. The method of claim 9, wherein said substrate material is a polymeric material selected from the group consisting of polyolefins, polyimides, fluorocarbon polymers, polyetheretherketones, polyamides and polysiloxanes.

27. The method of claim 9, where said withdrawing said excess reagent from said substrate through said selected porous regions comprises introducing a pressure differential across said substrate.

28. The method of claim 9, where said withdrawing said excess reagent from said substrate through said selected porous regions comprises use of osmotic pressure.

29. The method of claim 28, where said withdrawing said excess reagent from said substrate through said selected porous regions comprises use of electro-osmotic pressure.

30. The method of claim 9, where said withdrawing said excess reagent from said substrate through said selected porous regions comprises use of electric fields.

31. The method of claim 9, where said withdrawing said excess reagent from said substrate through said selected porous regions comprises use of capillary action.

32. The method of claim 9, where said withdrawing said excess reagent from said substrate through said selected porous regions comprises use of gravity.

33. The method of claim 9, wherein said providing said substrate comprises:

(a) providing a base; and

(b) joining said base to said substrate to define an enclosure between said base and said substrate.

34. The method of claim 33, wherein said providing said substrate further comprises providing a gasket configured to sealingly engage said substrate and said base.

35. The method of claim 9, wherein said contacting said isolated porous regions with said reagents is carried out with a liquid dispenser head.

36. The method of claim 33, wherein said providing said substrate further comprises providing support element for substrate, said support element including a plurality of holes, said substrate and said support element configured to align said plurality of isolated porous regions of said substrate with said plurality of holes of said support element.

37. The method of claim 9, wherein said isolated porous regions are present on said substrate at a density of between about 1 porous region per square centimeter and about 10 porous regions per square centimeter.

38. The method of claim 9, wherein said isolated porous regions are present on said substrate at a density of between about 10 porous regions per square centimeter and about 100 porous regions per square centimeter.

39. The method of claim 9, wherein said isolated porous regions are present on said substrate at a density of between about 100 porous regions per square centimeter and about 10000 porous regions per square centimeter.

40. The method of claim 9, wherein said isolated porous regions are present on said substrate at a density of between about 1000 porous regions per square centimeter and about 100000 porous regions per square centimeter.

41. The method of claim 9, wherein said isolated porous regions are present on said substrate at a density of between about 10000 porous regions per square centimeter and about 100000 porous regions per square centimeter.

42. The method of claim 9, wherein said isolated porous regions are present on said substrate at a density of between about 100000 porous regions per square centimeter and about 1000000 porous regions per square centimeter.

43. The method of claim 12, wherein said nucleic acid comprises of between about 2 nucleic acid bases and about 100 nucleic acid bases.

44. The method of claim 12, wherein said nucleic acid comprises of between about 100 nucleic acid bases and about 1000 nucleic acid bases.

45. The method of claim 12, wherein said nucleic acid comprises of between about 1000 nucleic acid bases and about 10000 nucleic acid bases.

46. The method of claim 12, wherein said nucleic acid comprises of between about 10000 nucleic acid bases and about 100000 nucleic acid bases.

62. The method of claim 33, further comprising coupling said enclosure to a vacuum source.