Substrates and optical systems and methods of use thereof
This invention provides analytical devices for use in various applications, including detection of single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates, dielectric omnidirectional reflectors, and optical couplers are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.
1 . An integrated analytical device for detecting single molecules, comprising:
a plurality of nanoholes disposed in a mask layer above a substrate;
an optical grating coupling an optical illumination energy source to the substrate;
a reflector positioned below the substrate; and
an optical detection system positioned to receive optical energy emitted from reaction sites of the nanoholes;
wherein the substrate is a waveguide substrate;
wherein the optical energy comprises a laser beam;
wherein the reflector is a dielectric omnidirectional reflector comprising a stack of dielectric layers;
wherein the reflector reflects illumination from the optical energy source; and
wherein the integrated analytical device is configured to detect single molecules in the reaction sites of the nanoholes.
2 . The analytical device of claim 1 , wherein the optical detection system comprises pixels.
3 . The analytical device of claim 1 or 2 , wherein the portion of the reflector that is positioned between the nanohole and a detector permits passage of optical energy emitted from nanoholes through the reflector to the optical detection system.
4 . The analytical device of claim 1 , further comprising a microlens array that directs light from the reaction sites to the pixels.
5 . The analytical device of claim 1 , wherein the mask layer is a metal.
6 . The analytical device of claim 1 , wherein the integrated analytical device is configured to perform single molecule nucleic acid sequencing.
7 . The analytical device of claim 1 , wherein the integrated analytical device is configured to detect protein interactions.
8 . A method of detecting single molecules, comprising:
a) providing an integrated analytical device comprising: a plurality of nanoholes disposed in a mask layer above a substrate;
an optical coupling an optical illumination energy source to the substrate;
a reflector positioned below the substrate; and
an optical detection system positioned to receive optical energy emitted from reaction sites of the nanoholes;
wherein the substrate is a waveguide substrate;
wherein the optical energy comprises a laser beam;
wherein the reflector is a dielectric omnidirectional reflector comprising a stack of dielectric layers;
wherein the reflector reflects illumination from the optical energy source; and wherein the integrated analytical device is configured to detect single molecules in the reaction sites of the nanoholes;
b) illuminating reaction sites of the nanoholes;
c) detecting, at the optical detection system, light emitted from single molecules of the reaction sites.
9 . The method of claim 8 , wherein the optical detection system comprises pixels.
10 . The method of claim 8 or 9 , wherein the portion of the reflector that is positioned between the nanohole and a detector permits passage of optical energy emitted from nanoholes through the reflector to the optical detection system.
11 . The method of claim 8 , wherein the integrated analytical device further comprises a microlens array that directs light from the reaction sites to the pixels.
12 . The analytical device of claim 1 , wherein the mask layer is a metal.
13 . The analytical device of claim 8 , wherein step c) comprises single molecule nucleic acid sequencing.
14 . The analytical device of claim 8 , wherein step c) comprises detecting protein interactions.