Arrays of integrated analytical devices and methods for production

• US 9,372,308 B1
• Filed: 06/17/2013
• Issued: 06/21/2016
• Est. Priority Date: 06/17/2012
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Ru, Michael Tzu, Foquet, Mathieu, Saxena, Ravi, Orimoto, Takashi Whitney, Grot, Annette, Chou, Hou-Pu
• Primary Examiner(s): Ahmed, Shamim
• Application Number:
  US13/920,037
• Time in Patent Office: 1,100 Days
• Field of Search: 216/24, 216/41, 385/15
• US Class Current: 1/1
• CPC Class Codes: B29D 11/0073 Optical laminates
• CPC Class Codes: B29D 17/007 Forming the relief pattern on a support larger than the record
• CPC Class Codes: B29L 2011/005 Fresnel lenses
• CPC Class Codes: B29L 2011/0066 Optical filters
• CPC Class Codes: B29L 2011/0075 Light guides, optical cables
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 2021/6467 Axial flow and illumination
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 2021/6478 Special lenses
• CPC Class Codes: G01N 2021/7713 in core
• 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 2201/0873 Using optically integrated constructions
• CPC Class Codes: G02B 2006/12038 Glass (SiO2 based materials)
• CPC Class Codes: G02B 2006/12109 Filter
• CPC Class Codes: G02B 5/189 Structurally combined with optical elements not having diffractive power
• CPC Class Codes: G02B 6/02123 characterised by the method of manufacture of the grating photolithography G03F7/0005
• CPC Class Codes: G02B 6/12002 Three-dimensional structures
• CPC Class Codes: G02B 6/12004 Combinations of two or more optical elements
• CPC Class Codes: G02B 6/124 Geodesic lenses or integrated gratings
• CPC Class Codes: G02B 6/136 : by etching

Abstract

Arrays of integrated analytical devices and their methods for production are provided. The arrays are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

Claims

1. A method for producing an array of integrated analytical devices comprising:

providing a substrate layer;

depositing a filter module layer on the substrate layer;

depositing a collection module layer on the filter module layer, wherein the collection module layer comprises a Fresnel lens structure configured to split a light beam into a plurality of light beams;

depositing a first layer of waveguide cladding material on the collection module layer;

depositing a waveguide core material on the first layer of waveguide cladding material;

depositing a second layer of waveguide cladding material on the waveguide core material to form an upper cladding and to complete a waveguide module layer;

depositing a zero-mode waveguide material on the surface of the waveguide module layer to form a zero-mode waveguide module layer;

patterning and etching the zero-mode waveguide module layer to define a plurality of nanometer-scale apertures penetrating into the upper cladding of the waveguide module layer.

2. The method of claim 1, further comprising the step of patterning and etching the waveguide core material to define a waveguide.

3. The method of claim 1, wherein the substrate layer is a detector layer.

4. The method of claim 1, wherein the substrate layer is a CMOS wafer.

5. The method of claim 1, wherein the filter module layer comprises a dielectric filter.

6. The method of claim 1, wherein the filter module layer comprises an absorptive filter.

7. The method of claim 3, wherein the detector layer comprises a color-separation layer.

8. The method of claim 1, wherein etching of the zero-mode waveguide module layer is stopped using an endpoint signal.

9. The method of claim 1, wherein the zero-mode waveguide module layer is etched until at least one nanometer-scale aperture fully penetrates the upper cladding of the waveguide module layer.

10. The method of claim 9, further comprising the step of partially backfilling at least one nanometer-scale aperture.

11. The method of claim 10, wherein the step of partially backfilling the at least one nanometer-scale aperture uses atomic layer deposition or low pressure chemical vapor deposition.

12. The method of claim 1, further comprising the step of depositing an etch hardmask on the waveguide core material prior to forming the upper cladding and completing the waveguide module layer.

13. The method of claim 1, wherein the second layer of waveguide cladding material is SiO₂.

14. The method of claim 1, wherein the waveguide core material is Si₃N₄.

15. The method of claim 1, wherein the plurality of nanometer-scale apertures comprise at least 100 nanometer-scale apertures.

16. The method of claim 1, wherein the plurality of nanometer-scale apertures have a density of at least 1000 apertures per cm².

17. The method of claim 1, wherein the Fresnel lens structure is a diffractive Fresnel lens structure.

18. The method of claim 1, wherein the Fresnel lens structure is a refractive Fresnel lens structure.

19. The method of claim 1, wherein the Fresnel lens structure combines refractive and diffractive features.

20. The method of claim 1, wherein the Fresnel lens structure is a phase Fresnel zone plate.

21. The method of claim 20, wherein the Fresnel lens structure is at least a two-phase Fresnel zone plate.

22. The method of claim 20, wherein the Fresnel lens structure is at least a four-phase Fresnel zone plate.