SUBSTRATES, SYSTEMS AND METHODS FOR ANALYZING MATERIALS

• US 20080128627A1
• Filed: 08/31/2007
• Published: 06/05/2008
• 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: Turner, Stephen, Lundquist, Paul
• Granted Patent: US 7,820,983 B2
• Time in Patent Office: Days
• US Class Current: 250/363.01
• CPC Class Codes: G01N 2021/7786 Fluorescence
• 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 21/6452 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: 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. An analytical device, comprising:

a substrate comprising a first surface and at least a first optical waveguide disposed upon the first surface; and

an analyte disposed sufficiently proximal to the first surface and external to the waveguide, to be illuminated by an evanescent field emanating from the waveguide when light is passed through the waveguide.

2. The device of claim 1, wherein the substrate comprises more than one waveguide disposed upon the first surface.

3. The device of claim 1, wherein the at least first waveguide is disposed within the first surface of the substrate.

4. The device of claim 1, wherein the substrate comprises at least 10 waveguides disposed upon the first surface.

5. The device of claim 1, wherein the substrate comprises at least 20 waveguides disposed upon the first surface.

6. The device of claim 1, wherein the substrate comprises at least 40 waveguides disposed upon the first surface.

7. The device of claim 2, wherein a plurality of the more than one waveguides disposed upon the first surface are optically coupled to a common originating waveguide.

8. The device of claim 1, wherein the substrate comprises SiO₂.

9. The device of claim 1, wherein the substrate comprises a polymer.

10. The device of claim 1, further comprising at least a first excitation radiation source optically coupled to the waveguide to pass excitation light therethrough.

11. The device of claim 10, wherein the at least first excitation radiation source is coupled to the first optical waveguide by at least a first optical fiber.

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

13. The device of claim 1, further comprising a mask layer disposed over the first surface of the substrate, the mask layer covering at least a first portion of the waveguide on the first surface and not covering at least a second portion of the waveguide on the first surface.

14. The device of claim 13, wherein the mask layer comprises a plurality of apertures disposed therethrough, the apertures providing access to the at least a portion of the waveguide on the first surface.

15. The device of claim 13, wherein the mask layer and the substrate layer comprise the same material.

16. The device of claim 15, wherein the same material comprises a silica based material.

17. The device of claim 16, wherein the silica based material comprises SiO₂.

18. The device of claim 13, wherein the mask layer comprises a polymer.

19. The device of claim 13, wherein the mask layer comprises a metal.

31. The system of claim 11, wherein the optical detection system receives and detects signals from a plurality of locations on the surface of the substrate.

20. A method of illuminating an analyte, comprising:

providing a substrate comprising a first surface and at least a first optical waveguide disposed upon the first surface;

providing an analyte disposed sufficiently proximal to the first surface and external to the waveguide, to be illuminated by an evanescent field emanating from the waveguide when light is passed through the waveguide; and

directing light through the first waveguide such that the evanescent field from the waveguide illuminates the analyte.

21. The method of claim 20, wherein the analyte is confined proximal to a selected portion of the first surface.

22. The method of claim 21, wherein a structural barrier confines the analyte proximal to the selected portion of the first surface.

23. The method of claim 24, wherein the structural barrier comprises a well in a mask layer disposed over the first surface, the well providing confinement of the analyte proximal to a portion of the first surface.

24. The method of claim 20, wherein the analyte is immobilized proximal to the first surface.

25. The method of claim 20, wherein the analyte comprises a fluorescent moiety, and the step of directing light comprises directing light having an excitation wavelength for the fluorescent moiety.

26. The method of claim 20, wherein the analyte is confined proximal to a portion of the first surface by a hydrophobic region of the first surface.

27. The method of claim 26, wherein the hydrophobic region surrounds the portion of the first surface.

28. The method of claim 20, wherein the substrate comprises at least a first fluidic channel disposed over and in fluid communication with the first surface, and the providing step comprises delivering the analyte proximal to the first surface through the first fluidic channel.

29. The method of claim 20, wherein the analyte comprises a complex of a polymerase enzyme, a target nucleic acid sequence, a primer sequence complementary to at least a portion of the target sequence, and a nucleotide or nucleotide analog.

30. A system for analyzing an analyte, comprising:

a substrate comprising a first surface and at least a first optical waveguide disposed upon the first surface;

at least a first light source optically coupled to the at least first waveguide to direct light into the first waveguide; and

an optical detection system positioned to receive and detect optical signals from an analyte disposed sufficiently proximal to the first surface and external to the waveguide to be illuminated by an evanescent field emanating from the waveguide when light from the light source is passed through the waveguide.

32. The system of claim 30, wherein the analyte comprises a fluorescent moiety that is excited by light of the wavelength provided by the first light source, and wherein the optical detection system comprises a detector for detecting fluorescent signals, and an optical train positioned to receive fluorescent signals from the first surface of the substrate and direct the fluorescent signals to the detector.

33. The system of claim 30, further comprising at least a second light source optically coupled to the at least first waveguide.

34. The system of claim 30, wherein the substrate comprises a plurality of optical waveguides disposed upon the first surface of the substrate.

35. The system of claim 30, wherein the substrate comprises at least 10 waveguides disposed upon the first surface.

36. The system of claim 30, wherein the substrate comprises at least 20 waveguides disposed upon the first surface.

37. The system of claim 30, wherein the substrate comprises at least 40 waveguides disposed upon the first surface.