Substrate preparation process

• US 6,706,875 B1
• Filed: 11/20/2000
• Issued: 03/16/2004
• Est. Priority Date: 04/17/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affyemtrix Incorporated
• Inventors: Morris, MacDonald, Rava, Richard P., McGall, Glenn, Goldberg, Martin, Tan, Jennifer, Ngo, Nam Quoc, Hubbell, Earl, Yamamoto, Mel, Diggelman, Martin
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/716,507
• Time in Patent Office: 1,212 Days
• Field of Search: 435/6, 536/22.1, 536/23.1, 536/25.3, 536/26.6
• US Class Current: 536/25.3
• 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 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential 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 2219/00608 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 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• 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: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries

Abstract

The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.

Claims

1. A method of preparing a solid substrate for forming polymer sequences thereon, comprising:

providing functional groups on a surface of said substrate;

coupling monomers to said functional groups on said surface of said substrate, said monomers prior to coupling including lipophilic phosphoramidite groups, the lipophilic phosphoramidite groups having at least one lipophilic moiety.

2. The method according to claim 1, wherein said monomer comprises a nucleotide protected with a lipophilic protecting group.

6. The method according to claim 2, wherein said monomer comprises a nucleoside Fmoc-phosphoramidite.

3. A method of preparing a solid substrate for forming polymer sequences thereon, comprising:

providing functional groups on a surface of said substrate;

coupling monomers to said functional groups on said surface of said substrate. said monomers prior to coupling including lipophilic phosphoramidite groups the lipophilic phosphoramidite groups having at least one lipophilic moiety, wherein said monomer comprises a nucleotide protected with a lipophilic protecting group, wherein said lipophilic protecting group is coupled to an exocyclic functional group in a nucleobase in said nucleotide.

4. The method according to claim 3, wherein said exocyclic functional group is protected with a DMT protecting group.

5. A method of preparing a solid substrate for forming polymer sequences thereon, comprising:

providing functional groups on a surface of said substrate;

coupling monomers to said functional groups on said surface of said substrate. said monomers prior to coupling including lipophilic phosphoramidite groups, the lipophilic phosphoramidite groups having at least one lipophilic moiety, wherein said monomer comprises a nucleotide protected with a liponhilic protecting group, wherein said lipophilic protecting group is a photolabile protecting group.

7. A method of minimizing a number of differential synthesis steps in forming an array of polymer sequences on a surface of a substrate by sequentially deprotecting and coupling monomers in regions of said surface of said substrate to produce a plurality of different polymer sequences in different known locations of said surface of said substrate, the method comprising aligning deprotection and coupling steps in adjacent regions to minimize a number of differential synthesis steps and to optimize polymer sequence similarity between said adjacent regions.

8. A method of minimizing the number of synthetic steps in probing a target sequence by utilizing an array of polymer sequences wherein each polymer sequence has a subsequence of monomers common to a sequence that is complementary to a target sequence, but wherein at least one position within said subsequence is substituted with each member of a basis set of monomers, the method comprising coupling all monomers in a same layer of a first of said polymer sequences in a same synthesis cycle with corresponding monomers in a second of said polymer sequences.

9. An array of polymers comprising:

a substrate having a layer including one or more of an index matching material, a light absorbing material or an antireflective material and a plurality of polymers disposed on the substrate.

10. The array of claim 9 wherein the antireflective material includes a member selected from the group consisting of magnesium fluoride, polymethylmethacrylate and polyimide.

11. The array of claim 9 wherein the antireflective material includes magnesium fluoride.

12. The array of claim 9 wherein the antireflective material includes polymethylmethacrylate.

13. The array of claim 9 wherein the antireflective material includes polyimide.

14. The array of claim 9 wherein the layer has a thickness of between about 1 μ

m to about 50 μ

m.

15. The array of claim 9 wherein the layer has a thickness of between about 5 μ

m to about 20 μ

m.

16. The array of claim 9 wherein the layer has a thickness of about 10 μ

m.

17. The array of claim 9 wherein the layer is removable.

18. The array of claim 9 wherein the substrate is a flat substrate, a planar substrate, an aerogel, a silica aerogel, a particle, a strand, a precipitate, a gel, a sheet, a tube, a glass tube, a capillary tube, a microcapillary tube, a container, a pad, a slice, a film, a plate, or a slide.

