Optical analyte detection systems and methods of use

Abstract

Various embodiments are drawn to systems and methods for detecting an analyte of interest in a sample including an optical sensor, a capture probe attached to a surface of the optical sensor wherein the capture probe is capable of binding to the analyte to form a duplex or complex, and an antibody capable of binding to the analyte, duplex, or complex. In several embodiments, systems and methods further include a particle attached to the antibody or capable of binding to the antibody. In several embodiments, systems and methods for analyte detection feature one or more of the following: high detection sensitivity and specificity, scalability and multiplex capacity, ability to analyze large analytes, and ability to detect or measure multiple individual binding events in real-time.

1 . A system for detecting a nucleic acid molecule of interest in a sample comprising:
 an optical sensor;   a nucleic acid capture probe attached to a surface of the optical sensor, wherein the capture probe is capable of hybridizing to the nucleic acid molecule of interest to form a duplex; and   an antibody capable of specifically binding to the duplex of the capture probe and nucleic acid molecule of interest,   wherein said optical sensor has an optical property that is altered when said antibody is bound to said duplex such that said optical sensor is configured to sense said antibody combined with said duplex.   
     
     
         2 . The system of  claim 1 , further comprising:
 a detector capable of detecting the optical property that is altered.   
     
     
         3 . (canceled) 
     
     
         4 . The system of  claim 1 , wherein the nucleic acid molecule of interest comprises deoxyribonucleic acid (DNA). 
     
     
         5 . The system of  claim 1 , wherein the nucleic acid molecule of interest comprises ribonucleic acid (RNA). 
     
     
         6 . The system of  claim 4 , wherein the capture probe comprises a DNA oligonucleotide. 
     
     
         7 . The system of  claim 6 , wherein the DNA oligonucleotide is complementary to the nucleic acid of interest. 
     
     
         8 . The system of  claim 6 , wherein the DNA oligonucleotide comprises a modified DNA nucleotide. 
     
     
         9 . The system of  claim 8 , wherein the modified DNA nucleotide comprises a locked nucleic acid (LNA). 
     
     
         10 . The system of  claim 8 , wherein the modified DNA nucleotide comprises a universal base. 
     
     
         11 . The system of  claim 1 , wherein the capture probe comprises an RNA oligonucleotide. 
     
     
         12 . The system of  claim 11 , wherein the RNA oligonucleotide is complementary to the nucleic acid of interest or analyte of interest. 
     
     
         13 . The system of  claim 11 , wherein the RNA oligonucleotide comprises a modified RNA nucleotide. 
     
     
         14 . The system of  claim 13 , wherein the modified RNA nucleotide comprises a locked nucleic acid (LNA). 
     
     
         15 . The system of  claim 14 , wherein the modified RNA nucleotide comprises a universal base. 
     
     
         16 . The system of  claim 1 , wherein the antibody binds to a sequence-independent DNA:RNA duplex and does not bind to the nucleic acid molecule of interest or analyte of interest prior to the formation of the duplex. 
     
     
         17 . The system of  claim 16 , wherein the antibody is S9.6. 
     
     
         18 . (canceled) 
     
     
         19 . (canceled) 
     
     
         20 . The system of  claim 1 , wherein the capture probe is covalently coupled to the surface of the optical sensor or optical ring resonator. 
     
     
         21 . The system of  claim 1 , wherein the optical sensor comprises a waveguide structure. 
     
     
         22 . The system of  claim 21 , wherein the optical sensor has an output portion configured to output an optical signal. 
     
     
         23 . The system of  claim 22 , wherein the optical output yields different outputs when said capture probe binds to the nucleic acid molecule of interest forming said duplex and said antibody binds said duplex, and when said antibody does not bind to said duplex. 
     
     
         24 . The system of  claim 1 , wherein the optical sensor comprises an input and an output portion each comprising portions of a waveguide. 
     
     
         25 . The system of  claim 24 , wherein the optical sensor comprises an input waveguide and an output waveguide having optical coupling region therebetween configured to increase coupling of a wavelength component from said input waveguide to said output waveguide when said capture probe binds to the nucleic acid molecule of interest forming said duplex and said antibody binds to said duplex. 
     
     
         26 . The system of  claim 1 , wherein said optical sensor is integrated on an integrated optical chip comprising optical waveguides. 
     
     
         27 . The system of  claim 1 , wherein the optical sensor comprises a resonator. 
     
     
         28 . The system of  claim 27 , wherein said resonator has a resonant wavelength that shifts when said capture probe binds to the nucleic acid molecule of interest forming said duplex and said antibody binds to said duplex. 
     
     
         29 . The system of  claim 27 , wherein the optical sensor comprises a waveguide structure. 
     
     
         30 . The system of  claim 27 , wherein the optical sensor comprises a ring resonator. 
     
     
         31 . The system of  claim 30 , wherein said ring resonator comprises a waveguide structure. 
     
     
         32 . The system of  claim 1 , wherein the antibody increases the sensitivity of the optical sensor in detecting the nucleic acid molecule of interest when the antibody binds to the duplex. 
     
     
         33 . The system of  claim 1 , wherein the antibody amplifies the optical property that is altered when the antibody binds to the duplex. 
     
     
         34 . A method for detecting a nucleic acid molecule of interest in a sample comprising:
 providing an optical sensor comprising a nucleic acid capture probe attached to a surface of the optical sensor, wherein the capture probe is capable of hybridizing to the nucleic acid molecule of interest to form a duplex;   applying a sample for which the presence or absence of the nucleic acid molecule of interest is to be determined to the optical sensor under conditions in which the nucleic acid molecule of interest, when present, and the capture probe sequence-specifically hybridize to form a duplex;   providing an antibody that specifically binds a duplex of nucleic acid molecules, wherein binding between the antibody and the duplex of the capture probe and nucleic acid molecule of interest alters an optical property of the optical sensor; and   determining the presence or absence of the nucleic acid molecule of interest by detecting the altered optical property of the optical sensor.   
     
     
         35 . The method of  claim 34 , wherein the nucleic acid molecule of interest comprises ribonucleic acid (RNA). 
     
     
         36 . The method of  claim 34 , wherein the optical sensor comprises a ring resonator. 
     
     
         37 . The method of  claim 36 , wherein said ring resonator comprises a waveguide structure. 
     
     
         38 - 87 . (canceled)