Method for concurrently processing multiple biological chip assays

Abstract

Methods for concurrently processing multiple biological chip assays by providing a biological chip plate comprising a plurality of test wells, each test well having a biological chip having a molecular probe array; introducing samples into the test wells; subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a biological chip plate reader that interrogates the probe arrays to detect any reactions between target molecules and probes.

What is claimed is:  
     
         1 . A method for concurrently processing multiple biological chip assays comprising the steps of: 
 (a) providing a biological chip plate comprising a plurality of test wells, each test well defining a space for the introduction of a sample, and comprising a biological array comprising a substrate and a surface to which an array of probes is attached, produced by light-directed probe synthesis said probes exposed to the space;    (b) manipulating the biological chip plate with a fluid handling device that automatically performs steps to carry out reactions between target molecules in a test sample and probes in a plurality of the test wells; and    (c) interrogating the probe arrays of the biological chip plate with a biological chip plate reader to detect reactions between target molecules and probes in a plurality of the test wells to generate assay results.    
     
     
         2 . The method of  claim 1  further comprising the step of processing the results with a computer.  
     
     
         3 . The method of  claim 2  wherein the results are processed into an image with the intensity in each region of the image varying according to the binding affinity between targets and probes.  
     
     
         4 . The method of  claim 1  wherein the probes are DNA or RNA molecules.  
     
     
         5 . The method of  claim 4  wherein 
 (a) the reactions are hybridization of target molecules to probes; and  
 (b) the results provide information regarding the nucleotide sequence of the target molecule.  
 
     
     
         6 . The method of  claim 5  wherein the assay is the detection or identification of a pathogenic organism.  
     
     
         7 . The method of  claim 6  wherein the pathogenic organism is HIV.  
     
     
         8 . The method of  claim 5  wherein the assay is the detection or identification of a human nucleic acid.  
     
     
         9 . The method of  claim 8  wherein the assay is the detection of a human gene variant.  
     
     
         10 . The method of  claim 8  wherein the human gene variant indicates the existence of, or predisposition to cystic fibrosis, diabetes, muscular dystrophy or cancer.  
     
     
         11 . The method of  claim 1  wherein the assay is the identification of a probe in a library that binds to a receptor and the reaction is the binding of a target molecule to a peptide probe.  
     
     
         12 . The method of  claim 1  wherein the reaction is the catalytic transformation of a probe molecule by a target catalyst.  
     
     
         13 . The method of  claim 1  further comprising controlling the temperature of the samples in the test wells and adding or removing fluids from the test wells at predetermined times.  
     
     
         14 . The method of  claim 1  wherein the target molecule is tagged with a fluorescent marker, a chemiluminescent marker, a light scattering marker or a radioactive marker.  
     
     
         15 . The method of  claim 14  wherein the marker is a fluorescent marker selected from the group consisting of fluorescein, rhodamine, or cyanine.  
     
     
         16 . The method of  claim 1  wherein the fluid handling device and the biological chip plate reader comprise 
 (a) a confocal detection device having a monochromatic or polychromatic light source;  
 (b) optics for directing an excitation light from the light source at the substrate;  
 (c) a temperature controller for controlling temperature of the substrate during a reaction; and  
 (d) a detector for detecting fluorescence emitted by the targets in response to the excitation light.  
 
     
     
         17 . The method of  claim 1  wherein the manipulating step comprises robotically controlling pipets for adding or removing fluids from the test wells at predetermined times.  
     
     
         18 . The method of  claim 1  wherein the interrogating step comprises detecting fluorescent emissions from the plate with a photomultiplier tube.  
     
     
         19 . The method of  claim 1  wherein the interrogating step comprises focusing the excitation light to a point on the plate and determining the region the fluorescence originated.  
     
     
         20 . The method of  claim 16  wherein the target is tagged with a fluorescent marker and the biological chip plate reader comprises a CCD array.  
     
     
         21 . The method of  claim 1  wherein the biological arrays each have at least about 2500 probe sites.  
     
     
         22 . The method of  claim 1  wherein the biological arrays each have at least about 50,000 probe sites.  
     
     
         23 . The method of  claim 1  wherein each test well comprises an individual probe array.  
     
     
         24 . The method of  claim 1  wherein said chip plate is made by the steps of mating a wafer to an array of open ended wells.  
     
