Analytic devices comprising optical waveguides and nanometer-scale apertures and methods of uses thereof

• US 9,222,123 B2
• Filed: 05/24/2013
• Issued: 12/29/2015
• 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, Foguet, Mathieu, Korlach, Jonas, Bayandorian, Hovig
• Primary Examiner(s): LE, QUE TAN
• Application Number:
  US13/902,113
• Publication Number:
  US 20130338013A1
• Time in Patent Office: 949 Days
• Field of Search: 250/573, 250/221, 250/559.4, 250/216, 250/227.11, 250/458.1, 385 11- 14, 385/123, 356/317, 356/318, 356244-246, 435/7.2, 4352871-2873, 436/518, 436/519
• US Class Current: 1/1
• 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 substrate comprising a first surface, wherein the first surface comprises a detection region;

at least one optical waveguide disposed within the substrate, wherein the optical waveguide traverses the detection region, and wherein the optical waveguide receives optical energy from an optical energy source at a first end, and further wherein the optical waveguide is configured to have a gradually increasing confinement of the optical energy in a propagation direction of the optical energy such that the confinement is lower at the first end than in the detection region; and

at least one nanometer-scale aperture in the detection region, wherein the nanometer-scale aperture penetrates into a first side of the substrate and extends toward a core of the optical waveguide such that a reaction site within the nanometer-scale aperture is sufficiently proximal to the core to be illuminated by an evanescent field emanating from the core when optical energy is passed through the optical waveguide.

2. The analytic device of claim 1, wherein a refractive index of the core is gradually increased along the propagation direction, thereby smoothly increasing the degree of confinement and relative field strength.

3. The analytic device of claim 1, wherein the core of the optical waveguide is tapered such that there is a gradual decrease in thickness along the propagation direction of the optical energy.

4. The analytic device of claim 3, wherein the optical waveguide is tapered in the top-to-bottom z direction.

5. The analytic device of claim 3, wherein the optical waveguide is tapered in the side-to-side y direction.

6. The analytic device of claim 1, wherein the optical waveguide comprises a cladding layer that separates the core from the reaction site, wherein the cladding layer is tapered above the core such that the core becomes gradually closer to the reaction site along the propagation direction of the optical energy.

7. The analytic device of claim 1, wherein a plurality of optical waveguides are disposed within the substrate.

8. The analytic device of claim 1, further comprising a plurality of nanometer-scale apertures in the detection region.

9. The analytic device of claim 8, further comprising a microlens array that collects optical energy signals from the plurality of nanometer-scale apertures and directs the optical energy signals so collected to a detector.

10. The analytic device of claim 1, further comprising a detector disposed proximal to the substrate on a side opposite the first side.

11. The analytic device of claim 1, wherein the at least one optical waveguide comprises a bend that changes the propagation direction of the optical energy.

12. The analytic device of claim 1, wherein the at least one optical waveguide comprises a bend that reduces background signal, thereby increasing a signal-to-background ratio.

13. The analytic device of claim 1, further comprising a reflective or absorptive layer disposed over the first surface of the substrate, wherein the nanometer-scale aperture extends through the reflective or absorptive layer.

14. A method of detecting a signal from an analyte, comprising:

a) providing the analytic device of claim 1;

b) disposing an optically resolvable individual analyte at the reaction site;

c) directing optical energy from the optical energy source into the optical waveguide at the first end such that the evanescent field illuminates the reaction site; and

d) detecting a signal from the optically resolvable individual analyte.

15. The method of claim 14, wherein the optically resolvable individual analyte comprises a fluorescent or fluorogenic label that is excited by the evanescent field.

16. The method of claim 14, wherein the optically resolvable individual analyte participates in an analytical reaction at the reaction site.

17. The method of claim 14, wherein the optically resolvable individual analyte is a differentially labeled nucleotide used by a polymerase enzyme to synthesize a nascent nucleic acid strand at the reaction site.

18. The method of claim 14, wherein said detecting a signal comprises disposing a detector proximal to a second surface of the substrate, wherein the second surface is on a second side that is opposite the first side;

and during said directing optical energy of c), detecting fluorescent or fluorogenic emissions from said optically resolvable individual analyte.

19. The method of claim 14, wherein the at least one optical waveguide comprises a bend that changes the propagation direction of the optical energy and reduces background signal.

20. The method of claim 14, wherein the analytic device further comprises a reflective or absorptive layer disposed over the first surface of the substrate, wherein the nanometer-scale aperture extends through the reflective or absorptive layer.