High density array fabrication and readout method for a fiber optic biosensor

Abstract

The invention relates to the fabrication and use of biosensors comprising a plurality of optical fibers each fiber having attached to its “sensor end” biological “binding partners” (molecules that specifically bind other molecules to form a binding complex such as antibody-antigen, lectin-carbohydrate, nucleic acid-nucleic acid, biotin-avidin, etc.). The biosensor preferably bears two or more different species of biological binding partner. The sensor is fabricated by providing a plurality of groups of optical fibers. Each group is treated as a batch to attach a different species of biological binding partner to the sensor ends of the fibers comprising that bundle. Each fiber, or group of fibers within a bundle, may be uniquely identified so that the fibers, or group of fibers, when later combined in an array of different fibers, can be discretely addressed. Fibers or groups of fibers are then selected and discretely separated from different bundles. The discretely separated fibers are then combined at their sensor ends to produce a high density sensor array of fibers capable of assaying simultaneously the binding of components of a test sample to the various binding partners on the different fibers of the sensor array. The transmission ends of the optical fibers are then discretely addressed to detectors—such as a multiplicity of optical sensors. An optical signal, produced by binding of the binding partner to its substrate to form a binding complex, is conducted through the optical fiber or group of fibers to a detector for each discrete test. By examining the addressed transmission ends of fibers, or groups of fibers, the addressed transmission ends can transmit unique patterns assisting in rapid sample identification by the sensor.

What is claimed is:  
     
         1 . A process for constructing a fiber optic bundle for sensing a plurality of biological binding partners within a sample, the process comprising the steps of: 
 providing a plurality of optical fibers with each fiber having a sensor end and a transmission end wherein each fiber has attached to its sensor end a species of biological binding partner;    combining said fibers with differing binding partners to form an optical fiber array wherein said fibers have commonly aligned sensor ends for simultaneous assay of a sample; and,    addressing the transmission end of the combined discrete fibers for interrogation to produce the fiber optic sensor for the sample.    
     
     
         2 . The process of  claim 1 , wherein said providing step comprises: 
 providing a plurality of optical fibers with each fiber having a sensor end and a transmission end;    placing the plurality of optical fibers in a plurality of fiber groups, each fiber group with commonly aligned sensor ends for simultaneous treatment;    providing a plurality of differing batches, each batch comprising a single species of biological binding partner suitable for attachment under treatment to the commonly aligned sensor ends of the optical fibers of a selected group of optical fibers;    placing and treating the commonly aligned sensor ends of differing fiber groups in differing batches with differing biological binding partners to produce a plurality of groups of optical fibers with the sensor ends of the optical fibers of each group having the same species of biological binding partner and the sensor ends of optical fibers of differing groups having differing species of biological binding partners; and    separating fibers from each group of fibers thereby providing a plurality of optical fibers with each fiber having a sensor end and a transmission end wherein each fiber has attached to its sensor end a species of biological binding partner.    
     
     
         3 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 1  wherein: 
 the binding partners are selected from a group consisting of nucleic acid, antibody, peptide, lectin, biotin, and avidin.  
 
     
     
         4 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 1  wherein: 
 the combining separated fibers with differing binding partners with commonly aligned sensor ends includes randomly gathering the sensor ends.  
 
     
     
         5 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 1  wherein: 
 the combining separated fibers with differing binding partners with commonly aligned sensor ends includes assembling said sensor ends to form a tiered sensor face.  
 
     
     
         6 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 1  wherein: 
 the combining separated fibers with differing binding partners with commonly aligned sensor ends includes assembling said sensor ends to form a planer sensor face.  
 
     
     
         7 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 1  wherein: 
 the addressing the transmission end of the recombined discrete fibers for interrogation includes addressing the transmission ends of each of the discrete fibers to an optical array.  
 
     
     
         8 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 1  wherein: 
 transmission ends of the optical fibers of each group having similar binding partners have similar markings for distinguishing the transmission ends corresponding to binding partners.  
 
     
     
         9 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 1  wherein: 
 the providing a plurality of batches of differing binding partners includes batches of nucleic acid binding partners to which nucleic acids in the sample might hybridize.  
 
     
     
         10 . A process for constructing a fiber optic bundle for sensing a plurality of binding partners within a sample according to  claim 9  wherein: 
 the nucleic binding partners each correspond to specific regions on chromosomes.  
 
