IP Library › Granted Patent US 12,241,122
Granted Patent B2
US 12,241,122 · App. 17/217,876 · Granted Mar 4, 2025

Illumination of integrated analytical systems

Inventors: Adrian Fehr (San Francisco, CA); Nathaniel Joseph McCaffrey (Mill Valley, CA); Stephen Turner (Eugene, OR)
Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
C12Q1/6874B01L3/502707B01L3/502715B82Y20/00C12Q1/6825C12Q1/6869G01N21/03G01N21/0303G01N21/05G01N21/64G01N21/6428G01N21/645G01N21/6452G01N21/6454G01N21/6456G01N21/648G01N21/75G01N21/77G01N33/54373G02B6/1226B01L2300/0654B01L2300/0663B01L2300/0816B01L2300/168G01N2021/0346G01N2021/6434G01N2021/6439G01N2021/6441G01N2021/6463G01N2021/757G01N2021/7786G01N2201/067G01N2201/068G01N2201/08Y10T436/143333
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Quick Facts
Patent No.
US 12,241,122
App. No.
17/217,876
Granted
Mar 4, 2025
Kind
B2
Abstract

An analytical device including an optically opaque cladding, a sequencing layer including a substrate disposed below the cladding, and a waveguide assembly for receiving optical illumination and introducing illumination into the device. The illumination may be received from a top, a side edge, and a bottom of the device. The waveguide assembly may include a nanoscale aperture disposed in the substrate and extending through the cladding. The aperture defines a reaction cell for receiving a set of reactants. In various aspects, the device includes a sensor element and the illumination pathway is through the sensor element. Waveguides and illumination devices, such as plasmonic illumination devices, are also disclosed. Methods for forming and operating the devices are also disclosed.

Claims (42)

1. An integrated device comprising:

a plurality of reaction cells to house reactants, wherein the plurality of reaction cells are formed on a surface of the integrated device;

at least one waveguide to receive optical energy; and

a plurality of coupling structures optically coupling the at least one waveguide with the plurality of reaction cells, wherein each respective coupling structure in the plurality of coupling structures is formed at or adjacent to a corresponding reaction cell in the plurality of reaction cells, and is configured to provide excitation energy to the corresponding reaction cell in response to the optical energy from a corresponding waveguide in the at least one waveguide, wherein

the respective coupling structure provides plasmonic energy to the corresponding reaction cell,

the respective coupling structure is a metal-insulator-metal (MIM) structure, and

the MIM structure is a gold-silicon dioxide-gold structure.

2. An integrated device comprising:

a plurality of reaction cells to house reactants, wherein the plurality of reaction cells are formed on a surface of the integrated device;

at least one waveguide to receive optical energy; and

a plurality of coupling structures optically coupling the at least one waveguide with the plurality of reaction cells, wherein each respective coupling structure in the plurality of coupling structures is formed at or adjacent to a corresponding reaction cell in the plurality of reaction cells, and is configured to provide excitation energy to the corresponding reaction cell in response to the optical energy from a corresponding waveguide in the at least one waveguide, wherein

the respective coupling structure provides plasmonic energy to the corresponding reaction cell,

the respective coupling structure is a metal-insulator-metal (MIM) structure, and

the MIM structure comprises one or more essentially concentric rings, wherein the corresponding reaction cell is positioned in or adjacent to a center of the one or more essentially concentric rings.

3. The integrated device of claim 2 , wherein the corresponding reaction cell is a zero mode waveguide (ZMW).

4. The integrated device of claim 2 , wherein the corresponding waveguide in the at least one waveguide is a planar waveguide.

5. The integrated device of claim 2 , wherein the plasmonic energy provided by the respective coupling structure enhances excitation of one or more fluorophores of a reactant housed in the corresponding reaction cell.

6. The integrated device of claim 2 , wherein the plasmonic energy provided by the respective coupling structure is applied to the corresponding reaction cell in bursts or essentially continuously.

7. The integrated device of claim 2 , wherein the respective coupling structure is configured to generate the plasmonic energy with a wavelength essentially equivalent to a dimension of the corresponding reaction cell.

8. The integrated device of claim 2 , wherein the corresponding reaction cell is defined by an aperture extending through the MIM structure.

9. The integrated device of claim 1 , further comprising:

a plurality of sensor elements in optical communication with the plurality of reaction cells to detect emitted signals from reactants housed in the plurality of reaction cells.

10. The integrated device of claim 1 , wherein the corresponding reaction cell is a zero mode waveguide (ZMW).

11. The integrated device of claim 1 , wherein the corresponding waveguide in the at least one waveguide is a planar waveguide.

12. The integrated device of claim 1 , wherein the plasmonic energy provided by the respective coupling structure enhances excitation of one or more fluorophores of a reactant housed in the corresponding reaction cell.

13. The integrated device of claim 1 , wherein the plasmonic energy provided by the respective coupling structure is applied to the corresponding reaction cell in bursts or essentially continuously.

14. The integrated device of claim 1 , wherein the respective coupling structure is configured to generate the plasmonic energy with a wavelength essentially equivalent to a dimension of the corresponding reaction cell.

15. The integrated device of claim 1 , wherein the corresponding waveguide extends around at least a portion of a circumference of the corresponding reaction cell.

16. The integrated device of claim 2 , further comprising:

a plurality of sensor elements in optical communication with the plurality of reaction cells to detect emitted signals from reactants housed in the plurality of reaction cells.

17. The integrated device of claim 2 , wherein the corresponding waveguide extends around at least a portion of a circumference of the corresponding reaction cell.

18. An integrated device comprising:

a plurality of reaction cells to house reactants, wherein the plurality of reaction cells are formed on a surface of the integrated device;

at least one waveguide to receive optical energy; and

a plurality of coupling structures optically coupling the at least one waveguide with the plurality of reaction cells, wherein each respective coupling structure in the plurality of coupling structures is formed at or adjacent to a corresponding reaction cell in the plurality of reaction cells, and is configured to affect coupling of the optical energy received by the at least one waveguide into the corresponding reaction cell, wherein

the respective coupling structure is a metal-insulator-metal (MIM) structure, and

the MIM structure comprises one or more essentially concentric rings, wherein the corresponding reaction cell is positioned in or adjacent to a center of the one or more essentially concentric rings.

19. The integrated device of claim 18 , further comprising:

a plurality of sensor elements in optical communication with the plurality of reaction cells to detect emitted signals from reactants housed in the plurality of reaction cells.

20. The integrated device of claim 18 , wherein the respective coupling structure is configured to provide plasmonic energy to the corresponding reaction cell in response to the optical energy from a corresponding waveguide in the at least one waveguide.

21. The integrated device of claim 18 , wherein the corresponding reaction cell is defined by an aperture extending through the MIM structure.

22. The integrated device of claim 18 , wherein the corresponding reaction cell is a zero mode waveguide (ZMW).

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jul 28, 2021
From: FEHR, ADRIAN; MCCAFFREY, NATHANIEL JOSEPH; TURNER, STEPHEN
To: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
Reel/Frame 057005/0434 →
Continuity (8)
Continuation 16200096 · Nov 26, 2018
Continuation 14844492 · Sep 3, 2015
Continuation 13895486 · May 16, 2013
Continuation 13031103 · Feb 18, 2011
Provisional Application 61410189 · Nov 4, 2010
Provisional Application 61387916 · Sep 29, 2010
Provisional Application 61306235 · Feb 19, 2010
Related Publication 20210340616A1 · Nov 4, 2021
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