Substrates, systems and methods for analyzing materials

• US 9,222,133 B2
• Filed: 12/12/2014
• Issued: 12/29/2015
• Est. Priority Date: 09/01/2006
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Lundquist, Paul, Turner, Stephen
• Primary Examiner(s): Kim, Kiho
• Application Number:
  US14/568,454
• Publication Number:
  US 20150203909A1
• Time in Patent Office: 382 Days
• US Class Current: 1/1
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 2021/6439 with indicators, stains, dyes, tags, labels, marks
• CPC Class Codes: G01N 2021/7786 Fluorescence
• CPC Class Codes: G01N 21/64 Fluorescence; Phosphorescence
• 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 21/645 Specially adapted constructive features of fluorimeters
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• 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 21/7743 the reagent-coated grating coupling light in or out of the waveguide
• CPC Class Codes: G01N 2201/08 Optical fibres; light guides
• 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 6/43 Arrangements comprising a plurality of opto-electronic elements and associated optical interconnections

Abstract

Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.

Claims

1. A method of monitoring an analytical reaction, comprising:

a) providing a substrate comprising;

i) a first surface and at least a first optical waveguide disposed beneath but sufficiently proximal to the first surface that when excitation radiation is passed through the first optical waveguide, an evanescent field emanating from the first optical waveguide reaches above the first surface;

ii) a mask layer disposed over the first surface of the substrate, the mask layer comprising a plurality of apertures that pass through the mask layer and expose the first surface; and

iii) an individual, optically resolvable analyte disposed within one of the apertures sufficiently proximal to the first surface and external to the waveguide to be illuminated by the evanescent field;

b) directing optical energy through the first optical waveguide, thereby generating said evanescent field and further illuminating the individual, optically resolvable analyte; and

c) detecting a signal from the individual, optically resolvable analyte, wherein the signal is indicative of the analytical reaction, thereby monitoring the analytical reaction.

2. The method of claim 1, further comprising optically coupling at least a first excitation radiation source to the first optical waveguide to pass excitation light therethrough.

3. The method of claim 2, wherein the first excitation radiation source is optically coupled to the first optical waveguide by at least a first optical fiber.

4. The method of claim 1, further comprising optically coupling at least two excitation radiation sources to the first optical waveguide to pass excitation light therethrough, each of the two excitation radiation sources providing light of a different spectrum.

5. The method of claim 1, wherein said one of the apertures is an optical confinement.

6. The method of claim 1, wherein said one of the apertures has a cross-sectional dimension between 50 and 200 nm.

7. The method of claim 1, wherein said one of the apertures is a zero mode waveguide.

8. The method of claim 1, wherein the mask layer comprises at least one material selected from the group consisting of a metal, a polymeric material, and a silica-based material.

9. The method of claim 1, wherein the mask layer is a transparent mask layer.

10. The method of claim 1, wherein the mask layer blocks the evanescent field above portions of the first optical waveguide.

11. The method of claim 1, wherein the individual, optically resolvable analyte is immobilized on the first surface via interaction with an immobilized complex.

12. The method of claim 11, wherein the immobilized complex comprises an enzyme.

13. The method of claim 12, wherein the enzyme is a polymerase enzyme.

14. The method of claim 1, wherein said detecting a signal comprises using a detector selected from the group consisting of a PMT, a photodiode, a photodiode array, a CCD, an EMCCD, an ICCD, and a photographic film.

15. The method of claim 1, wherein the individual, optically resolvable analyte comprises a fluorescently labeled nucleotide or nucleotide analog.

16. The method of claim 15, wherein the fluorescently labeled nucleotide or nucleotide analog comprises a terminating group.

17. The method of claim 1, further comprising delivering the individual, optically resolvable analyte proximal to the first surface via a first fluidic channel disposed over and in fluid communication with the first surface.

18. The method of claim 1, wherein each the first optical waveguide is exposed at the first surface of the substrate.

19. The method of claim 1, wherein each the first optical waveguide is not exposed at the first surface of the substrate.

20. The method of claim 1, wherein the substrate further comprises at least one integrated optical functionality selected from the group consisting of mask layers, lenses, filters, gratings, antireflective coatings, optical switching components, or attenuation components.