19. The array of claim 9 wherein the polymers have known sequences and are disposed on the substrate at positionally distinct locations.

20. The array of claim 9 wherein the polymers comprise peptides or nucleic acids.

25. The array of claim 9 wherein the index matching material has a refractive index approximately equal to that of the substrate.

26. The array of claim 9 wherein the index matching material has a refractive index within approximately 10% of the refractive index of the substrate.

27. The array of claim 9 wherein the index matching material has a refractive index within approximately 5% of the refractive index of the substrate.

28. The array of claim 9 wherein the index matching material has a refractive index approximately equal to that of a glass substrate.

29. The array of claim 9 wherein the light absorbing material absorbs light having a wavelength approximately equal to that of light used during photolysis.

30. The array of claim 9 wherein the light absorbing material absorbs ultraviolet light.

31. The array of claim 9 wherein the light absorbing material absorbs light within the wavelength range of about 280 nm to about 400 nm.

45. The array of claim 9 wherein the layer is a vapor-deposed layer or a spray-applied layer.

21. An array of polymers comprising:

a substrate having a layer including one or more of an index matching material, a light absorbing material or an antireflective material and a plurality of nucleic acids or peptides disposed on the substrate at positionally distinct locations.

22. The array of claim 21 wherein the substrate is a flat substrate, a planar substrate, an aerogel, a silica aerogel, a particle, a strand, a precipitate, a gel, a sheet, a tube, a glass tube, a capillary tube, a microcapillary tube, a container, a pad, a slice, a film, a plate, or a slide.

32. The array of claim 21 wherein the index matching material has a refractive index approximately equal to that of the substrate.

33. The array of claim 21 wherein the index matching material has a refractive index within approximately 10% of the refractive index of the substrate.

34. The array of claim 21 wherein the index matching material has a refractive index within approximately 5% of the refractive index of the substrate.

35. The array of claim 21 wherein the index matching material has a refractive index approximately equal to that of a glass substrate.

36. The array of claim 21 wherein the light absorbing material absorbs light having a wavelength approximately equal to that of light used during photolysis.

37. The array of claim 21 wherein the light absorbing material absorbs ultraviolet light.

38. The array of claim 21 wherein the light absorbing material absorbs light within the wavelength range of about 280 nm to about 400 nm.

23. An array of polymers comprising:

a substrate including different polymers disposed on the substrate at positionally distinct locations and wherein the polymers have known sequences and wherein it is known which polymer is at which location, and

a coating on the substrate wherein the coating is selected to match the refractive index of the substrate so as (1) to prevent refraction of light passing through the substrate during photolysis or (2) to absorb light at the wavelength of light used during photolysis to prevent back reflection.

24. The array of claim 23 wherein the polymers are peptides or nucleic acids.

39. An array of polymers comprising:

a substrate having a layer including a material having a refractive index within about 10% of the refractive index of the substrate and which absorbs ultraviolet light and a plurality of polymers disposed on the substrate.

40. The array of claim 39 wherein the material has a refractive index within approximately 5% of the refractive index of the substrate.

41. The array of claim 39 wherein the material has a refractive index approximately equal to that of a glass substrate.

42. The array of claim 39 wherein the material absorbs light having a wavelength approximately equal to that of light used during photolysis.

43. The array of claim 39 wherein the material absorbs ultraviolet light.

44. The array of claim 39 wherein the material absorbs light within the wavelength range of about 280 nm to about 400 nm.

46. A method of coating a surface of a substrate comprising

coating the surface of a substrate with a curable solution of one or more of an index matching material, a light absorbing material or an antireflective material;

heating the substrate at a first temperature for a first period of time, then

heating the substrate at a second temperature higher than the first temperature and for a second period of time longer than the first period of time in a manner to form a cured layer of an index matching material, a light absorbing material or an antireflective material.

47. The method of claim 46 wherein the first temperature is about 85°

C.

48. The method of claim 46 wherein the first time period is about 5 minutes.

49. The method of claim 46 wherein the second temperature is between about 220°

C. and 360°

C.

50. The method of claim 46 wherein the second time period is about 60 minutes.

51. The method of claim 46 wherein the curable solution is coated onto the substrate by vapor deposition.

52. The method of claim 46 wherein the curable solution is coated onto the substrate by spray application.