Analytical biochemistry system with robotically carried bioarray

Abstract

An analytical biochemistry system featuring a substrate with reactants immobilized thereon at fixed, known locations, a holder supporting the substrate and a manipulator for transporting the holder to a fixed sample and to an inspection station. The reactants are binding agents for a target biomolecule in a sample which forms a bound substance having a detectable characteristic. The holder may be a standard pipettor, optionally carried by a robot arm or hand as the manipulator to contact the sample for detection of the presence of target biomolecules within the sample. In one embodiment, the holder is a pipette tip within which the substrate is housed, or it may be a pipette adapter which bears the substrate and fits within the sample wells of a standard microtiter plate.

1 . A system for detecting the presence of a target biomolecule within a sample comprising: 
 a support surface treated with distinct reactants immobilized thereon in a spaced-apart relation, forming a substrate having a plurality of spaced-apart active sites, at least one of the reactants being reactive with a target biomolecule to form a bound complex having a detectable characteristic,    holder means for supporting the substrate,    an inspection station having means for probing the spaced-apart active sites of the substrate for said detectable characteristic of the sample, and    manipulator means for bringing the holder means into contact with the sample and into said inspection station.    
     
     
         2 - 76 . (canceled)  
     
     
         77 . An apparatus for conducting chemical reactions, said apparatus comprising: (a) a plurality of wells in a housing and (b) a channel in said housing, said channel surrounding said plurality of wells and adapted for being filled with an amount of a fluid to form a convex meniscus extending above the top of said channel.  
     
     
         78 . An apparatus according to  claim 77  wherein said plurality of wells is in the form of a pattern in said housing.  
     
     
         79 . An apparatus according to  claim 77  wherein each of said wells has variable depth.  
     
     
         80 . An apparatus according to  claim 79  wherein each of said wells has a fluid circulation mechanism associated therewith.  
     
     
         81 . An apparatus according to  claim 80  wherein said fluid circulation mechanism comprises a member selected from the group consisting of sources for generating a thermal gradient causing convective flow and sources of mechanical energy.  
     
     
         82 . An apparatus according to  claim 81  wherein said member is a source for generating a thermal gradient selected from the group consisting of electrical current sources, infrared radiation sources, radio frequency sources, electrical resistance heaters, and semiconductor junction heaters, and Peltier cooling devices or said member is a source of mechanical energy selected from the group consisting of electric pulses, audio mechanical pulses, sub-audio mechanical impulses, vibration sources, ultrasonic pulses, and continuous wave acoustic sources.  
     
     
         83 . An apparatus according to  claim 77  wherein the surface properties surrounding each of said wells is different than the surface properties of said wells.  
     
     
         84 . An apparatus according to  claim 77  wherein each of said wells has a groove around its perimeter.  
     
     
         85 . A method for conducting chemical reactions, said method comprising: (a) placing one or more liquid samples in separate wells in a housing surface comprising a plurality of said wells wherein the volume of said liquid sample in each of said wells is sufficient to form a convex meniscus at the surface of each of said wells, and (b) contacting said liquid samples with a plurality of arrays of chemical compounds wherein each of said arrays corresponds to a respective well in said housing.  
     
     
         86 . A method according to  claim 85  wherein said liquid samples are contacted with a substrate surface having a plurality of arrays of chemical compounds arranged on said substrate surface wherein each of said arrays corresponds to a respective well in said housing and wherein said substrate surface compresses each convex meniscus without cross-contact between adjacent liquid samples.  
     
     
         87 . A method according to  claim 86  further comprising, during said contacting, forming a seal between said substrate surface and said housing surface around the perimeter of said wells.  
     
     
         88 . A method according to  claim 87  wherein said seal is selected from the group consisting of fluid seals and seals is formed by placing a liquid in a channel in said housing surface surrounding said wells prior to contacting said substrate surface with said housing surface wherein the amount of said liquid is sufficient to form a convex meniscus.  
     
     
         89 . A method according to  claim 86  wherein said plurality of wells is in the form of a pattern in said housing.  
     
     
         90 . A method according to  claim 86  further comprising circulating said liquid sample in each of said wells.  
     
     
         91 . A method according to  claim 90  wherein the bottom of said wells is slanted and said method further comprises a step generating a thermal gradient causing convective flow in said liquid samples or a step of applying mechanical energy to said liquid samples sufficient to cause circulation therein.  
     
     
         92 . A method according to  claim 91  wherein said step is generating a thermal gradient causing convective flow selected from the group of steps consisting of (i) applying heat to said liquid samples sufficient to cause circulation in said samples from a heat source selected from the group consisting of electrical current sources, infrared radiation sources, radio frequency sources, electrical resistance heaters, and semiconductor junction heaters, and (ii) cooling said samples by means of a Peltier cooling device sufficient to cause circulating in said liquid samples or said step is applying mechanical energy selected from the group of steps consisting of (i) applying an electrical pulse to said liquid samples sufficient to cause circulating in said liquid samples, (ii) applying an audio or sub-audio mechanical impulse or vibration to said liquid samples sufficient to cause circulating in said liquid samples, and (iii) applying an ultrasonic pulse or continuous wave acoustic signal to said liquid samples sufficient to cause circulating in said liquid samples.  
     
