Integrated device with external light source for probing detecting and analyzing molecules

• US 9,885,657 B2
• Filed: 08/07/2015
• Issued: 02/06/2018
• Est. Priority Date: 08/08/2014
• Status: Active Grant

• Current Assignee: Quantum-Si Incorporated
• Original Assignee: Quantum-Si Incorporated
• Inventors: Rothberg, Jonathan M., Kabiri, Ali, Sickler, Jason W., Gyarfas, Brett J., Lackey, Jeremy, Schmid, Gerard, West, Lawrence C., Fife, Keith G., Cipriany, Benjamin, Ghasemi, Farshid
• Primary Examiner(s): Ayub, Hina F
• Application Number:
  US14/821,688
• Publication Number:
  US 20160084761A1
• Time in Patent Office: 914 Days
• Field of Search: 356244
• 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 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• CPC Class Codes: G01N 2021/6439 with indicators, stains, dyes, tags, labels, marks
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 2021/6463 Optics
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 21/6408 with measurement of decay time, time resolved 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 21/6454 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 2201/064 Stray light conditioning
• CPC Class Codes: G01N 2201/0696 Pulsed
• CPC Class Codes: G01N 2201/08 Optical fibres; light guides
• CPC Class Codes: G01N 2201/12 Circuits of general importance; Signal processing

Abstract

System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device. One of multiple markers distinguishable by temporal parameters of the emission energy may label the sample and configuration of the sensor within a pixel may allow for detection of a temporal parameter associated with the marker labeling the sample.

Claims

1. An integrated device comprising:

a pixel region comprising;

a plurality of pixels, a pixel of the plurality of pixels having;

a sample well disposed on a substrate surface, wherein the sample well is configured to receive a sample;

at least one sensor configured to receive luminescence from the sample well; and

at least one waveguide for delivering excitation energy to a vicinity of the sample well; and

an excitation source coupling region comprising;

a coupling component including a grating coupler disposed beneath the substrate surface, wherein the grating coupler is configured to receive excitation energy incident on the substrate surface from an external excitation energy source and couple the excitation energy into the at least one waveguide; and

a reflector layer disposed proximate to a side of the grating coupler and positioned to reflect excitation energy passing through the grating coupler towards the grating coupler.

2. The integrated device of claim 1, wherein the sample well is configured to isolate a molecule from a sample containing a plurality of molecules.

3. The integrated device of claim 1, wherein the reflector layer includes at least one hole and the excitation source coupling region further includes at least one monitoring sensor positioned to receive excitation energy through the at least one hole in the reflector layer and measure an intensity of the received excitation energy.

4. The integrated device of claim 3, wherein the intensity of the received excitation energy provides a signal as part of a feedback loop for an alignment process of the excitation energy to the grating coupler.

5. The integrated device of claim 1, wherein the pixel further comprises at least one coupling element between the sample well and the at least one waveguide for coupling excitation energy from the at least one waveguide to the sample well.

6. The integrated device of claim 5, wherein the at least one coupling element is a microcavity.

7. The integrated device of claim 5, wherein the at least one coupling element is a bullseye grating.

8. The integrated device of claim 1, wherein the pixel further comprises a baffle for suppressing excitation energy from being detected by the at least one sensor.

9. The integrated device of claim 1, wherein the pixel region further comprises at least one excitation filter positioned between the at least one waveguide and the at least one sensor for selectively filtering excitation energy while transmitting luminescence energy from the sample well.

10. The integrated device of claim 1, wherein the grating coupler has a width that tapers in the direction of the at least one waveguide.

11. The integrated device of claim 1, wherein the sample well comprises a nanoaperture formed in a metallic material.

12. The integrated device of claim 11, wherein the pixel further comprises a concentric ring grating comprising a plurality of rings formed from the metallic material, wherein the nanoaperture is located within an innermost ring of the plurality of rings.

13. The integrated device of claim 1, wherein the at least one waveguide is configured to provide excitation energy to an excitation region within the sample well, and a sample located within the excitation region emits emission energy in response to excitation energy illuminating the excitation region.

14. The integrated device of claim 1, wherein the at least one waveguide is configured to deliver excitation energy to a vicinity of a sample well for each pixel of a portion of pixels among the plurality of pixels.

15. The integrated device of claim 1, wherein a pixel of the plurality of pixels further comprises at least one excitation-coupling structure configured to couple with the at least one waveguide and direct excitation energy to a vicinity of a sample well.

16. The integrated device of claim 1, wherein a pixel of the plurality of pixels further comprises at least one surface-energy coupling element configured to couple with emission energy emitted by a sample located within a sample well.

17. A method of forming an integrated device comprising:

forming a plurality of sensor regions, wherein a sensor region of the plurality of sensor regions includes at least one sensor;

forming a plurality of sample wells on a substrate surface, wherein a sample well of the plurality of sample wells aligns with a corresponding one of the plurality of sensor regions;

forming at least one waveguide configured to couple excitation energy separate from the plurality of sample wells and direct excitation energy to at least one sample well of the plurality of sample wells;

forming, in a region separate from the plurality of sample wells, a grating coupler configured to receive excitation energy incident on the substrate surface from at least one excitation energy source external to the integrated device and couple the excitation energy to the at least one waveguide; and

forming a reflector layer proximate to a side of the grating coupler and positioned to reflect excitation energy passing through the grating coupler towards the grating coupler.

18. The method of claim 17, wherein the method further comprises:

forming at least one monitoring sensor positioned to receive excitation energy passing through the reflector layer.

19. The method of claim 18, wherein the method further comprises:

forming at least one hole through the reflector layer, wherein the at least one monitoring sensor is positioned to receive excitation energy passing through the at least one hole.

20. The method of claim 18, wherein the at least one monitoring sensor is configured to generate a signal indicative of an alignment of the at least one external excitation source to the grating coupler.