Apparatus for assay, synthesis and storage, and methods of manufacture, use, and manipulation thereof

Abstract

The invention features methods of making devices, or “platens”, having a high-density array of through-holes, as well as methods of cleaning and refurbishing the surfaces of the platens. The invention further features methods of making high-density arrays of chemical, biochemical, and biological compounds, having many advantages over conventional, lower-density arrays. The invention includes methods by which many physical, chemical or biological transformations can be implemented in serial or in parallel within each addressable through-hole of the devices. Additionally, the invention includes methods of analyzing the contents of the array, including assaying of physical properties of the samples.

We claim:  
     
         1 . A method of making a platen of a desired thickness having a plurality of through-holes, the method comprising: 
 a) providing a plurality of plates having upper and lower surfaces, wherein one or both of the upper and lower surfaces of at least some of said plurality of plates has continuous, substantially parallel grooves running the length of said surfaces;    b) bonding the upper surfaces of all but one of said plurality of plates to the lower surfaces of the other plates; and    c) if necessary to achieve the desired thickness, slicing the platen substantially perpendicularly to the through-holes, thereby creating a platen of a desired thickness having a plurality of through-holes.    
     
     
         2 . The method of  claim 1 , further comprising repeating step c) to make a plurality of platens.  
     
     
         3 . The method of  claim 1 , wherein the plates are bonded in a configuration in which the grooves of one plate are substantially parallel to the grooves of each of the other plates.  
     
     
         4 . A device for the immobilization of probes, cells, or solvent, said device comprising a platen having a plurality of through-holes, wherein at least some of said through-holes contain a porous material for the immobilization of probes, cells, or solvent.  
     
     
         5 . A method of making a platen having opposing hydrophobic surfaces and a plurality of hydrophilic through-holes, the method comprising: 
 (a) coating a plate with a material that reacts with amphiphilic molecules;    (b) forming through-holes; and    (c) treating the plate with a solution or vapor of an amphiphilic molecule to provide a platen having hydrophobic coating on surfaces of the platen but not on the walls of the through-holes.    
     
     
         6 . A platen made by the method of  claim 5 .  
     
     
         7 . A method of regenerating the hydrophobic coating on the platen of  claim 6  after use, the method comprising: 
 (a) removing residual hydrophobic coating, if any; and  
 (b) treating the platen with a solution or vapor of an amphiphilic molecule to regenerate the hydrophobic coating.  
 
     
     
         8 . A method of selectively making a coating on the surfaces of a platen having a plurality of through-holes, the method comprising: 
 (a) selectively coating the surfaces of the platen with a material that reacts with amphiphilic molecules; and    (b) treating the platen with a solution or vapor of an amphiphilic molecule to regenerate the hydrophobic coating.    
     
     
         9 . A device comprising: 
 a platen having two opposing surfaces and a plurality of through-holes extending between the surfaces, wherein the through-holes have walls, and wherein the surfaces and walls have different chemical properties, so that the walls and surfaces can be independently functionalized.    
     
     
         10 . A method of making a plastic platen of a desired thickness with through-holes, the method comprising: 
 a) potting a plurality of capillaries in the through-holes of a stack of platens comprising at least two platens having through holes;    b) separating adjacent platens by a distance equal to the desired thickness;    c) injecting a plastic-forming material into the space between the separated platens;    d) forming the plastic; and    e) slicing at the interface between the platens and the plastic to form the chips.    
     
     
         11 . A method of making a plastic platen of a desired thickness with through-holes, the method comprising: 
 a) potting a plurality of fibers or wires in the through-holes of a stack of platens comprising at least two platens having through holes;    b) separating adjacent platens by a distance equal to the desired thickness;    c) injecting a plastic-forming material into the space between the separated platens;    d) forming the plastic;    e) withdrawing the fibers or wires from the plastic to form through-holes; and    f) slicing at the interface between the platens and the plastic to form the chips.    
     
     
         12 . A method of creating a chemical array, the method comprising: 
 a) providing a platen having a plurality of through-holes and two opposing surfaces;    b) applying a mask to one or both surfaces of the platen to block at least some of the through-holes, while leaving other through-holes open;    c) exposing a surface of the platen to a reagent so that the reagent enters at least one of the open through-holes; and    d) repeating steps b) and c) with at least one different mask and at least one different reagent to create a chemical array.    
     
