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

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.

What is claimed is: 
     
         1 . An apparatus comprising:
 a plurality of pixels, each pixel comprising:
 a sample well configured to receive a sample; 
 a sensor configured to receive emission light from the sample well; and 
 a lens configured to focus the emission light from the sample well toward the sensor. 
   
     
     
         2 . The apparatus as claimed in  claim 1  wherein the sample well is configured to receive excitation light causing the sample to emit the emission light. 
     
     
         3 . The apparatus of  claim 1 , wherein the lens includes a refractive lens. 
     
     
         4 . The apparatus of  claim 3 , wherein the lens is positioned between the sample well and the sensor. 
     
     
         5 . The apparatus of  claim 4 , wherein the lens is centered between the sample well and the sensor. 
     
     
         6 . The apparatus of  claim 5 , wherein the lens is disposed approximately 5 microns from the sample well. 
     
     
         7 . The apparatus of  claim 3 , wherein the lens has a convex surface facing the sample well and a planar surface facing the sensor. 
     
     
         8 . The apparatus of  claim 1 , further including a lens layer in which the lens is formed. 
     
     
         9 . The apparatus of  claim 8 , further including a layer of dielectric material positioned between the lens layer and the sample well. 
     
     
         10 . The apparatus of  claim 9 , wherein the layer of dielectric material includes silicon oxide and the lens layer includes silicon nitride. 
     
     
         11 . The apparatus of  claim 9 , wherein the layer of dielectric material has a thickness of approximately 5 microns. 
     
     
         12 . A chip comprising:
 an array of sample wells, each of at least some of the sample wells configured to receive a sample which emits emission light upon excitation; and   a plurality of lenses, each of at least some of the lenses configured to direct emission light from a sample well to a corresponding sensor.   
     
     
         13 . A method of forming a chip comprising:
 forming an array of sample wells, each of at least some of the sample wells configured to receive a sample which emits emission light upon excitation; and   forming a plurality of lenses, each of at least some of the lenses configured to direct emission light from a sample well to a corresponding sensor.   
     
     
         14 . The method of  claim 13 , further including forming a lens layer between the sample wells and sensors in which lens layer the lenses are formed. 
     
     
         15 . The method of  claim 14 , further including forming a dielectric layer between the lens layer and sample wells. 
     
     
         16 . The method of  claim 13 , wherein the lenses are formed such that individual lenses align with corresponding individual sample wells. 
     
     
         17 . The method of  claim 13 , wherein forming the plurality of lenses includes forming each of at least some lenses to include a convex surface facing a corresponding sample well. 
     
     
         18 . The method of  claim 13 , wherein forming the plurality of lenses includes forming each of at least some lenses to include a planar surface facing a corresponding sensor. 
     
     
         19 . The method of  claim 13 , wherein forming an array of sample wells includes:
 forming at least one metal layer; and   etching into the metal layer to form the plurality of sample wells.   
     
     
         20 . The method of  claim 19 , wherein the etching includes etching tapered sidewalls of each of at least some of the sample wells.