Analytic device comprising a nanohole extending through an opaque mask layer and into a waveguide cladding

• US 10,697,012 B2
• Filed: 02/28/2019
• Issued: 06/30/2020
• Est. Priority Date: 09/16/2008
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Zhong, Cheng Frank, Lundquist, Paul, Foquet, Mathieu, Korlach, Jonas, Bayandorian, Hovig
• Primary Examiner(s): Le, Que Tan
• Application Number:
  US16/289,513
• Publication Number:
  US 20190292590A1
• Time in Patent Office: 488 Days
• Field of Search: 250573, 250221, 250239
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 2021/6463 Optics
• CPC Class Codes: G01N 2021/6478 Special lenses
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6454 using an integrated detector array
• CPC Class Codes: G01N 21/648 using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
• CPC Class Codes: G01N 21/7703 using reagent-clad optical fibres or optical waveguides using measurement of total internal reflection or attenuated total reflection G01N21/552; optical fibres or waveguides per se G02B
• CPC Class Codes: G01N 2201/06113 Coherent sources; lasers
• CPC Class Codes: G01N 2201/0638 Refractive parts
• CPC Class Codes: G01N 2201/08 Optical fibres; light guides
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings

Abstract

This invention provides substrates for use in various applications, including single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates and dielectric omnidirectional reflectors are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.

Claims

1. An analytic device, comprising:

a waveguide substrate comprising a waveguide core and a waveguide cladding;

an opaque mask layer deposited on a top surface of the waveguide substrate; and

a nanohole extending through the opaque mask layer and into the waveguide cladding but not into the waveguide core;

wherein the nanohole comprises an analyte region disposed sufficiently proximal to the waveguide core to be illuminated by an evanescent field emanating from the waveguide core when optical energy is passed therethrough.

2. The analytical device of claim 1, wherein the waveguide core is a planar weveguide.

3. The analytical device of claim 1, wherein the waveguide core is a channel weveguide.

4. The analytical device of claim 3, wherein the waveguide substrate comprises two or more discreet channel waveguides.

5. The analytic device of claim 4, wherein each of the two or more discrete channel waveguides comprises a grating of uniform characteristics configured to couple free space light between a source of free space light and the waveguides and wherein the optical gratings disposed within each of the two or more discrete channel waveguides normalize the optical energy intensity among the two or more waveguides.

6. The analytic device of claim 5, further comprising a source of a single beam of optical energy and a diffractive optical element for splitting the single beam of optical energy into two or more beams of optical energy, wherein the diffractive optical element is in optical communication with the optical gratings.

7. The analytic device of claim 6, wherein at least one of the two or more discrete channel waveguides further comprises a second optical grating, wherein the first optical grating and the second optical grating form a diffraction grating pair, wherein the diffraction grating pair flanks a portion of the waveguide that is proximal to the analyte region, and wherein the diffraction grating pair intensifies optical energy of at least one desired wavelength within the portion of the waveguide.

8. The analytic device of claim 1, wherein the nanohole has a cross-sectional dimension between 50 and 200 nm.

9. The analytic device of claim 1, wherein the nanohole is a tapered nanohole.

10. The analytic device of claim 1, wherein the opening at the top of the nanohole through the mask layer has a submicrometer diameter that prevents the evanescent field emanating from the waveguide core from entering the area above the opaque mask layer.

11. The analytic device of claim 1, where the opaque mask layer is a metal mask layer.

12. The analytic device of claim 11, wherein the metal mask layer is from about 40 nm to about 250 nm thick.

13. The analytic device of claim 11, wherein the metal mask layer is formed from aluminum, gold, platinum, silver, chromium, or combinations thereof.

14. The analytic device of claim 1, wherein the waveguide substrate comprises a plurality of nanoholes.

15. The analytical device of claim 14, wherein the waveguide substrate further comprises a multi-sensor array beneath the waveguide core, wherein each sensor in the multi-sensor array detects optical energy signals emitted from the analyte region of a single one of the plurality of nanoholes.

16. The analytical device of claim 15, wherein the waveguide substrate further comprises a microlens array positioned between the waveguide core and the multi-sensor array, wherein the microlens array collects optical energy signals emitted from each of the analyte regions and directs the collected optical energy signals to its corresponding sensor.