Waveguide-Based Optical Scanning Systems

• US 20090068668A1
• Filed: 09/12/2008
• Published: 03/12/2009
• Est. Priority Date: 09/12/2007
• Status: Active Grant

• Current Assignee: LDIP, LLC
• Original Assignee: PLC Diagnostics, Inc.
• Inventors: Duer, Reuven
• Granted Patent: US 8,288,157 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2201/024 Modular construction
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

A scanning sensor system, methods of use and kits for detecting a biologically active analyte are provided. The scanning sensor system includes a light source, a detector, a substrate comprising a plurality of waveguides and a plurality of optical sensing sites in optical communication with one or more waveguide of the substrate, and at least one adapter configured to couple with the substrate and provide optical communication between the light source, the waveguides of the substrate, and the detector.

Claims

1. A scanning sensor system for detecting a biologically active analyte comprising:

a light source;

a detector;

a substrate comprising a plurality of waveguides and a plurality of optical sensing sites in optical communication with one or more waveguide of the substrate; and

at least one adapter configured to couple with the substrate and provide optical communication between the light source, the waveguides of the substrate, and the detector.

2. The system of claim 1, wherein the substrate and the at least one adapter are substantially planar and comprise a planar lightwave circuit.

3. The system of claim 1, wherein the at least one adapter is further configured to removably couple with the substrate.

4. The system of claim 1, wherein the at least one adapter is further coupled to at least one of the light source and the detector.

5. The system of claim 1, wherein the at least one adapter is a single adapter further coupled to the light source and the detector.

6. The system of claim 4 or claim 5, wherein the coupling is by fiber optic.

7. The system of claim 5, wherein the adapter comprises a plurality of edges and wherein coupling to the light source and the detector comprises coupling to a first edge of the adapter and coupling to the substrate comprises coupling at a second edge of the adapter.

8. The system of claim 5, wherein the adapter comprises a plurality of optical elements comprising at least one lens and at least one filter, wherein the plurality of optical elements are configured to manipulate and couple light from the light source to the substrate and further configured to manipulate and couple light from the substrate to the detector.

9. The system of claim 5, wherein the plurality of waveguides comprise in-coupling waveguides and out-coupling waveguides.

10. The system of claim 9, wherein the in-coupling waveguides are coupled to the out-coupling waveguides through a combiner.

11. The system of claim 10, wherein the substrate further comprises at least one combiner.

12. The system of claim 10, wherein the adapter further comprises at least one combiner.

13. The system of claim 1, wherein the at least one adapter is a single adapter, the plurality of waveguides comprise in-coupling waveguides and out-coupling waveguides, wherein the in-coupling waveguides are coupled to the out-coupling waveguides through a combiner, wherein the light source comprises a light generator element coupled to at least one in-coupling waveguide, and wherein the detector comprises a detector element coupled to at least one out-coupling waveguide.

14. The system of claim 1, wherein the optical sensing site further comprises a sensor configured to transduce a first light wave generated by the light source in a waveguide, resulting in a second light wave in the same waveguide, the second light wave being detectable by the detector.

15. The system of claim 14, wherein the plurality of waveguides comprise in-coupling waveguides coupled to out-coupling waveguides by way of combiners, and wherein the first light wave is carried by an in-coupling waveguide and the second light wave is carried by an out-coupling waveguide.

16. The system of claim 15, wherein both the adapter and substrate comprise inter-coupling optically communicating in-coupling waveguides and out-coupling waveguides and wherein the substrate further comprises the combiners.

17. The system of claim 14, wherein the sensor comprises a biologically active analyte in a sample, and wherein a measurable change in the first light wave results when the sensor discriminates or interacts with the biologically active analyte.

18. The system of claim 1, wherein the sensor is adapted to support an immunoassay.

19. The system of claim 18, wherein the immunoassay supported is an enzyme-linked immunosorbent assay (ELISA).

20. The system of claim 18, wherein the immunoassay supported is a fluorescent immunoassay.

21. The system of claim 1, wherein the sensor is selected from the group consisting of a fluorescence well, an absorption cell, an interferometric sensor, a diffractive sensor and surface plasmon resonance sensor.

22. The system of claim 1, wherein the biologically active analyte is selected from the group consisting of a nucleic acid, a protein, an antigen, an antibody, a microorganism, a gas, a chemical agent and a pollutant.

23. The system of claim 22, wherein the nucleic acid is produced via an amplification reaction.

24. The system of claim 1, wherein the waveguides are single-mode.

25. The system of claim 1, wherein the waveguides are multi-mode.

26. The system of claim 1, wherein the waveguides are single-mode in the vertical dimension and multi-mode in the lateral dimension.

27. The system of claim 1, wherein the optical sensing sites comprise wells.

28. The system of claim 1, wherein the optical sensing sites comprise the surface of the substrate above the waveguides.

29. The system of claim 1, wherein the optical sensing sites comprise biochemical interaction sites.

30. The system of claim 1, wherein the optical sensing sites comprise optical transducers.

31. The system of claim 30, wherein the optical transducers comprise fluorescence wells comprising fluorescent or luminescent compounds, wherein light waves guided by a waveguide of the plurality of waveguides excite the fluorescent or luminescent compound in the wells in the presence of a biologically active analyte, and the same waveguide collects and guides light emitted from the wells to the detector.

32. The system of claim 1, wherein the number of optical sensing sites is greater than 10.

33. The system of claim 1, wherein the number of optical sensing sites is greater than 200.

34. The system of claim 1, wherein the number of optical sensing sites is greater than 5,000.

35. The system of claim 1, wherein the light source comprises a chip containing an array of light generators coupled to an array of waveguides.

36. The system of claim 1, wherein the light source comprises a passive light source.

37. The system of claim 36, wherein the light source is a passive 1×

N splitter with N being between 1 and 1000.

