Silicon-based photonic crystal fluorescence enhancement and laser line scanning instrument
A silicon-based photonic crystal includes a silicon substrate, a first dielectric with a grating structure formed therein, and a second dielectric with a higher index of refraction that covers at least a portion of the grating structure. The first dielectric can be formed on the silicon substrate, or a Fabry-Perot optical cavity can be formed between the silicon substrate and the first dielectric. An instrument can excite a fluorophore coupled to the photonic crystal by focusing collimated incident light that includes the fluorophore's excitation wavelength to a focal line on the surface of the photonic crystal such that the focal line is substantially parallel to the grating direction and can detect fluorescence radiation emitted by the fluorophore in response to the incident light. To provide for fluorescence enhancement, the excitation wavelength and/or emission wavelength of the fluorophore can couple to an optical resonance of the photonic crystal.
1. A photonic crystal structure, comprising:
a silicon substrate;
a first dielectric having a first index of refraction, wherein the first dielectric has a first surface facing the silicon substrate and a second surface opposite the first surface, wherein the second surface has a grating structure formed therein;
a second dielectric having a second index of refraction that is higher than the first index of refraction, wherein the second dielectric covers at least a portion of the grating structure such that the first and second dielectrics together define a photonic crystal having an optical resonance; and
a Fabry-Perot optical cavity between the photonic crystal and the silicon substrate, wherein the Fabry-Perot optical cavity couples to the optical resonance of the photonic crystal.
2. The photonic crystal structure of claim 1 , wherein the first dielectric comprises silicon oxide.
3. The photonic crystal structure of claim 1 , wherein the second dielectric comprises titanium oxide.
4. The photonic crystal structure of claim 1 , further comprising one or more intermediate layers between the silicon substrate and the first surface of the first dielectric.
5. The photonic crystal structure of claim 4 , wherein the one or more intermediate layers define the Fabry-Perot optical cavity between the photonic crystal and the silicon substrate.
6. The photonic crystal structure of claim 5 , wherein the one or more intermediate layers includes a reflective metal layer on the silicon substrate.
7. The photonic crystal structure of claim 1 , further comprising a fluorophore coupled to the photonic crystal, wherein the fluorophore is configured to emit fluorescence radiation at an emission wavelength at an emission angle in response to receiving excitation radiation at an excitation wavelength at an excitation angle.
8. The photonic crystal structure of claim 7 , wherein the optical resonance of the photonic crystal has a resonance wavelength at the excitation angle that corresponds to the excitation wavelength of the fluorophore.
9. The photonic crystal structure of claim 7 , wherein the optical resonance of the photonic crystal has a resonance wavelength at the emission angle that corresponds to the emission wavelength of the fluorophore.
10. A method, comprising:
exposing a functionalized photonic crystal structure to a sample to provide a sample-exposed photonic crystal structure, wherein the functionalized photonic crystal structure comprises a silicon substrate, a photonic crystal having an optical resonance, a Fabry-Perot optical cavity between the photonic crystal and the silicon substrate, wherein the Fabry-Perot optical cavity couples to the optical resonance of the photonic crystal, and a capture ligand coupled to a surface of the photonic crystal, wherein the capture ligand is configured to bind to a target in the sample to form a fluorescent complex, wherein the fluorescent complex comprises a fluorophore configured to emit fluorescence radiation at an emission wavelength in response to receiving excitation radiation at an excitation wavelength;
exposing the sample-exposed photonic crystal structure to incident light from a light source at an angle of incidence, wherein the incident light includes light at the excitation wavelength; and
detecting, by a detector, fluorescence radiation emitted from the fluorescent complex at an emission angle in response to the incident light from the light source.
