ZERO-MODE WAVEGUIDES WITH NON-REFLECTING WALLS

• US 20110117637A1
• Filed: 09/08/2010
• Published: 05/19/2011
• Est. Priority Date: 09/11/2009
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Popovich, Natasha, Cicero, Ronald L., Dudek, Stephen, Gray, Jeremy, Grot, Annette
• Granted Patent: US 8,906,670 B2
• Time in Patent Office: Days
• US Class Current: 435/287.2
• CPC Class Codes: C23F 1/00 Etching metallic material by chemical means manufacture of printing surfaces B41C; manufacture of printed circuits H05K
• CPC Class Codes: C23F 17/00 Multi-step processes for surface treatment of metallic material involving at least one process provided for in class C23 and at least one process covered by subclass C21D or C22F or class C25 coating for obtaining at least two superposed coatings either by methods not provided for in a single one of main groups C23C2/00 - C23C26/00, or by combinations of methods providedfor in subclasses C23C and C25D, C23C28/00
• CPC Class Codes: C25D 11/022 Anodisation on selected surface areas
• CPC Class Codes: C25D 11/04 of aluminium or alloys based thereon
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/7743 the reagent-coated grating coupling light in or out of the waveguide
• CPC Class Codes: G02B 6/10 of the optical waveguide type G02B6/02, G02B6/24 take precedence; devices or arrangements for the control of light by electric, magnetic, electro-magnetic or acoustic means G02F1/00; transferring the modulation of modulated light G02F2/00; optical logic elements G02F3/00; optical analogue/digital converters G02F7/00
• CPC Class Codes: G02B 6/107 Subwavelength-diameter waveguides, e.g. nanowires
• CPC Class Codes: G02B 6/136 by etching

Abstract

The application relates to improved optical containment structures, methods of manufacture and use, and systems for employing same. The optical containment structures generally comprise zero-mode waveguide structures having non-reflective walls. The non-reflective walls allow the preparation of optical containment regions in which the optical containment dimensions can be decoupled from the solution containment dimensions. The application also relates to methods for producing islands of functionality within nanoscale apertures.

Claims

1. A zero-mode waveguide structure comprising:

a) a transparent substrate having a top surface;

b) an opaque layer disposed upon the top surface of the transparent substrate;

c) an array of apertures extending through the opaque layer to the transparent substrate whereby the apertures comprise wells having walls and bases, the bases of the wells comprising portions of the top surface of the transparent substrate; and

d) a non-reflective layer disposed on the walls of the wells wherein the thickness of the non-reflective layer is greater than about 5 nm.

2. The zero-mode waveguide structure of claim 1 wherein the thickness of the non-reflective layer is greater than about 10 nm.

3. The zero-mode waveguide structure of claim 1 wherein the non-reflective layer comprises an oxide.

4. The zero mode waveguide of claim 3 wherein the opaque layer comprises a metal, and the non-reflective layer comprises an oxide of such metal.

5. The zero-mode waveguide structure of claim 3 wherein the oxide is formed by oxidation of the opaque layer.

6. The zero-mode waveguide structure of claim 1 wherein the opaque layer comprises a reflective layer.

7. The zero-mode waveguide of claim 5 wherein the non-reflective layer comprises phosphorous.

8. The zero-mode waveguide of claim 5 wherein the opaque layer comprises aluminum, and the non-reflective layer comprises aluminum oxide.

9. The zero-mode waveguide structure of claim 1 wherein the non-reflective layer comprises an organic polymer.

10. The zero-mode waveguide structure of claim 1 wherein the non-reflective layer comprises a silica-based material.

11. The zero-mode waveguide structure of claim 10 wherein the non-reflective layer comprises a silane polymer.

12. The zero :

mode waveguide structure of claim 1 wherein the apertures comprise cylinders.

13. The zero-mode waveguide structure of claim 1 wherein the apertures comprise conical structures.

14. A zero-mode waveguide structure comprising:

a) a transparent substrate having a top surface;

b) a reflective layer deposed upon the top surface of the transparent substrate;

c) an array of apertures extending through the reflective layer to the transparent substrate whereby the apertures comprise wells having walls and bases, the bases of the wells comprising portions of the top surface of the transparent substrate; and

d) a non-reflective layer disposed on the walls of the wells wherein the thickness of the non-reflective layer is greater than about 10% of the largest cross-sectional dimension of the wells.

15. The zero-mode waveguide of claim 14 wherein the wells comprise cylindrical structures, whereby the largest cross-sectional dimensions comprise the diameters of the cylinders.

16. A zero-mode waveguide wherein the solution volume of the zero-mode waveguide is less than about 80% of the ZMW volume of the zero-mode waveguide.

