Selectively functionalized arrays

• US 8,501,406 B1
• Filed: 06/09/2010
• Issued: 08/06/2013
• Est. Priority Date: 07/14/2009
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Gray, Jeremy, Kearns, Gregory, Dudek, Stephen, Popovich, Natasha, Sebra, Robert, Cicero, Ronald
• Primary Examiner(s): CROW, ROBERT THOMAS
• Application Number:
  US12/797,260
• Time in Patent Office: 1,154 Days
• Field of Search: 435/6, 435/6.1, 435/283.1, 435/287.1, 435/287.2, 514/44, 424/482
• US Class Current: 435/6.1
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00443 Thin film deposition
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• 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 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6869 Methods for sequencing

Abstract

Methods, substrates, and devices related to arrays of optical confinements having surfaces with high levels of bias. Substrates having transparent or silica based portions and opaque or reflective portions are treated with 1) a selective passivating agent, that selectively coats the opaque or reflective regions, 2) a functionalizing agent such as a coupling agent, and 3) a selective removal agent, which selectively removes functionalizing agent from the passivated opaque or reflective surfaces.

Claims

1. A method for selectively functionalizing a surface of a substrate having both silica-based portions and metal or metal oxide portions comprising:

a) exposing a surface of a substrate having both silica-based portions and metal or metal oxide portions to an agent that preferentially binds to the metal or metal oxide portions to produce passivated metal or metal oxide portions of the surface;

b) exposing the surface of the substrate to a silica functionalizing agent that binds to both the silica-based portions and the passivated metal or metal oxide portions of the surface, then rinsing the surface of the substrate; and

c) after step b), exposing the silica-based portions and the passivated metal or metal oxide portions of the surface of the substrate to a selective removal compound that preferentially removes the silica functionalizing agent from the passivated metal or metal oxide portions of the surface.

2. The method of claim 1 wherein the agent that preferentially binds to the metal or metal oxide portions comprises phosphate or phosphonate functionality.

3. The method of claim 1 wherein the silica functionalizing agent comprises a silane coupling agent.

4. The method of claim 1 wherein the selective removal compound comprises an acidic compound.

5. The method of claim 1 wherein the selective removal compound comprises a compound having a pK_a of less than 6.

6. The method of claim 1 wherein the selective removal compound comprises a polymer.

7. The method of claim 6 wherein the polymer comprises carboxylate, sulfonate, sulfate, phosphonate or phosphate functionality.

8. The method of claim 6 wherein the polymer comprises a homopolymer or copolymer of one or more of the monomers vinyl(acrylic acid), vinyl(sulfonic acid), vinyl(phosphonic acid), vinyl(styrenesulfonic acid), maleic acid, or salts thereof.

9. The method of claim 6 wherein the polymer comprises poly(vinylsulfonic acid) or

10. The method of claim 1 wherein the silica-based portions comprise optical confinement regions.

11. The method of claim 1 wherein the substrate comprises an array of optical confinement regions wherein the silica-based portions comprise bases of apertures though a metal or metal oxide layer on a transparent silica-based substrate.

12. A method for selectively functionalizing a surface of a substrate having both silica-based portions and metal or metal oxide portions comprising;

a) treating a surface of a substrate having both silica-based portions and metal or metal oxide portions with a compound comprising phosphate or phosphonate groups to produce passivated metal or metal oxide portions of the surface;

b) treating the surface of the substrate with a silica functionalizing agent that binds to both the silica-based and the passivated metal or metal oxide portions of the surface; and

c) treating the surface of the substrate with an acidic compound having a pK_a of less than 6 to remove silica functionalizing agent from the passivated metal or metal oxide portions of the surface.

15. The method of claim 12 wherein the silica functionalizing agent comprises a silane coupling agent.

16. The method of claim 12 wherein the acidic compound comprises a polymer.

17. The method of claim 16 wherein the polymer comprises carboxylate, sulfonate, sulfate, phosphonate or phosphate functionality.

18. The method of claim 16 wherein the polymer comprises a homopolymer or copolymer of one or more of the monomers vinyl(acrylic acid), vinyl(sulfonic acid), vinyl(phosphonic acid), vinyl(styrenesulfonic acid), maleic acid, or salts thereof.

19. The method of claim 16 wherein the polymer comprises poly(vinylsulfonic acid) or

20. The method of claim 12 wherein the silica-based portions comprise optical confinement regions.

21. The method of claim 12 wherein the substrate comprises an array of optical confinement regions wherein the silica-based portions comprise bases of apertures though a metal or metal oxide layer on a transparent silica-based substrate.

13. A method for attaching a desired molecule to a silica-based portion of a surface of a substrate having both silica-based portions and metal or metal oxide portions comprising;

a) exposing a surface of a substrate having both silica-based portions and metal or metal oxide portions to an agent that preferentially binds to the metal or metal oxide portions to produce passivated metal or metal oxide portions of the surface;

b) exposing the surface of the substrate to a coupling agent that binds to both the silica-based portions and the passivated metal or metal oxide portions of the surface, then rinsing the surface of the substrate;

c) after step b), exposing the silica-based portions and the passivated metal or metal oxide portions of the surface of the substrate to a selective removal compound that preferentially removes the coupling agent from the passivated metal or metal oxide portions of the surface; and

d) attaching the desired molecule to the coupling agent bound to the silica-based portions of the surface.

14. A method for attaching a desired molecule to a silica-based portion of a surface of a substrate having both silica-based portions and metal or metal oxide portions comprising;

a) treating a surface of a substrate having both silica-based portions and metal or metal oxide portions with a compound comprising phosphate or phosphonate groups to produce passivated metal or metal oxide portions of the surface;

b) treating the surface of the substrate with a coupling agent that binds to both the silica-based and the passivated metal or metal oxide portions of the surface;

c) treating the surface of the substrate with an acidic compound having a pK_a of less than 6 to remove coupling agent from the passivated metal or metal oxide portions of the surface; and

d) attaching the desired molecule to the coupling agent bound to the silica-based portions of the surface.