     
     
         11 . A sensor for detecting a multiplicity of analytes, the sensor comprising in combination: 
 a plurality of fibers, each fiber including a sensot-end and a transmission end;    the sensor end of at least one first fiber having attached a first biological binding partner;    the sensor end of at least one second fiber having attached a second biological binding partner;    a transmission array having first and second positions for addressing the transmission ends of the first and second fibers; and    means for addressing the transmission ends of the first and second fibers to the transmission array.    
     
     
         12 . The sensor of  claim 11 , further comprising an optical interrogation means adjacent the transmission ends for examining the attachment of analytes at the sensor ends of said fibers.  
     
     
         13 . The sensor of  claim 11 , wherein said sensor ends are arranged to form a tiered sensor face.  
     
     
         14 . The sensor of  claim 11 , wherein said first and second binding partners are nucleic acids.  
     
     
         15 . The sensor of  claim 14 , wherein the nucleic acids are mapped to specific regions in human chromosomes.  
     
     
         16 . The sensor of  claim 14 , wherein the nucleic acids are DNA.  
     
     
         17 . The sensor of  claim 14 , wherein the nucleic acids are cDNA.  
     
     
         18 . The sensor of  claim 14 , wherein the target nucleic acids are about 1000 to about 1,000,000 nucleotides in complexity.  
     
     
         19 . The sensor of  claim 11 , wherein said first and second binding partners are antibodies.  
     
     
         20 . A method for comparing copy number of nucleic acid sequences in two or more collections of nucleic acid molecules, said method comprising: 
 (a) providing a biosensor wherein said biosensor comprises a plurality of optical fibers, each fiber including sensor end and a transmission end where the sensor ends of the optical fibers bear target nucleic acids such that the sensor end of at least one first fiber has attached a first target nucleic acid and the sensor end of at least one second fiber has attached a second target nucleic acid;    (b) contacting said biosensor with 
 (i) a first collection of labelled nucleic acid comprising a sequence substantially complementary to a target nucleotide sequence, and  
 (ii) at least a second labelled nucleic acid comprising a sequence complementary to the target nucleotide sequence;  
   wherein the first and second labels are distinguishable from each other; and    (c) detecting the amount of binding of the first and second labelled complementary nucleic acids to the target nucleic acids.    
     
     
         21 . The method of  claim 20 , wherein the target nucleic acids are DNA.  
     
     
         22 . The method of  claim 20 , wherein the target nucleic acids are cDNA.  
     
     
         23 . The method of  claim 20 , wherein the target nucleic acids are RNA.  
     
     
         24 . The method of  claim 20 , wherein the target nucleic acids are mapped to specific regions in human chromosomes.  
     
     
         25 . The method of  claim 20 , wherein the target nucleic acids are about 1000 to about 1,000,000 nucleotides in complexity.  
     
     
         26 . The method of  claim 20 , wherein the complexity of the sequence complementary to the target nucleic acid sequence is less than 1% of the total complexity of the sequences in the sample.  
     
     
         27 . The method of  claim 20 , wherein the first and second labels are fluorescent labels.  
     
     
         28 . The method of  claim 20 , wherein the first labeled nucleic acids comprise mRNA or cDNA from a test cell and the second labeled nucleic acids comprise mRNA are DNA from a reference cell.  
     
     
         29 . The method of  claim 20 , wherein the first labeled nucleic acids are from a test genome and the second labeled nucleic acids are from a normal reference genome.  
     
     
         30 . The method of  claim 29 , wherein the test genome comprises nucleic acids from fetal tissue.  
     
     
         31 . The method of  claim 29 , wherein the test genome comprises nucleic acids from a tumor.  
     
     
         32 . The method of  claim 20 , wherein the first and second collections of nucleic acids are treated to inhibit the binding of repetitive sequences.  
     
     
         33 . The method of  claim 32 , wherein the first and second collections of nucleic acids are mixed with unlabeled blocking nucleic acids comprising repetitive sequences.  
     
     
         34 . A detector for detecting an array of light sources, said detector comprising a multiplicity of simple lenses joined together to form a compound lens wherein each simple lens is positioned such that each light source of said array of light sources is located at the focal point of a single simple lens of said compound lens.  
     
     
         35 . The detector of  claim 34 , further comprising a beam positioned positioned to direct an excitation light through each simple lens of said compound lens.  
     
     
         36 . The detector of  claim 35 , further comprising an excitation light source to provide said excitation light, said excitation light source.