Printing molecular library arrays

• US 6,239,273 B1
• Filed: 10/26/1999
• Issued: 05/29/2001
• Est. Priority Date: 02/27/1995
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Rava, Richard P., Goldberg, Martin J., McGall, Glenn, Winkler, James L., Fodor, Stephen P. A., Pease, R. Fabian, Stryer, Lubert, Goss, Virginia
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US09/427,850
• Time in Patent Office: 581 Days
• Field of Search: 536/221, 536/23.1, 536/25.3, 530/350, 530/587.1
• 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 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00382 Stamping
• CPC Class Codes: B01J 2219/00385 Printing
• CPC Class Codes: B01J 2219/00427 using masks
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00454 by chemical cleavage from the solid support
• 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 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• 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: B41M 3/00 : Printing processes to produce particular kinds of printed work, e.g. patterns printing apparatus or machines of special type or for particular purposes B41F17/00; special designs or pictures per se B44F; manufacturing printed circuits using printing techniques H05K3/12 ; manufacturing organic semiconductor devices using printing techniques H10K71/13
• 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 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
• CPC Class Codes: G03F 7/00 : Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printing surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor using photoresist structures for special production processes, see the relevant places, e.g. B44C, H01L, e.g. H01L21/00, H05K

Abstract

A method and apparatus for selectively applying a print material onto a substrate for the synthesis of an array of oligonucleotides at selected regions of a substrate. The print material includes a barrier material, a monomer sequence, a nucleoside, a deprotection agent, a carrier material, among other materials. The method and apparatus also relies upon standard DMT based chemistry, and a vapor phase deprotection agent such as solid TCA and the like.

Claims

1. A method of forming selected polymers on a substrate, said method comprising:

providing a substrate comprising a layer of linker molecules thereon, each of said linker molecules having a protective group at its distal end away from the substrate;

applying a barrier layer overlying said linker molecule layer, said applying step forming selected exposed regions of said linker molecule layer;

exposing said selected exposed regions of said linker molecule layer to a deprotecting agent solely in a vapor phase, solely to remove the protective group; and

coupling selected monomers to form said selected polymers on the substrate.

2. The method of claim 1, wherein said applying step comprises a printing method selected from the group consisting of:

relief press printing, letter press printing, gravure printing, intaglio printing, stencil printing, ion beam proximity printing, ink jet printing, bubble jet printing, lithography, and xerography.

3. The method of claim 1, wherein said applying step comprises a print method selected from the group consisting of stencil printing and lithography.

4. The method of claim 2, wherein said printing method uses a print medium comprising a barrier material, a receptor, a deprotection agent, a monomer, a carrier material, an activator, or a combination thereof.

5. The method of claim 4, wherein said barrier material is selected from the group consisting of:

a lacquer, an epoxy, an oil, a polyester, and a polyurethane.

6. The method of claim 4, wherein said barrier material is a liquid.

7. The method of claim 4, wherein the substrate has a top surface and the print medium is selectively applied to said top surface of the substrate.

8. The method of claim 7, wherein said selectively applying step occurs through a drop-on-demand printhead.

9. The method of claim 1, wherein said deprotection agent is an acidic vapor selected from the group consisting of trichloroacetic acid, dichloroacetic acid, hydrochloric acid and any other acidic vapor.

10. The method of claim 1, wherein said deprotection agent comprises water vapor or a carrier gas.

11. The method of claim 1, wherein said deprotection agent is mixed with a carrier gas.

12. The method of claim 1, wherein said deprotection occurs at atmospheric pressure or at a pressure lower than atmospheric pressure.

13. The method of claim 1, wherein said deprotection occurs at a pressure ranging from about 10⁻

5 torr to about 1 torr.

14. The method of claim 1, wherein said deprotection agent is at a temperature ranging from about 20°

C. to about 50°

C.

15. The method of claim 1, wherein the polymer is selected from the group consisting of:

nucleic acids, polynucleotides, oligonucleotides, polypeptides, polysaccharides, oligosaccharides, phospholipids, polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneimines, polyarylene sulfides, polysiloxanes, polyimides, and polyacetates.