17. The zero-mode waveguide of claim 16 wherein the solution volume of the zero-mode waveguide is less than about 75% of the ZMW volume of the zero-mode waveguide.

18. The zero-mode waveguide of claim 16 wherein the solution volume of the zero-mode waveguide is less than about 70% of the ZMW volume of the zero-mode waveguide.

19. A zero-mode waveguide comprising an aperture having a solution cross-sectional area and a ZMW cross-sectional area, wherein the solution cross-sectional area is less than about 80% of the cross-sectional area of the zero-mode waveguide.

20. The zero-mode waveguide of claim 19 wherein the solution cross-sectional area is less than about 75% of the cross-sectional area of the zero-mode waveguide.

21. The zero-mode waveguide of claim 19 wherein the solution cross-sectional area is less than about 70% of the cross-sectional area of the zero-mode waveguide.

22. A method for forming a zero-mode waveguide structure comprising:

a) providing a substrate having a lower transparent layer and an upper metal layer, wherein the metal layer comprises an array of apertures disposed through the reflective layer to the transparent layer, the apertures having side walls, and

b) exposing the substrate to oxidizing conditions whereby an oxide layer is formed on the side walls of the apertures under conditions whereby an oxide having a thickness of greater than 5 nm is produced.

23. The method of claim 22 wherein the oxide is formed by chemical oxidation.

24. The method of claim 22 wherein the oxide is formed electrochemically.

25. The method of claim 22 wherein the oxide is formed with an oxygen plasma.

26. The method of claim 22 wherein the metal comprises aluminum, silver, or titanium.

27. A method for forming a zero-mode waveguide array structure comprising:

a) providing an electrochemical system comprising a working electrode, a counter electrode, and optionally a reference electrode;

b) providing a substrate having a lower transparent layer and an upper electrically conductive reflective layer, wherein the electrically conductive reflective layer comprises an array of apertures disposed through the reflective layer to the transparent layer;

the apertures having side walls, wherein the electrically conductive reflective layer comprises the working electrode; and

c) applying a voltage to the working electrode such that a layer of non-reflective material is formed onto the side walls of the aperture.

28-33. -33. (canceled)

34. A method for analyzing a luminescent species comprising:

a) disposing a luminescent species in an aperture that extends through an upper reflective layer that is disposed on a lower transparent layer, wherein the aperture comprises side walls, and a non-reflective layer on the side walls of the aperture having a thickness of greater than 5 nm; and

b) detecting emitted light from the luminescent species wherein the emitted light passes through the transparent layer.

35-40. -40. (canceled)

41. An apparatus for obtaining nucleic acid sequence information comprising:

a) a zero-mode waveguide array structure comprising;

i. a transparent substrate having a top surface, and a reflective layer disposed upon the top surface of the transparent substrate;

ii. an array of apertures extending through the reflective layer to the transparent substrate wherein the apertures comprise wells having walls and bases, the bases of the wells comprising portions of the top surface of the transparent layer; and

iii. a non-reflective layer disposed on the walls of the wells wherein the thickness of the non-reflective layer is greater than about 5 nm;

the zero-mode waveguide structure incorporated into a device configured to hold an analysis solution in contact with the zero-mode waveguide structure, whereby the wells comprise the analysis solution which comprises reagents for carrying out reactions for which nucleic acid sequence information can be derived;

including polymerase enzyme, nucleotides, and nucleic acid template, the solution further comprising fluorescent species;

b) an illumination system that illuminates the wells through the transparent layer;

c) a detection system that detects emitted light over time from the fluorescent species within the wells, wherein the emitted light passes through the transparent layer; and

d) a computing system that analyzes the emitted light over time in order to obtain sequence information.

42-43. -43. (canceled)

44. A method for producing a zero-mode-waveguide array comprising:

a) providing an electrochemical cell having a working electrode, a counter electrode, and optionally a reference electrode, wherein the working electrode comprises a metallic upper layer of a substrate also having a transparent lower layer, wherein the metallic upper layer comprises an array of apertures extending through metallic upper layer to the transparent lower layer;

b) contacting the working electrode with a solution comprising a phosphorous containing compound; and

c) passing current through the electrochemical cell whereby a phosphorous containing material is deposited onto the metallic upper layer of the substrate.

45-63. -63. (canceled)

64. A method for forming an array of nanopores comprising:

a) providing a substrate comprising an array of apertures extending therethrough, each of the apertures having one or more cross-sectional dimension; and

b) oxidizing the substrate whereby an oxide layer is formed on the substrate and whereby the formed oxide lowers one or more cross sectional dimensions of the apertures to 20 nm or less.

65-81. -81. (canceled)