     
         25 . The method of  claim 5 , wherein the samples are from a plurality of patients.  
     
     
         26 . The method of  claim 25  further comprising the step of using information from the results to determine which of the patients exhibit a genetic disease or characteristic.  
     
     
         27 . The method as recited in  claim 1  wherein the interrogating step comprises the steps of: 
 (a) directing excitation light through a bottom surface of said plate; and  
 (b) detecting where targets bound on said probe arrays.  
 
     
     
         28 . The method as recited in  claim 1  wherein said arrays of probes are made by repeating the steps of: 
 (a) selectively directing light at said surface to remove photoremovable protecting groups; and  
 (b) selectively coupling monomers to said surface.  
 
     
     
         29 . The method of  claim 1  wherein the interrogating step comprises determining the on- or off-rates of binding between target molecules in a sample and probes.  
     
     
         30 . A system for concurrently processing multiple biological chip assays comprising: 
 (a) a biological chip plate comprising a plurality of test wells, each test well defining a space for the introduction of a sample, and comprising a biological array comprising a substrate and a surface to which an array of at least 100 probes at known sites is attached, said probes exposed to the space;    (b) a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes in a plurality of the test wells; and    (d) a biological chip plate reader that interrogates the probe arrays to detect any reactions between target molecules and probes in a plurality of the test wells to produce assay results.    
     
     
         31 . The system of  claim 30  further comprising a computer comprising a program for processing the assay results.  
     
     
         32 . The system of  claim 30  wherein the probes are DNA or RNA molecules.  
     
     
         33 . The system of  claim 30  wherein the fluid handling device and the biological chip plate reader comprise 
 (a) a confocal detection device having a monochromatic or polychromatic light source;  
 (b) means for directing an excitation light from the light source at the substrate;  
 (c) means for controlling temperature of the substrate during a reaction; and  
 (d) means for detecting fluorescence emitted by the targets in response to the excitation light.  
 
     
     
         34 . The system of  claim 33  wherein the fluid handling device comprises 
 robotically controlled pipets for adding or removing fluids from the test wells at predetermined times; and wherein 
 (a) the means for detecting the fluorescent emissions from the substrate comprise a photomultiplier tube;  
 (b) the means for focusing the excitation light to a point on the substrate and determining the region the fluorescence originated from comprise an x-y-z translation table; and  
 (c) wherein translation of the x-y-z table, temperature control and data collection are managed and recorded by a digital computer.  
 
 
     
     
         35 . The system of  claim 33  wherein the means for directing excitation light and means for detecting are arranged to illuminate and read the test wells through a bottom side of the test wells.  
     
     
         36 . The system of  claim 30  wherein the biological chip plate reader comprises a line scanner.  
     
     
         37 . The system of  claim 30  wherein the biological chip plate reader comprises a CCD array.  
     
     
         38 . The system of  claim 30  wherein the biological chips have at least about 2500 probe sites.  
     
     
         39 . The system of  claim 30  wherein the biological chips have at least about 50,000 sites.  
     
     
         40 . The system of  claim 30  wherein the biological chip plate comprises about 96 test wells.  
     
     
         41 . A biological chip plate comprising a plurality of test wells, each test well defining a space for the introduction of a sample, and each test well comprising a biological chip produced by light-directed probe synthesis comprising a substrate and a surface to which an array of at least  100  probes are attached, the probes being exposed to the space.  
     
     
         42 . The biological chip plate of  claim 41  wherein the substrate comprises functionalized glass or silica comprising Si, Ge, GaAs, GaP, SiO 2 , SiN 4  or modified silicon.  
     
     
         43 . The biological chip plate of  claim 41  wherein the surface comprises polymers, plastics, resins, polysaccharides, silica or silica-based materials, carbon, metals, inorganic glasses, membranes, polymerized Langmuir Blodgett film, functionalized glass, (poly)tetrafluoro-ethylene, (poly)vinylidenedifluoride, polystyrene or polycarbonate.  
     
     
         44 . The biological chip plate of  claim 41  comprising a body having test wells, wherein each test well comprises an individual biological chip.  
     
     
         45 . The biological plate of  claim 44  wherein the body comprises (poly)tetrafluoroethylene, (poly)vinylidenedi-fluoride, polypropylene, polystyrene, polycarbonate, or combinations thereof.  
     