11. The method of claim 10 , wherein the capture ligand comprises an antibody or an oligonucleotide.
12. The method of 10 , wherein a plurality of different capture ligands are bound to the surface of the photonic crystal at a plurality of discrete locations such that each capture ligand is configured to bind to a respective target in the sample to form a respective fluorescent complex, further comprising:
sequentially exposing each discrete location in the sample-exposed photonic crystal structure to incident light from the light source at the angle of incidence; and
sequentially detecting, by the detector, fluorescence radiation emitted at the emission angle from each respective fluorescent complex in each discrete location.
13. The method of claim 10 , wherein the optical resonance of the photonic crystal has a resonance wavelength at the angle of incidence that corresponds to the excitation wavelength of the fluorophore.
14. The method of claim 10 , wherein the optical resonance of the photonic crystal has a resonance wavelength at the emission angle that corresponds to the emission wavelength of the fluorophore.
15. The method of claim 10 , wherein the fluorophore is present in the functionalized photonic crystal structure prior to exposing the functionalized photonic crystal structure to the sample.
16. The method of claim 10 , wherein the fluorophore is present in the sample prior to exposing the functionalized photonic crystal structure to the sample.
17. The method of claim 10 , wherein the photonic crystal comprises a grating structure having a grating direction, and wherein the incident light from the light source is focused to a focal line on the surface of the photonic crystal such that the focal line is substantially parallel to the grating direction.
18. The method of claim 17 , wherein the light from the light source is collimated at the focal line in a direction substantially perpendicular to the grating direction.
19. An instrument for exciting a fluorophore coupled to a surface of a photonic crystal having an optical resonance, wherein the fluorophore is configured to emit fluorescence radiation at an emission wavelength in response to receiving excitation radiation at an excitation wavelength, and wherein the photonic crystal comprises a grating structure having a grating direction, the instrument comprising:
a light source, wherein the light source is configured to emit incident light that includes light at the excitation wavelength of the fluorophore;
a collimator for collimating the incident light from the light source to provide collimated incident light;
a focusing system for directing the collimated incident light onto the surface of the photonic crystal at an angle of incidence and for focusing the collimated incident light to a focal line on the surface of the photonic crystal such that the focal line is substantially parallel to the grating direction and the collimated incident light at the focal line is collimated in a direction substantially perpendicular to the grating direction; and
a detection system configured to detect fluorescence radiation emitted by the fluorophore at an emission angle in response to the collimated incident light directed onto the surface of the photonic crystal.
20. The instrument of claim 19 , wherein the optical resonance has a resonance wavelength at the angle of incidence that corresponds to the excitation wavelength of the fluorophore.
21. The instrument of claim 19 , wherein the optical resonance has a resonance wavelength at the emission angle that corresponds to the emission wavelength of the fluorophore.
22. The instrument of claim 19 , wherein the detection system comprises a CCD camera and a filter, wherein the filter is configured to pass light at the emission wavelength and block light at the excitation wavelength.
23. The instrument of claim 19 , wherein the focusing system comprises a cylindrical lens and an objective lens, wherein the cylindrical lens has a cylindrical-lens focus at a location in a focal plane of the objective lens, and wherein the location of the cylindrical-lens focus in the focal plane of the objective lens defines the angle of incidence.
24. The instrument of claim 23 , wherein the objective lens is configured to collect fluorescence radiation emitted from the focal line on the photonic crystal and to direct the collected fluorescence radiation toward the detection system.
25. The instrument of claim 24 , wherein the focusing system comprises a dichroic mirror configured to reflect light at the excitation wavelength and to transmit light at the emission wavelength, and wherein the objective lens is configured to direct the collected fluorescence radiation toward the detection system through the dichroic mirror.
26. The instrument of claim 24 , wherein the fluorophore is coupled to the surface of the photonic crystal at a plurality of discrete locations, and wherein the instrument comprises a movable stage for moving the photonic crystal relative to the objective lens such that each of the discrete locations is exposed to the collimated incident light and the objective lens collects fluorescence radiation emitted from each of the discrete locations and directs the fluorescence radiation collected from each of the discrete locations toward the detection system.