Printing molecular library arrays

• US 20030175409A1
• Filed: 03/13/2003
• Published: 09/18/2003
• Est. Priority Date: 02/27/1995
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Goldberg, Martin. J., Goss, Virginia, Fodor, Stephen P.A., Rava, Richard P., McGall, Glenn, Winkler, James L., Pease, R. Fabian, Stryer, Lubert
• Application Number:
  US10/387,969
• Publication Number:
  US 20030175409A1
• Time in Patent Office: Days
• US Class Current: 427/2.11
• 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 2219/00454 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 2219/0061 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 2219/00637 by coating it with another layer
• 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 2219/00722 : Nucleotides
• 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: 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: C40B 40/06 : Libraries containing nucleotides or polynucleotides, 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 polymers having diverse monomer sequences on a substrate, said method comprising:

providing a substrate comprising a linker molecule layer thereon, said linker molecule layer comprising a linker molecule and a protective group;

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

exposing said selected exposed regions of said linker molecule layer to a vapor comprising a deprotecting agent.

2. The method of claim 1 wherein said deprotection agent is an acidic vapor selected from a group consisting of TCA, DCA, and HCl.

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

C. to about 50°

C.

4. The method of claim 1 wherein said applying step is selected from a group consisting of relief press printing, letter press printing, gravure printing, intaglio printing, stencil printing, and lithography.

5. The method of claim 1 wherein said barrier layer is selected from a group consisting of a lacquer, an epoxy, an oil, a polyester, and a polyurethane.

6. The method of claim 1 wherein said barrier layer is a liquid.

7. The method of claim 1 wherein said deprotection agent comprises a carrier gas.

8. The method of claim 1 wherein said deprotection agent comprises a water vapor.

9. 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 vapor deprotection agent to selected regions of said linker molecule layer.

10. The method of claim 9 wherein said deprotection agent is selected from a group consisting of TCA, DCA, and HCl.

11. The method of claim 9 wherein said deprotection agent is at a temperature ranging from about 20°

C. to about 50°

C.

12. The method of claim 9 wherein said applying step occurs through forced convention.

13. The method of claim 9 wherein said deprotection agent comprises a carrier gas.

14. The method of claim 9 wherein said deprotection agent comprises a water vapor.

15. A method of applying a medium in selected regions of a substrate, 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 medium comprising an element selected from a group consisting of a barrier material, a receptor, a deprotection agent, a monomer group, a carrier material, and an activator to selected regions of said substrate top surface.

16. The method of claim 15 wherein said medium is selected from a group consisting of TCA, DCA, HCL, and any other acidic vapor.

17. The method of claim 15 wherein said medium is at a temperature ranging from about 20°

C. to about 50°

C.

18. The method of claim 15 wherein said medium is a deprotection agent.

19. The method of claim 18 wherein said deprotection agent comprises a carrier gas.

20. The method of claim 18 wherein said deprotection agent comprises a water vapor.

21. The method of claim 15 wherein said selectively applying step is selected from a group consisting of relief press printing, letter press printing, gravure printing, intaglio printing, and stencil printing.

22. The method of claim 15 wherein said selectively applying step occurs through a drop-on-demand printhead.

23. A method of synthesizing an oligonucleotide comprising the steps of:

coupling a first portion of said oligonucleotide to said substrate, said first portion of said oligonucleotide comprising a removable protecting group;

removing said protecting group with a vapor phase deprotection agent to expose a functional group on said first portion of said oligonucleotide; and

covalently bonding a second portion of said oligonucleotide to said first portion of said oligonucleotide.

24. The method as recited in claim 23 wherein said surface of said substrate is selectively protected by a mask during said removing step.

25. The method as recited in claim 24 further comprising repeating said removing and covalently bonding steps to form an array of oligonucleotides.

26. The method of claim 24 wherein said vapor phase deprotection agent is selected from a group consisting of TCA, DCA, and HCl.

27. The method of claim 24 wherein said mask is selected from a group consisting of an epoxy, a silicone oil, a metal, a silicon material, a lacquer, a oil, and a polyester.

28. The method of claim 24 wherein said mask is held in place by electrostatic force.