Substrates and optical systems having a waveguide, nanometer-scale apertures, a lens array, and sensing regions and methods of use thereof

• US 10,280,457 B2
• Filed: 06/21/2017
• Issued: 05/07/2019
• 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:
  US15/629,631
• Publication Number:
  US 20170362652A1
• Time in Patent Office: 685 Days
• Field of Search: 250239, 2505594
• 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 integrated optical system comprising:

a waveguide comprising a cladding layer and an optical waveguide layer;

a plurality of nanoholes in the cladding layer;

a microlens array; and

a detector comprising a plurality of sensing regions;

wherein the plurality of nanoholes and the microlens array are positioned on opposite sides of the optical waveguide, wherein the plurality of nanoholes are positioned to be illuminated by an evanescent field emanating from the optical waveguide when optical energy is propagated therethrough, and wherein the microlens array is configured to collect optical energy signals emitted from each of the plurality of nanoholes and send the collected optical energy signals to the plurality sensing regions of the detector.

2. The integrated optical system of claim 1, wherein the plurality of nanoholes penetrate a core of the optical waveguide.

3. The integrated optical system of claim 1, wherein the nanoholes are zero-mode waveguides.

4. The integrated optical system of claim 1, wherein the optical waveguide is a planar waveguide.

5. The integrated optical system of claim 1, wherein the optical waveguide comprises at least one channel waveguide.

6. The integrated optical system of claim 1, wherein the microlens array comprises a first microlens array and a second microlens array, wherein the first microlens array is configured to collect emitted optical energy from each of the plurality of nanoholes and send a collimated beam of the emitted optical energy to the second mircolens array, wherein the second microlens array is configured to send the collimated beam of emitted optical energy from each of the plurality of nanoholes to the plurality of sensing regions of the detector.

7. The integrated optical system of claim 6, further comprising a notch filter positioned between the first and second microlens array, wherein the notch filter is configured to reject optical energy emitted from the optical waveguide, unwanted scattered optical energy, optical noise, or any combination thereof.

8. The integrated optical system of claim 1, wherein each of the plurality of sensing regions of the detector comprises a pixel.

9. The integrated optical system of claim 8, wherein the pitch of the microlens array matches the pitch of the pixels of the detector.

10. The integrated optical system of claim 1, wherein each of the plurality of sensing regions receives collected optical energy emitted from a corresponding single one of the plurality of nanoholes.

11. The integrated optical system of claim 10, wherein each of the plurality of sensing regions comprises a single pixel.

12. The integrated optical system of claim 1, wherein the optical energy is illumination light.

13. The integrated optical system of claim 1, wherein each of the plurality of nanoholes comprises an analyte region.