     
         93 . A method according to  claim 86  wherein the surface properties surrounding each of said wells is different than the surface properties of said wells.  
     
     
         94 . A method according to  claim 86  wherein each of said wells has a groove around its perimeter.  
     
     
         95 . A method according to  claim 86  wherein said chemical reactions involve biopolymers.  
     
     
         96 . A method according to  claim 86  further comprising reading the arrays.  
     
     
         97 . A method according to  claim 96  comprising forwarding data representing a result obtained from reading one of the arrays.  
     
     
         98 . A method according to  claim 97  wherein the data is transmitted to a remote location.  
     
     
         99 . A method according to  claim 97  comprising receiving data representing a result of an interrogation obtained by reading one of the arrays.  
     
     
         100 . A method of testing multiple liquid samples with multiple biopolymer arrays, said method comprising: (a) placing each of a multiple liquid samples in all or less than all separate wells in a housing surface comprising a plurality of said wells wherein the volume of said liquid sample in each of said wells is sufficient to form a convex meniscus at the surface of each of said wells, wherein the bottom of said wells is slanted, (b) placing a liquid in a channel in said housing surface surrounding said wells wherein the amount of said liquid is sufficient to form a convex meniscus, (c) contacting said liquid samples with a substrate surface having multiple biopolymer arrays arranged on said substrate surface wherein each of said arrays corresponds to a respective well in said housing and wherein said substrate surface compresses each convex meniscus without cross-contact between adjacent liquid samples and wherein forming a seal between said substrate surface and said housing surface around the perimeter of said wells, (d) causing circulation in said liquid samples, and (e) observing said substrate surface for the presence of reactions between said biopolymer arrays and said liquid samples.  
     
     
         101 . A method according to  claim 100  wherein said plurality of wells is in the form of a pattern in said housing.  
     
     
         102 . A method according to  claim 100  wherein said circulation is caused by generating a thermal gradient causing convective flow in said liquid samples or by applying mechanical energy to said liquid samples sufficient to cause circulation therein.  
     
     
         103 . A method according to  claim 102  wherein said circulation is caused by generating a thermal gradient causing convective flow selected from the group of steps consisting of (i) applying heat to said liquid samples sufficient to cause circulation in said samples from a heat source selected from the group consisting of electrical current sources, infrared radiation sources, radio frequency sources, electrical resistance heaters, and semiconductor junction heaters, and (ii) cooling said samples by means of a Peltier cooling device sufficient to cause circulating in said liquid samples or said circulation is caused applying mechanical energy selected from the group of steps consisting of (i) applying an electrical pulse to said liquid samples sufficient to cause circulating in said liquid samples, (ii) applying an audio or sub-audio mechanical impulse or vibration to said liquid samples sufficient to cause circulating in said liquid samples, and (iii) applying an ultrasonic pulse or continuous wave acoustic signal to said liquid samples sufficient to cause circulating in said liquid samples.  
     
     
         104 . A method according to  claim 100  wherein the surface properties surrounding each of said wells is different than the surface properties of said wells.  
     
     
         105 . A method according to  claim 100  wherein each of said wells has a groove around its perimeter.  
     
     
         106 . A method according to  claim 100  wherein said biopolymers are polynucleotides or polypeptides.  
     
     
         107 . A kit for analyzing multiple biopolymer arrays on the surface of a substrate, said kit comprising in packaged combination: (a) an apparatus for conducting chemical reactions, said apparatus comprising: (i) a plurality of wells in a housing and (ii) a channel in said housing, said channel surrounding said plurality of wells and adapted for being filled with an amount of a fluid to form a convex meniscus extending above the top of said channel, and (b) a substrate having on a surface thereof a plurality of biopolymer arrays.  
     
     
         108 . A method for conducting chemical reactions, said method comprising: (a) placing one or more liquid samples in separate wells in a housing surface comprising a plurality of said wells wherein each of the wells has a depth which varies within the well, and (b) contacting said liquid samples with a plurality of arrays of chemical compounds wherein each of said arrays corresponds to a respective well in said housing.  
     
     
         109 . A method according to  claim 108  wherein said liquid samples are contacted with a substrate surface placed over well openings, and which surface has the plurality of arrays of chemical compounds arranged on said substrate surface.  
     
     
         110 . An integrated microfluidic array device comprising: a microfluidic component having a microfluidic feature for carrying a fluid of interest; and an array component comprising a flexible array substrate supporting an addressable collection of probes, said array component in operable association with said microfluidic feature of the microfluidic component for analyzing said fluid of interest.  
     
     
         111 . The integrated microfluidic array device of  claim 110  wherein said flexible any substrate comprises a flexible base supporting, in order, a reflective layer, a transparent layer, and the addressable collection of probes.  
     
     
         112 . The integrated microfluidic array device of  claim 110  wherein said flexible array substrate further comprises a flexible support supporting the flexible base.  
     
