Apparatus and method for performing nucleic acid analysis

Abstract

The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.

1 . An array for the optical analysis of an analyte in a solution comprising:
 a) a transparent substrate having disposed on its surface a transparent layer, the index of refraction of the transparent substrate and the transparent layer selected to provide for total internal reflection when illuminated through the transparent substrate;   b) nanoscale holes disposed through the transparent layer to the surface of the transparent substrate; and   c) a solution comprising an analyte, the analyte disposed on top of the transparent layer and extending into the nanoscale holes, wherein the transparent layer physically prevents the solution from contact with the surface except where the nanoscale holes are disposed, wherein each of the nanoscale holes provides a degree of lateral confinement given by its diameter.   
     
     
         2 . The array of  claim 1 , wherein the transparent layer has an index of refraction nearly identical to that of the solution. 
     
     
         3 . The array of  claim 1 , wherein the transparent layer comprises a polymer. 
     
     
         4 - 5 . (canceled) 
     
     
         6 . The array of  claim 1 , wherein the transparent substrate is a high index transparent substrate. 
     
     
         7 - 33 . (canceled) 
     
     
         34 . An array for the optical analysis of an analyte in a solution comprising:
 a) a substrate comprising arrayed nanoscale optical confinements, each of the arrayed nanoscale optical confinements having an effective observation volume that permits resolution of individual molecules;   b) a solution comprising an analyte, the solution disposed on top of the substrate and extending into the arrayed nanoscale optical confinements; and   c) a waveguide in optical communication with the arrayed nanoscale optical confinements, wherein the waveguide is an optical transmission element that channels the incident light to the arrayed nanoscale optical confinements.   
     
     
         35 . The array of  claim 34 , wherein the analyte is fluorescently labeled. 
     
     
         36 . (canceled) 
     
     
         37 . The array of  claim 34 , wherein each of the arrayed nanoscale optical confinements has an effective observation volume that is less than one nanoliter. 
     
     
         38 . The array of  claim 34 , wherein the waveguide is a planar waveguide. 
     
     
         39 . The array of  claim 34 , wherein the waveguide is an integral part of the substrate. 
     
     
         40 . (canceled) 
     
     
         41 . An analytical system comprising:
 a) a substrate comprising arrayed nanoscale optical confinements, each of the arrayed nanoscale optical confinements having an effective observation volume that permits resolution of individual molecules;   b) a solution comprising an analyte, the solution disposed on top of the substrate and extending into the arrayed nanoscale optical confinements;   c) an excitation source that generates incident light used to optically excite the analyte;   d) a waveguide in optical communication with the arrayed nanoscale optical confinements, wherein the waveguide is an optical transmission element that channels the incident light to the arrayed nanoscale optical confinements; and   e) a photon detector operatively coupled to the arrayed nanoscale optical confinements.   
     
     
         42 . The analytical system of  claim 41 , wherein the analyte is fluorescently labeled. 
     
     
         43 - 44 . (canceled) 
     
     
         45 . The analytical system of  claim 41 , wherein each of the arrayed nanoscale optical confinements have an effective observation volume that is less than one nanoliter. 
     
     
         46 . The analytical system of  claim 41 , wherein the waveguide is a planar waveguide. 
     
     
         47 . The analytical system of  claim 41 , wherein the waveguide is an integral part of the substrate. 
     
     
         48 . (canceled) 
     
     
         49 . The analytical system of  claim 41 , wherein the photon detector detects optical signals emitted from individual molecules of the analyte within the arrayed nanoscale optical confinements. 
     
     
         50 . (canceled) 
     
     
         51 . The analytical system of  claim 41 , further comprising at least one additional optical transmission element selected from the group consisting of diffraction gratings, arrayed waveguide gratings, optic fibers, optical switches, mirrors, lenses, collimators, optical attenuators, polarization filters, wavelength filters, wave-plates, prisms, and delay lines. 
     
     
         52 . A method of optically analyzing an analyte in a solution comprising:
 a) providing a substrate comprising arrayed nanoscale optical confinements, each of the arrayed nanoscale optical confinements having an effective observation volume that permits resolution of individual molecules;   b) disposing a solution comprising an analyte on top of the substrate and into the arrayed nanoscale optical confinements;   c) generating incident light of a wavelength that optically excites the analyte;   d) channeling the incident light to the arrayed nanoscale optical confinements through a waveguide that is in optical communication with the arrayed nanoscale optical confinements; and   e) detecting optical signals emitted from individual molecules of the analyte within the arrayed nanoscale optical confinements.   
     
     
         53 . The method of  claim 52 , wherein the analyte is fluorescently labeled. 
     
     
         54 - 55 . (canceled) 
     
     
         56 . The method of  claim 52 , wherein each of the arrayed nanoscale optical confinements have an effective observation volume that is less than one nanoliter. 
     
     
         57 . The method of  claim 52 , wherein the waveguide is a planar waveguide. 
     
     
         58 . The method of  claim 52 , wherein the waveguide is an integral part of the substrate. 
     
     
         59 . (canceled) 
     
     
         60 . The method of  claim 52 , wherein the detecting is performed using an optical system comprising a photon detector that detects optical signals emitted from individual molecules of the analyte within the arrayed nanoscale optical confinements. 
     
     
         61 . (canceled) 
     
     
         62 . The method of  claim 60 , wherein the optical system further comprises at least one additional optical transmission element selected from the group consisting of diffraction gratings, arrayed waveguide gratings, optic fibers, optical switches, mirrors, lenses, collimators, optical attenuators, polarization filters, wavelength filters, wave-plates, prisms, and delay lines. 
     
     
         63 . The array of  claim 34 , wherein the individual molecules are present at a concentration greater than one micromolar.