     
         13 . The method of  claim 12 , wherein the mask is made of a polymer, an elastomer, paper, glass, or a semiconductor material.  
     
     
         14 . The method of  claim 12 , wherein the mask comprises mechanical valves, pin arrays, or gas jets.  
     
     
         15 . The method of  claim 12 , wherein the applying step forms a hermetic seal between the mask and the platen.  
     
     
         16 . The method of  claim 12 , wherein the reagent is a liquid, a gas, a solid, a powder, a gel, a solution, a suspension, a cell culture, a virus preparation, or electromagnetic radiation.  
     
     
         17 . The method of  claim 12 , wherein the mask is translated to expose different through-holes.  
     
     
         18 . The method of  claim 12 , wherein the mask has co-registration pins and holes such that alignment of pins and holes in the mask register with the through-holes in the platen.  
     
     
         19 . The method of  claim 12 , wherein the mask comprises a flexible material.  
     
     
         20 . The method of  claim 19 , wherein multiple masks are part of a flexible tape, and the multiple masks are registered with the through-holes of the platen by advancing the tape.  
     
     
         21 . An array created by the method of  claim 12 .  
     
     
         22 . A method of creating a chemical array, the method comprising: 
 a) providing a platen having a plurality of through-holes and two opposing surfaces;    b) applying a mask that has one or more reagents on its surface to one or both surfaces of the platen to transfer the reagent from the mask to at least some of the through-holes; and    c) repeating step b) with at least one different mask and at least one different reagent to create a chemical array.    
     
     
         23 . A method for separating samples within a chemical array in a platen, the method comprising: 
 a) providing a platen having a plurality of through-holes and two opposing surfaces;    b) electrophoretically transporting a charged reagent into at least some of the through-holes by placing the platen into an electrophoresis apparatus containing the reagent and applying an electric field parallel to the through-holes; and    c) repeating step b) with at least one different reagent to create a chemical array.    
     
     
         24 . A method of creating a spatially addressable array, the method comprising: 
 a) providing a platen having a spatially addressable plurality of discrete through-holes each having an inner wall, wherein said platen has opposing hydrophobic surfaces; and    b) covalently or non-covalently immobilizing at least one reagent or probe on the inner walls of at least some of the through-holes or on a bead contained within at least one of the through-holes to form a spatially addressable array.    
     
     
         25 . The method of  claim 24 , wherein the through-holes are non-communicating through holes.  
     
     
         26 . The method of  claim 24 , wherein the through-holes are selectively communicating through-holes.  
     
     
         27 . The method of  claim 24 , further comprising: 
 c) flowing reagents into or through a predetermined subset of the through holes.    
     
     
         28 . A method of creating a stochastic array, the method comprising: 
 a) providing a platen having a plurality of through-holes; and    b) applying each of a plurality of reagents to the through-holes in a random or semi-random manner to create a stochastic array.    
     
     
         29 . The method of  claim 28 , wherein said applying step comprises providing a plurality of dispensing devices addressing at least some of the through-holes, dispensing different combinations of reagent solutions into each through-hole, and repositioning the dispensing devices at least once to address a different set of through-holes.  
     
     
         30 . The method of  claim 29 , further comprising dispensing a fluid that is immiscible with the reagent solutions into at least one through-hole.  
     
     
         31 . A method of identifying combinations of reagents having a biological, chemical or physical property of interest, the method comprising: 
 a) creating a stochastic array using the method of  claim 28;     b) assaying the stochastic array for combinations having a property of interest; and    c) identifying the reagents that have the property of interest.    
     
     
         32 . A method of loading a platen having a plurality of through-holes, where the platen has opposing surfaces, the method comprising: 
 a) dipping the platen into a liquid sample comprising a sample to be loaded into the through-holes, thereby loading at least some of the through-holes with the sample; and    b) passing the platen through a liquid that has an affinity for the surfaces of the platen but that is immiscible with the liquid sample, thereby cleaning the surface of the platen of excess sample mixture.    
     