38. The system of claim 1, wherein the light source comprises a switchable light source.

39. The system of claim 38, wherein the switchable light source comprises a dynamic light source.

40. The system of claim 38, wherein the switchable light source is an optical switch comprising a light generator coupled to one or more input of the optical switch.

41. The system of claim 40, wherein the optical switch further comprises a branched architecture.

42. The system of claim 41, wherein the optical switch further comprises one or more inputs and multiple outputs.

43. The system of claim 42, wherein the optical switch further comprises greater than about 10 outputs.

44. The system of claim 42, wherein the optical switch further comprises greater than about 100 outputs.

45. The system of claim 42, wherein the optical switch further comprises greater than about 1,000 outputs.

46. The system of claim 42, wherein the optical switch further comprises substantially between 20 and 200 outputs.

47. The system of claim 40, wherein the light generator provides variable wavelengths of light.

48. The system of claim 40, wherein the light generator is selected from the group consisting of a broad-band source, a source with one or more discrete spectral lines and a tunable source.

49. The system of claim 1, wherein the light source is butt-coupled to one or more of the at least one adapter.

50. The system of claim 1, wherein the light source comprises one or more waveguide and is evanescently coupled to the at least one adapter through a proximate arrangement of the one or more light source waveguide and one or more waveguide of the at least one adapter.

51. The system of claim 1, wherein the detector is a photodetector array.

52. The system of claim 1, wherein the detector is a plurality of detectors.

53. The system of claim 52, wherein two or more detectors are coupled to and in optical communication with one or more waveguide of the at least one adapter at one or more edges of the at least one adapter.

54. The system of claim 1, wherein the system further comprises a thermal transfer element in thermal communication with the substrate.

55. The system of claim 54, wherein the thermal transfer element is a thermoelectric cooler.

56. The system of claim 1, wherein each optical sensing site comprises a thermal transfer element in thermal communication with the optical sensing site.

57. The system of claim 56, wherein the thermal transfer element comprises a thin-film heater.

58. The system of claim 56, wherein each optical sensing site further comprises a thermistor in thermal communication with the optical sensing site.

59. The system of claim 1, wherein the substrate further comprises one or more microchannel and one or more reservoirs in fluid communication with one or more optical sensing site.

60. The system of claim 1, wherein the system further comprises a fluidics layer coupled to the substrate and comprising one or more microchannel and one or more reservoirs in fluid communication with one or more optical sensing site.

61. A scanning sensing method comprising:

coupling a removable substrate comprising a plurality of in-coupling waveguides, a plurality of out-coupling waveguides and combiners for coupling the in-coupling and out-coupling waveguides, wherein the substrate is coupled in optical communication with an adapter, a light source, and a detector to provide a scanning sensor system, wherein the adapter is coupled to the light source and the detector;

delivering a sample suspected of containing a biologically active analyte to be detected to an optical sensing site of the substrate;

providing a first light wave using a light source to one or more of the plurality of in-coupling waveguides of the substrate, wherein the in-coupling waveguides are in optical communication with the optical sensing site, wherein the first light wave is transducable by a sensor associated with the optical sensing site to a second light wave carried to an out-coupling waveguide; and

detecting a measurable change in the second light wave using the detector, wherein a measurable change in the first light waves occurs when the sensor interacts with the biologically active analyte.

62. The method of claim 61, wherein scanning sensing further comprises switching one or more input light wave from the light source into the substrate to produce the first light wave in one or more of the in-coupling waveguides.

63. The method of claim 61, wherein the light source comprises an optical switch for controlled switching of one or more input light wave, the optical switch can multicast light to a plurality of outputs and into the substrate to controllably produce the first light wave in one or more of the in-coupling waveguides.

64. The method of claim 61, wherein the light source comprises an array of individually controlled light generators for controlled switching of one or more input light wave, to controllably produce the first light wave in one or more of the in-coupling waveguides.

65. The method of claim 61, further comprising simultaneously detecting the second light wave with the detector wherein the detector comprises a photodetector array.

66. The method of claim 61, wherein, a portion of the sensing sites comprise reference sample material for calibration and/or normalization.

67. The method of claim 61, wherein the biologically active analyte is selected from the group consisting of a nucleic acid, a protein, an antigen, an antibody, a microorganism, a gas, a chemical agent and a pollutant.

68. The method of claim 61, wherein the biologically active analyte is a protein.

69. The method of claim 61, wherein a SNP is detected in the biologically active analyte.

70. The method of claim 61, wherein expression of a gene is detected upon detection of the biologically active analyte.

71. The method of claim 61, wherein the sensor is adapted to support an immunoassay and wherein the sensor interacting with the biologically active analyte comprises an outcome of an immunoassay.

72. The method of claim 71, wherein the immunoassay supported is an enzyme-linked immunosorbent assay (ELISA).

73. The method of claim 71, wherein the immunoassay supported is a fluorescent immunoassay.

74. The method of claim 61, wherein detecting a measurable change in the second lightwave provides a diagnostic result.

75. The method of claim 61, further comprising conducting a real-time PCR reaction at the optical sensing site.

76. A kit for assaying a sample for a biologically active analyte comprising:

a scanning sensor system comprising a light source, a detector, a substrate comprising a plurality of waveguides and a plurality of optical sensing sites in optical communication with one or more waveguide of the substrate, and at least one adapter configured to couple with the substrate and provide optical communication between the light source, the waveguides of the substrate, and the detector;

packaging; and

instructions for use of the system.

77. The kit of claim 76, wherein the adapter and substrate comprises a planar lightwave circuit.

78. The kit of claim 76, wherein the optical sensing sites comprise a sensor adapted to support an immunoassay, and wherein the kit further comprises one or more immunoassay reagents.