     
         46 . The biological chip plate of  claim 41  comprising a wafer and a body, the wafer comprising a plurality of biological chips and the body comprising a plurality of channels, wherein the body is attached to the surface of the wafer so that a plurality of the channels each cover an array of probes and the wafer closes one end of a plurality of the channels, thereby forming the test wells.  
     
     
         47 . The biological plate of  claim 46  wherein the body comprises (poly)tetrafluoroethylene, (poly)vinylidenedi-fluoride, polypropylene, polystyrene, polycarbonate, or combinations thereof.  
     
     
         48 . The biological chip plate of  claim 41  comprising a wafer having a plurality of probe arrays and a material resistant to the flow of a liquid sample that surrounds each probe array.  
     
     
         49 . The biological chip of  claim 48  wherein the material is a hydrophobic material.  
     
     
         50 . The biological chip plate of  claim 41  comprising  96  wells arranged in  8  rows and  12  columns.  
     
     
         51 . The biological chip plate of  claim 41  wherein the probes are DNA or RNA molecules.  
     
     
         52 . The biological chip plate of  claim 51  wherein the DNA or RNA molecules comprise sequences directed to pathogenic organisms.  
     
     
         53 . The biological chip plate of  claim 52  wherein the pathogenic organism is HIV.  
     
     
         54 . The biological chip plate of  claim 51  wherein the nucleic acids comprise sequences directed to human DNA.  
     
     
         55 . The biological chip plate of  claim 52  wherein the sequences are directed to a human gene variant that indicates the existence of or predisposition to a genetic disease.  
     
     
         56 . The biological chip plate of  claim 53  wherein the disease is cystic fibrosis, diabetes, muscular dystrophy or cancer.  
     
     
         57 . The biological chip plate of  claim 41  wherein the array of probes in each test well is the same.  
     
     
         58 . The biological chip plate of  claim 41  wherein the test wells are arranged in rows and columns and the rows contain biological chips with the same probe array and the columns contain biological chips with a different probe array.  
     
     
         59 . The biological chip plate of  claim 41  wherein the probe arrays comprise at least 1000 features.  
     
     
         60 . The biological chip plate of  claim 41  wherein the probe arrays comprise at least 10,000 features.  
     
     
         61 . The biological chip plate of  claim 41  wherein the probe arrays comprise at least 100,000 features.  
     
     
         62 . The biological chip plate of  claim 41  wherein the probe arrays comprise at least  1 , 000 , 000  features.  
     
     
         63 . A method for making a biological chip plate comprising the steps of providing a wafer and a body, the wafer comprising a substrate having a surface to which is attached a plurality of arrays of probes, and the body comprising a plurality of channels; and attaching the body to the surface of the wafer whereby a plurality of the channels each cover an array of probes and the wafer closes one end of the plurality of channels, thereby forming test wells defining spaces for receiving samples.  
     
     
         64 . The method of  claim 63  wherein the probes are DNA or RNA molecules.  
     
     
         65 . A method for making a biological chip plate comprising the steps of: 
 (a) providing a body comprising a plurality of wells defining spaces;    (b) providing a plurality of biological arrays comprising a substrate having a surface to which is attached the plurality of probe arrays;    (c) attaching the substrate to the wells so that the probes are exposed to the spaces.    
     
     
         66 . The method of  claim 65  wherein the probes are DNA or RNA molecules.  
     
     
         67 . A method for making a biological chip plate comprising the steps of providing a wafer having a plurality of probe arrays; and applying a material resistant to the flow of a liquid sample so as to surround the probe arrays, thereby creating test wells.  
     
     
         68 . The method of  claim 67  wherein the probes are DNA or RNA molecules.  
     
     
         69 . A wafer comprising a substrate and a surface to which are attached a plurality of probe arrays, wherein the probe arrays are arranged on the wafer surface in rows and columns, wherein the probe arrays in each row are the same and the probe arrays in each column are different.  
     
     
         70 . The wafer of  claim 69  wherein the probes are DNA or RNA molecules.  
     
     
         71 . The wafer of claim  70  wherein the DNA or RNA molecules comprise sequences of HIV.  
     
     
         72 . The wafer of claim  70  wherein the probe arrays in the columns comprise sequences for screening a plurality of genetic diseases.  
     
     
         73 . The wafer of claim  72  wherein the genetic diseases comprise cystic fibrosis, diabetes, muscular dystrophy or cancer.