     
         33 . A method of loading a platen having a plurality of through-holes, where the platen has opposing surfaces, the method comprising: 
 a) dipping the platen into a liquid sample comprising a sample to be loaded into the through-holes, thereby loading at least some of the through-holes with the sample; and    b) contacting the platen with a liquid that has an affinity for the surfaces of the platen but is immiscible with the liquid sample, thereby cleaning the surface of the platen of excess sample mixture.    
     
     
         34 . A method of maintaining the viability of an aerobic organism in a platen having a plurality of through-holes, the method comprising: 
 a) loading the aerobic organism into at least some of the-through-holes of the platen, and    b) submerging the platen into a gas permeable liquid.    
     
     
         35 . The method of  claim 34 , wherein the organism is in a fluid and the gas permeable liquid is immiscible with the fluid.  
     
     
         36 . The method of  claim 34 , further comprising assaying one or more physical properties of the aerobic organism.  
     
     
         37 . The method of  claim 34 , wherein the aerobic organism is a cell.  
     
     
         38 . The method of  claim 34 , wherein the gas permeable liquid is a fluorocarbon, a silicone polymer, or a monolayer.  
     
     
         39 . A method of mixing volatile samples with other samples, the method comprising: 
 a) providing a platen having a plurality of through-holes;    b) optionally loading some or all of the through-holes with one or more non-volatile samples;    c) loading at least some of the through-holes of the platen with one or more volatile samples to allow the samples in each through-hole to mix with other samples in the same through-hole; and    d) submerging the platen in a liquid immiscible with the volatile samples, where steps b), c) and d) can be performed in any order.    
     
     
         40 . The method of  claim 39 , wherein the samples to be mixed are initially provided in two separate platens that are contacted while submerged in said immiscible liquid to allow mixing.  
     
     
         41 . The method of  claim 39 , wherein steps c) and d) are performed in reverse order.  
     
     
         42 . The method of  claim 39 , wherein the immiscible liquid is fluorocarbon, a silicone polymer, mineral oil, or an alkane.  
     
     
         43 . A method of mixing an array of samples, the method comprising: 
 a) providing a platen having a plurality of through-holes, wherein at least some of the through holes are loaded with a first sample or set of samples;    b) providing a substantially flat surface comprising an array of a second sample or set of samples, wherein the second sample or set of samples on the flat surface can be registered with the sample in the platen;    c) registering the platen with the array of the second sample or set of samples on the flat surface; and    d) contacting the platen with the flat surface, wherein the sample in the platen is aligned with the sample on the flat surface.    
     
     
         44 . The method of  claim 43 , wherein the first sample or set of samples comprises one or more probes.  
     
     
         45 . The method of  claim 43 , wherein the second sample or set of samples comprises one or more probes.  
     
     
         46 . The method of  claim 43 , further comprising analyzing a physical property of a sample contained in the platen.  
     
     
         47 . The method of  claim 43 , wherein the flat surface includes a hydrophobic pattern matching the pattern of the platen array.  
     
     
         48 . A method for transferring a reagent or probe to a receptacle from a specific through-hole of a platen comprising a plurality of through-holes, the method comprising: 
 a) placing the platen over the receptacle; and    b) applying a burst of gas, liquid, solid, or a pin to said specific through-hole to transfer said reagent or probe into the receptacle.    
     
     
         49 . The method of  claim 48 , wherein the burst of gas, liquid, or solid is generated with a syringe.  
     
     
         50 . The method of  claim 48 , wherein the burst of gas is generated by depositing a photodynamic or photothermal material in or above the through-hole, and then exposing the photodynamic or photothermal material to a laser beam of frequency and intensity suitable to activate the photodynamic or photothermal material.  
     
     
         51 . A device for filling or draining through-holes in a platen having a plurality of through-holes, the device comprising: 
 a) a holder adapted to accept the platen;    b) a nozzle having an aperture of a suitable size to inject a sample into a single through-hole in said platen; and    c) a valve that controls a flow of a sample through said nozzle, wherein the holder and nozzle can move with respect to each other.    
     
     
         52 . The device of  claim 51 , wherein the nozzle is positioned so as to contact the platen.  
     
     
         53 . The device of  claim 51 , further comprising a microplate positioned to receive samples from the platen.  
     
     
         54 . The device of  claim 51 , further comprising a computer that controls the valve and controls the positions of the holder and nozzle relative to each other.  
     
