Optical system and assay chip for probing, detecting and analyzing molecules

• US 9,863,880 B2
• Filed: 11/17/2014
• Issued: 01/09/2018
• Est. Priority Date: 11/17/2013
• 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, Cipriany, Benjamin, Jewell, Jack, West, Lawrence, Ferrigno, Michael, Glenn, Paul E., Cohen, Adam E., Bellofiore, Anthony
• Primary Examiner(s): Bhat, Narayan
• Application Number:
  US14/543,867
• Publication Number:
  US 20150177150A1
• Time in Patent Office: 1,149 Days
• CPC Class Codes: B01L 2200/12 Specific details about manufacturing devices
• CPC Class Codes: B01L 2300/0829 Multi-well plates; Microtitration plates
• CPC Class Codes: B01L 2300/0887 Laminated structure
• CPC Class Codes: B01L 2300/0893 having a very large number of wells, microfabricated wells
• CPC Class Codes: B01L 2300/168 Specific optical properties, e.g. reflective coatings
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• 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: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2537/157 A reaction step characterised by the number of molecules incorporated or released
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 2021/6478 Special lenses
• CPC Class Codes: G01N 21/64 Fluorescence; Phosphorescence
• CPC Class Codes: G01N 21/645 Specially adapted constructive features of fluorimeters
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• 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 21/6486 : Measuring fluorescence of biological material, e.g. DNA, RNA, cells G01N21/6428 takes precedence
• CPC Class Codes: G01N 21/7743 : the reagent-coated grating coupling light in or out of the waveguide
• CPC Class Codes: G01N 21/7746 : the waveguide coupled to a cavity resonator
• CPC Class Codes: G01N 2201/02 : Mechanical
• CPC Class Codes: G01N 2201/06113 : Coherent sources; lasers
• CPC Class Codes: G01N 2201/0612 : Laser diodes
• CPC Class Codes: G01N 2201/062 : LED's
• CPC Class Codes: G01N 2201/068 : Optics, miscellaneous
• CPC Class Codes: G01N 2201/125 : Digital circuitry
• CPC Class Codes: Y10T 29/49016 : Antenna or wave energy "plumbing" making

Abstract

Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.

Claims

1. An assay chip comprising:

a sample well configured to receive a sample, which, when excited, emits emission energy;

at least one element that directs the emission energy in a particular direction, wherein the at least one element is selected from the group consisting of a refractive element, a diffractive element, a plasmonic element and a resonator;

a ferromagnetic frame configured to detachably couple to at least one magnetic component on an instrument having a sensor; and

a light path along which the emission energy travels from the sample well and exits a surface of the assay chip opposite to the sample well, wherein the emission energy travels toward the sensor when the ferromagnetic frame is coupled to the instrument.

2. The assay chip of claim 1, wherein the assay chip is configured to be used in only a single biological assay prior to disposal.

3. The assay chip of claim 1, wherein the at least one element comprises at least one lens configured to direct the emission energy towards the sensor.

4. The assay chip of claim 3, wherein the at least one lens is a refractive lens.

5. The assay chip of claim 3, wherein the at least one lens is a diffractive lens.

6. The assay chip of claim 1, wherein the light path comprises at least one antireflection layer configured to reduce the reflection of the emission energy at one or more interfaces of the assay chip.

7. The assay chip of claim 1, wherein the at least one element comprises a concentric ring grating.

8. The assay chip of claim 7, wherein the concentric ring grating is configured to increase the amount of excitation light from an excitation light source that couples into the sample well and excites the sample.

9. The assay chip of claim 8, wherein the concentric ring grating is further configured to direct the emission energy towards the sensor.

10. The assay chip of claim 7, wherein the concentric ring grating is an aperiodic concentric ring grating.

11. The assay chip of claim 1, wherein the at least one element comprises a dielectric resonator antenna.

12. An instrument configured to interface with an assay chip comprising a plurality of sample wells, each sample well of the plurality of sample wells configured to receive a sample, the instrument comprising:

a housing configured to detachably couple to a frame of the assay chip, wherein the housing has an opening, and the assay chip is configured to align with the opening when the frame is coupled to the housing;

at least one magnetic component positioned proximate to the opening and configured to position the assay chip in alignment with the opening when the frame is coupled to the housing;

at least one excitation light source configured to excite the sample of at least a portion of the plurality of sample wells;

a plurality of sensors, each sensor of the plurality of sensors corresponding to a sample well of the plurality of sample wells, wherein each sensor of the plurality of sensors is configured to detect emission energy from the sample in a respective sample well; and

at least one optical element configured to direct the emission energy from each sample well of the plurality of sample wells towards a respective sensor of the plurality of sensors.

