Printing oligonucleotide arrays using deprotection agents solely in the vapor phase

• US 5,831,070 A
• Filed: 04/19/1996
• Issued: 11/03/1998
• 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: Winkler, James L., Rava, Richard P., Goldberg, Martin J., McGall, Glenn, Fodor, Stephen P. A., Pease, R. Fabian, Stryer, Lubert, Goss, Virginia
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US08/635,272
• Time in Patent Office: 928 Days
• Field of Search: 536/25.4, 536/25.3, 536/25.31, 536/25.32, 536/25.33, 536/25.34, 436/518, 435/91.1, 530/333, 530/334, 530/335
• 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 2219/00454 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 different 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, 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;

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

coupling selected monomers to form selected polymers on the substrate.

2. A method of forming polymers having different 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 selected from a group consisting of a lacquer, an epoxy, an oil, a polyester, and a polyurethane, 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, to remove the protective group; and

coupling selected monomers to form selected polymers on the substrate.

3. The method of claim 2, wherein one or more of a print medium comprising an element selected from a group consisting of the barrier material, a receptor, the deprotection agent, the monomer, a carrier material, and an activator is selectively applied to selected regions of said substrate top surface, 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.

4. The method of claim 3 wherein said selectively applying step occurs through a drop-on-demand printhead.

5. 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 deprotection agent in a vapor phase to expose a functional group on said first portion of said oligonucleotide, wherein said surface of said substrate is selectively protected by a mask; and

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

6. The method of claim 5 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.

7. The method of claim 5 wherein said mask is held in place by electrostatic force.