     
         55 . The device of  claim 53 , further comprising a computer that controls the valve and controls the positions of the microplate and holder relative to each other.  
     
     
         56 . The method of  claim 53 , wherein the microplate, the holder, and the nozzle can be moved independently of each other in at least two dimensions.  
     
     
         57 . The method of  claim 51 , wherein the nozzle is held in a single position and the holder and nozzle can be moved independently of each other in at least two dimensions.  
     
     
         58 . A method of analyzing the kinetics of one or more reactions occurring in at least one of the through holes of a platen, the method comprising: 
 a) providing a first platen having a plurality of through-holes, wherein the through-holes are loaded with a first sample or set of samples;    b) introducing the platen into a detection device;    c) introducing a second platen having a plurality of through-holes into the detection device, wherein the through holes are loaded with sample or reagent;    d) registering and contacting the platens such that contents of the through-holes of said first platen can mix with contents of corresponding through-holes of said second platen; and    e) detecting a change in a physical property of the contents of at least some of the through-holes over time.    
     
     
         59 . A method of analyzing a physical property of a sample in an array, the method comprising: 
 a) providing a platen having a plurality of through-holes, wherein the through-holes are loaded with a sample;    b) placing the platen between two partially transmitting mirrors;    c) illuminating the samples through one of the mirrors; and    d) detecting optical output from the sample.    
     
     
         60 . The method of  claim 59 , wherein said imaging step comprises measuring light emanating from the array.  
     
     
         61 . The method of  claim 59 , wherein the platen is within a laser cavity and an optical gain medium is positioned between the two mirrors.  
     
     
         62 . The method of  claim 59 , wherein said imaging step comprises measuring light emitted from the mirror opposite from the illumination source.  
     
     
         63 . A method of measuring sample output from an array, the method comprising: 
 a) providing a platen having a plurality of through-holes, wherein the through-holes are loaded with sample;    b) introducing the sample into an array of capillaries;    c) eluting the samples through the capillaries using pulse pressure, creating a non-continuous flow;    d) spotting the eluting samples onto a surface that is moving relative to the capillaries, wherein the spots are discrete and no mixing of the samples occurs; and    e) analyzing a physical property of the spots.    
     
     
         64 . A method of storing a plurality of samples in an assay-ready, high-density format, the method comprising: 
 a) providing a platen having a plurality of through-holes;    b) loading the through-holes with said samples dissolved in a mixture comprising two solvents, a first solvent having a low vapor pressure and a second solvent having a higher vapor pressure; and    c) evaporating the second solvent to result in a plurality of samples in first solvent.    
     
     
         65 . The method of  claim 64 , wherein the volume of the first solvent in each solution is less than about 25 nl.  
     
     
         66 . A method of forming a high throughput assay, the method comprising: 
 a) providing a platen having a plurality of through-holes, wherein at least some of the through-holes contain a sample dissolved in a solvent having a low vapor pressure;    b) cooling the platen to a temperature sufficient to freeze the dissolved sample,    c) dipping the platen into a solution comprising a reagent, wherein the temperature of the solution is less than the freezing point of the sample, but greater than the freezing point of the reagent solution,    d) removing the platen from the reagent solution, and    e) warming the platen to a temperature greater than the freezing point of the sample.    
     
     
         67 . The method of  claim 66 , wherein said providing step comprises: 
 a) providing a platen having a plurality of through-holes;    b) loading the through-holes with samples dissolved in a mixture comprising two solvents, a first solvent having a low vapor pressure and a second solvent having a higher vapor pressure; and    c) evaporating the first solvent.    
     
     
         68 . The method of  claim 66 , wherein the reagent solution is an aqueous solution.  
     
     
         69 . A filtration device comprising first and second platens, each having a plurality of through-holes, and a semi-permeable membrane, wherein the platens are aligned such that the through-holes of the first platen are substantially aligned with the through-holes of the second platen and the membrane is sandwiched in between the two platens.  
     
     
         70 . The method of  claim 69 , wherein the semi-permeable membrane is a nitrocellulose membrane.  
     
     
         71 . The method of  claim 69 , wherein the semi-permeable membrane comprises a layer of cells.  
     
     
         72 . The method of  claim 69 , wherein the platens have hydrophobic surfaces.