13. The instrument of claim 12, further comprising:

a polychroic mirror configured to reflect excitation light from the at least one excitation light source towards the assay chip and transmit the emission energy from the plurality of sample wells towards the plurality of sensors.

14. The instrument of claim 12, wherein the at least one optical element comprises a relay lens.

15. The instrument of claim 12, wherein the at least one excitation light source comprises a plurality of light sources, each light source of the plurality of light sources emitting excitation light at one or more of a plurality of wavelengths.

16. The instrument of claim 15, further comprising a wavelength combiner for spatially overlapping the light emitted from each of the plurality of light sources.

17. The instrument of claim 12, wherein the at least one excitation light source comprises a pulsed light source.

18. The instrument of claim 12, further comprising at least one spectral filter configured to transmit the emission energy and absorb and/or reflect excitation light from the at least one excitation light source.

19. The instrument of claim 12, further comprising at least one spectral sorting element for spatially separating emission energy of a first wavelength from emission energy of a second wavelength.

20. The instrument of claim 19, wherein the at least one spectral sorting element comprises a diffractive optical element.

21. The instrument of claim 20, wherein the diffractive optical element both chromatically disperses the emission energy and focuses the emission energy.

22. The instrument of claim 20, wherein the diffractive optical element comprises an offset Fresnel lens.

23. The instrument of claim 19, wherein the at least one spectral sorting element is a light-filtering element.

24. The instrument of claim 12, further comprising a control system that is programmed to (i) direct excitation light to the plurality of sample wells, (ii) detect signals at the plurality of sensors from the plurality of sample wells, and (iii) use a spatial distribution pattern of the signals to identify the sample and/or a subunit of the sample.

25. An apparatus comprising:

an assay chip comprising a frame and a plurality of pixels, each of the plurality of pixels comprising;

a sample well configured to receive a sample, which, when excited, emits emission energy;

at least one element for directing the emission energy in a particular direction, wherein the at least one element is selected from the group consisting of a refractive element, a diffractive element, a plasmonic element and a resonator; and

a light path along which the emission energy travels from the sample well and exits a surface of the assay chip opposite to the sample well; and

an instrument configured to interface with the assay chip, the instrument comprising;

a housing configured to detachably couple to the frame, wherein the housing has an opening, and the assay chip is configured to align with the opening when the frame is coupled to the housing;

at least one magnetic component positioned proximate to the opening and configured to position the assay chip in alignment with the opening when the frame is coupled to the housing;

at least one excitation light source configured to excite the sample in each sample well;

a plurality of sensors, each sensor of the plurality of sensors corresponding to a respective sample well, wherein each sensor of the plurality of sensors is configured to detect emission energy from the sample in the respective sample well; and

at least one optical element configured to direct the emission energy, when the frame is coupled to the instrument, from each sample well towards a respective sensor of the plurality of sensors.

26. The apparatus of claim 25, wherein, when the assay chip is connected to the instrument, the optical distance between a sample well of the plurality of sample wells and the corresponding sensor of the plurality of sensors is less than 30 cm.

27. The apparatus of claim 25, wherein, when the assay chip is connected to the instrument, the optical distance between a sample well of the plurality of sample wells and the corresponding sensor of the plurality of sensors is less than 5 cm.

28. The apparatus of claim 25, wherein, when the assay chip is connected to the instrument, the optical distance between a sample well of the plurality of sample wells and the corresponding sensor of the plurality of sensors is less than 1 cm.

29. The apparatus of claim 25, wherein the instrument is portable.

30. The apparatus of claim 25, wherein:

each sample comprises a luminescent tag that emits the emission energy within one wavelength band of a plurality of wavelength bands; and

each sensor of the plurality of sensors comprises a sub-sensor configured to detect the emission energy at each of the plurality of wavelength bands.

31. The apparatus of claim 30, wherein each sensor of the plurality of sensors comprises at least two sub-sensors.

32. The apparatus of claim 31, wherein each sensor of the plurality of sensors comprises at least four sub-sensors.

33. The apparatus of claim 30, wherein the instrument further comprises at least one wavelength dependent element that directs emission energy of a first wavelength towards a first sub-sensor of the at least two sub-sensors and directs emission energy of a second wavelength towards a second sub-sensor of the at least two sub-sensors.

34. The apparatus of claim 33, wherein the at least one wavelength dependent element is a diffractive optical element.

35. The apparatus of claim 33, wherein the at least one wavelength dependent element is a spectral filter.

36. The apparatus of claim 30, wherein:

a first luminescent tag associated with a first sample is excited by light of a first wavelength but is not excited by light of a second wavelength; and

a second luminescent tag associated with a second sample is excited by light of the second wavelength but is not excited by light of the first wavelength.

37. The apparatus of claim 25, wherein the at least one excitation source emits pulsed light.