     
         113 . The integrated microfluidic array device of  claim 110  wherein the microfluidic component includes an identifier.  
     
     
         114 . The integrated microfluidic array device of  claim 110  wherein the integrated microfluidic array device is flexible.  
     
     
         115 . The integrated microfluidic array device of  claim 110  wherein the integrated microfluidic array device is rigid.  
     
     
         116 . The integrated microfluidic array device of  claim 110 , wherein said microfluidic component further comprises a reservoir for holding one of a washing buffer, a sample fluid, or a reagent solution, the reservoir in fluid communication with the microfluidic feature.  
     
     
         117 . The integrated microfluidic array device of  claim 110 , wherein said microfluidic component further comprises a valve for controlling fluid flow, the valve in operable relation to the microfluidic feature.  
     
     
         118 . The integrated microfluidic array device of  claim 110  wherein said flexible array substrate comprises a polymer material selected from the group consisting of polyacrylamide, polyetheretherketone, polyacrylate, polymethacrylate, polyesters, polyolefins, polyethylene, polytetrafluoroethylene, polypropylene, poly (4-methylbutene), polystyrene, poly(ethylene terephthalate), nitrocellulose, cellulose acetate, poly (vinyl chloride), polyamides, nylon, poly(vinyl butyrate), cross-linked dextran, and agarose.  
     
     
         119 . The integrated microfluidic array device of  claim 110  wherein said microfluidic component and said array component are modular.  
     
     
         120 . The integrated microfluidic array device of  claim 110  wherein said microfluidic feature is a microfluidic sipper structure.  
     
     
         121 . The integrated microfluidic array device of  claim 110 , wherein said microfluidic feature is adapted to perform at least one of a reaction, concentration, or separation process.  
     
     
         122 . The integrated microfluidic device of  claim 110  wherein the microfluidic component includes a chamber in fluid communication with the microfluidic feature, the flexible array substrate disposed within the chamber.  
     
     
         123 . The integrated microfluidic array device of  claim 110  further comprising a chamber defined in part by the flexible array substrate, the chamber in fluid communication with the microfluidic feature.  
     
     
         124 . The integrated microfluidic array device of  claim 110  wherein the array component comprises a plurality of addressable collections of probes, each addressable collection of probes associated with its own separate chamber defined in pan by the array substrate.  
     
     
         125 . The integrated microfluidic array device of  claim 110  wherein more than one array component is joined to the microfluidic component.  
     
     
         126 . The integrated microfluidic array device of  claim 110  wherein more than one microfluidic component is joined to the array component.  
     
     
         127 . The integrated microfluidic array device of  claim 110 , the array component further comprising an interface surface and the microfluidic component further comprising a mating surface, wherein the interface surface and the mating surface are adapted to fit together to form a fluid tight seal when the army component is in operable association with the microfluidic component.  
     
     
         128 . The integrated microfluidic device of  claim 127  wherein the array component is bonded to the microfluidic component using an adhesive.  
     
     
         129 . The integrated microfluidic device of  claim 127  wherein the array component is joined to the microfluidic component using ultrasonic welding.  
     
     
         130 . The integrated microfluidic array device of  claim 110 , wherein said microfluidic component is adapted for interfacing to a standard multi-well plate.  
     
     
         131 . The integrated microfluidic array device of  claim 110  further comprising fiducial marks supported on the flexible array substrate.  
     
     
         132 . The integrated microfluidic array device of  claim 110  wherein the flexible array substrate has a thickness of less than about 800 microns.  
     
     
         133 . A method of producing an integrated microfluidic array device comprising: a) forming a plurality of arrays by fabricating a plurality of addressable collections of probes on a flexible array substrate; b) forming a microfluidic component having a microfluidic feature; and c) placing at least one of said arrays in fluid communication with said microfluidic feature of said microfluidic component.  
     
     
         134 . The method of  claim 133 , further comprising, before step c), cutting the flexible array substrate to provide said at least one of said arrays for step c).  
     
     
         135 . A method of performing a hybridization assay on a sample comprising: a) obtaining an integrated microfluidic array device comprising a microfluidic component having a microfluidic feature, the microfluidic array device further comprising an array comprising a flexible array substrate supporting an addressable collection of probes in fluid communication with said microfluidic feature; b) introducing said sample to the integrated microfluidic array device; and c) contacting the addressable collection of probes with the sample for a time and under conditions sufficient to allow the sample to react with the probes, thereby performing the hybridization assay.  
     
     
         136 . The method of  claim 135 , fisher comprising interrogating the array.  
     
     
         137 . The method of  claim 135 , further comprising removing the array from the integrated microfluidic device prior to interrogating.  
     
     
         138 . The method of  claim 135 , wherein the microfluidic array device further comprises a cover covering the array, the method further comprising removing the cover prior to interrogating the array.  
     
     
         139 . The method of  claim 135  further comprising mixing said sample during said reaction.  
     
     
         140 . The method of  claim 135  further comprising washing said array.  
     
     
         141 . The method of  claim 135  further comprising reading an identifier on the microfluidic device.