Zero-mode waveguides with non-reflecting walls

• US 8,906,670 B2
• Filed: 09/08/2010
• Issued: 12/09/2014
• 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: Gray, Jeremy, Cicero, Ronald L., Grot, Annette, Popovich, Natasha, Dudek, Stephen
• Primary Examiner(s): Beisner, William H
• Application Number:
  US12/877,764
• Publication Number:
  US 20110117637A1
• Time in Patent Office: 1,553 Days
• Field of Search: 435/288.7
• 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 comprising a metal 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 comprising an oxide formed by oxidation of the metal disposed on the walls of the wells wherein the thickness of the non-reflective layer is greater than about 10 nm.

2. The zero-mode waveguide of claim 1 wherein the opaque layer comprises aluminum, and the non-reflective layer comprises aluminum oxide.

3. The zero-mode waveguide structure of claim 1 wherein the apertures comprise cylinders.

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

5. The zero-mode waveguide structure of claim 1 wherein the thickness of the non-reflective layer is greater than about 10% of the largest cross-sectional dimension of the wells.

6. The zero-mode waveguide of claim 5 wherein the wells comprise cylindrical structures, whereby the largest cross-sectional dimensions comprise the diameters of the cylinders.

7. The zero-mode waveguide structure of claim 1 wherein the solution volume of the zero-mode waveguide is less than about 80% of the ZMW volume of the zero-mode waveguide.

8. The zero-mode waveguide structure of claim 1 wherein the aperture has 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.

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

a) a zero-mode waveguide array structure of claim 1;

the zero-mode waveguide structure in contact with an analysis solution, 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 excitation illumination source that illuminates the wells through the transparent layer;

c) a detector array 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 computer that analyzes the emitted light over time in order to obtain sequence information.