16. The method of claim 1, wherein said polymer is selected from the group consisting of:

nucleic acids, polynucleotides, oligonucleotides, polypeptides, and polysaccharides.

17. A method of deprotecting selected regions of a substrate, said method comprising:

providing a substrate comprising a layer of linker molecules thereon, each of said linker molecules having a protective group;

applying a deprotection agent solely in vapor phase solely to remove the protective group to selected regions of said linker molecule layer, wherein said deprotection occurs at atmospheric pressure or at a pressure lower than atmospheric pressure.

18. The method of claim 17, wherein said deprotection occurs at a pressure ranging from about 10⁻

5 torr to about 1 torr.

19. The method of claim 17, wherein said deprotection agent is an acidic vapor selected from the group consisting of trichloroacetic acid, dichloroacetic acid, hydrochloric acid and any other acidic vapor.

20. The method of claim 17 wherein said deprotection agent is at a temperature ranging from about 20°

C. to about 50°

C.

21. The method of claim 17, wherein said deprotection agent comprises water vapor or a carrier gas.

22. The method of claim 17, wherein said deprotection agent is mixed with a carrier gas.

23. The method of claim 17, wherein said applying step occurs through heat driven forced convection.

24. A method of applying a print medium which is solely in a vapor phase in selected regions of a substrate, solely to remove a protective group, said method comprising the steps of:

providing a partially completed substrate comprising an array of monomers, said partially completed substrate having a top surface;

selectively applying a print medium comprising a barrier material, a receptor, a deprotection agent, a monomer group, a carrier material, an activator, or a combination thereof, to selected regions of said substrate top surface, wherein

said selectively applying step comprises a printing method selected from the group consisting of;

relief press printing, letter press printing, gravure printing, intaglio printing, stencil printing, ion beam proximity printing, inkjet printing, bubble jet printing, lithography, and xerography.

25. The method of claim 24, wherein said print medium is a deprotection agent selected from the group consisting of:

trichloroacetic acid, dichloroacetic acid, hydrochloric acid and any other acidic vapor.

26. The method of claim 24, wherein said print medium is a deprotection agent comprising water vapor or a carrier gas.

27. The method of claim 24, wherein said print medium is a deprotection agent is mixed with a carrier gas.

28. The method according to claim 24, wherein said print medium is a deprotection agent and said deprotection occurs at atmospheric pressure or at a pressure lower than atmospheric pressure.

29. The method of claim 24, wherein said print medium is a deprotection agent and said deprotection occurs at a pressure ranging from about 10⁻

5 torr to about 1 torr.

30. The method of claim 24, wherein sai d selectively applying step is stencil printing.

31. The method according to claim 24, wherein said lithography is an ion beam projection lithography.

32. The method of claim 24, wherein said monomer is selected from the group consisting of:

nucleoside, nucleotide, amino acid, monosaccharide, phospholipid, urethane, ester, carbonate, urea, amide, ethyleneimine, arylene sulfide, siloxane, imide, and acetate.

33. A method of synthesizing a nucleic acid or a polynucleotide comprising the steps of:

a) providing an oligonucleotide having a proximal end and a distal end, said proximal end coupled to a substrate having a surface, and said distal end having a removable protecting group;

b) removing said protecting group with a deprotection agent solely in vapor phase solely to expose a functional group; and

c) covalently bonding an oligonucleotide to said exposed fumctional group.

34. The method of claim 33, wherein the oligonucleotide of step c) has a proximal end and a distal end, the proximal end is bonded to said exposed functional group of step b), and said distal end having a removable protecting group, and wherein the method further comprises repeating the steps b) and c).

35. The method of claim 33, wherein in step a), a plurality of oligonucleotides are coupled to the substrate to form an array.

36. The method of claim 33, wherein said deprotection agent is selected from the group consisting of trichloroacetic acid, dichloroacetic acid, hydrochloric acid and any other acidic vapor.

37. The method of claim 33, wherein said surface of said substrate is selectively protected by a mask during said removing step.

38. The method of claim 37, wherein said mask is selected from a group consisting of an epoxy, a silicone oil, a metal, a silicon material, a lacquer, an oil, a polyester, and a polyurethane.

39. The method of claim 37, wherein said mask is held in place by electrostatic force.