Guided deposition in spatial arrays

Abstract

An apparatus and method is provided for preparing and using a very large and diverse array of compounds on a substrate having rapidly accessible locations. The substrate contains cells in which the compounds of the array are located. Surrounding the cells is a non-wetable surface that prevents the solution in one cell from moving to adjacent cells. The compounds are delivered to the individual cells of the array by a micropipette attached to an X-Y translation stage.

1 . A method for conducting a plurality of reactions on a substrate, said substrate having a plurality of cells at predefined locations thereon, the location of each cell being encoded by information readable with electrical, magnetic or electromagnetic sensing means, said method comprising the following steps: 
 (a) selecting a first set of cells;    (b) decoding the locations of said first set of cells by said sensing means and delivering a first reactant to each of said first set cells;    (c) selecting a second set of cells;    (d) decoding the locations of said second set of cells by said sensing means and delivering a second reactant to each of said second set of cells; and    (e) simultaneously reacting said first reactant in each of said first set of cells and said second reactant in each of said second set of cells, wherein the first reactant is prevented from contacting the second set of cells and the second reactant is prevented from contacting the first set of cells.    
     
     
         2 - 20 . (canceled)  
     
     
         21 . An apparatus for assaying biological materials comprising: a substrate having a surface, an outer edge and a center; and a plurality of discrete features bound to an annular region on the surface of the substrate, the plurality of discrete features comprising a first biological material.  
     
     
         22 . The apparatus of  claim 21 , wherein the plurality of discrete features further comprises: a second biological material chemically associated with the first biological material; and a signal producing system chemically associated with the plurality of discrete features.  
     
     
         23 . The apparatus of  claim 22 , wherein the second biological material is complementary to the first biological material.  
     
     
         24 . The apparatus of  claim 23 , wherein the first biological material is an oligonucleotide probe and the second biological material is a target nucleotide sequence.  
     
     
         25 . The apparatus of  claim 21 , wherein the plurality of discrete features are in an annular pattern in the annular region of the substrate surface.  
     
     
         26 . The apparatus of  claim 25 , wherein the annular pattern is a plurality of annular rings.  
     
     
         27 . The apparatus of  claim 26 , wherein the plurality of annular rings are concentric annular rings of decreasing diameter from the outer edge of the substrate to the center.  
     
     
         28 . The apparatus of  claim 26 , wherein the plurality of annular rings are segmented.  
     
     
         29 . The apparatus of  claim 25 , wherein the annular pattern is a spiral pattern having one end adjacent to the outer edge of the substrate and an opposite end adjacent to the center of the substrate.  
     
     
         30 . The apparatus of  claim 21 , further comprising a housing for holding the substrate and the plurality of discrete features bound to the substrate surface.  
     
     
         31 . The apparatus of  claim 30 , wherein the housing comprises: a plate having an outer edge, a first side and a second side opposite to the first side, the plate comprising: a port extending from the first side to the second side of the plate, a first recess in the first side coaxial with the port, a second recess in the first side having an annular shape and being coaxial with the first recess, a third recess in the first side having an annular shape and being coaxial with the second recess, the third recess for receiving the substrate, wherein the first recess and the second recess in the plate and the substrate define a chamber in the housing for receiving the second biological material and ancillary materials through the port, the plurality of discrete features being adjacent to a region in the chamber corresponding to the second recess and being visible from the first side of the plate; and a recess extending radially from the outer edge of the plate inward being in communication with the second recess; and a valve assembly in the radially extending recess, the valve assembly comprising an actuator, a biasing means and a cap, the cap being attached to the outer edge of the plate such that the radially extending recess forms a valve chamber inside the plate.  
     
     
         32 . The apparatus of  claim 31 , wherein the port comprises a septum for allowing the second biological material and ancillary materials to pass into the chamber, the septum preventing the materials from exiting the chamber through the port.  
     
     
         33 . The apparatus of  claim 31 , wherein the housing further comprises: a second radially extending recess located diametrically opposite to the first mentioned radially extending recess; a second valve assembly similar to the first mentioned valve assembly enclosed in the second radially extending recess; a fourth recess in the second side of the plate having an annular shape; and a ring frame attached to the second side of the plate, the ring frame enclosing the fourth recess, the fourth recess and the ring frame forming an annular cavity within the housing, wherein the first radially extending recess and the second radially extending recess intersect with the fourth recess and are in communication with the annular cavity, and wherein at least one of the first and second radially extending recesses being in communication with the exterior of the plate adjacent to the second side.  
     
     
         34 . A system for synthesizing an annular array of biological materials comprising: a holder for holding a substrate; a spinner assembly for rotating the holder; an enclosure for enclosing at least the holder and substrate; a deposition assembly for depositing biological material onto a surface of the substrate; a dispenser assembly for providing ancillary materials to the surface of the substrate; and a controller for automatically controlling the deposition assembly, the spinner assembly and the dispenser assembly.  
     
     
         35 . The system of  claim 34 , wherein the spinner assembly comprises a spindle and a motor, the spindle being attached to the holder, the motor imparting rotational motion to the spindle and the holder incrementally and continuously, and providing variable rotational speed.  
     
     
         36 . The system of  claim 34 , wherein the deposition assembly comprises: a deposition tool having a plurality of nozzles to deposit a plurality of monomers of the biological material as discrete features in an annular region on the surface of the substrate as the substrate is rotated in the holder by the spinner assembly, wherein there is one nozzle for each different monomer of the biological material to be deposited; a plurality of reservoirs of biological materials to be deposited, wherein there is one reservoir for each different monomer to be deposited; and a conduit for each reservoir of the plurality of reservoirs for carrying a respective monomer to a respective nozzle.  
     
     
         37 . The system of  claim 34 , wherein the deposition assembly comprises: a plurality of deposition tools to deposit a plurality of monomers of the biological material as discrete features in an annular pattern on the surface of the substrate as the substrate is rotated in the holder by the spinner assembly, wherein there is one deposition tool of the plurality of deposition tools for each different monomer of the biological material to be deposited, wherein each deposition tool has a plurality of nozzles aligned in a row on the deposition tool radially over the substrate to provide the annular pattern; a plurality of reservoirs of biological materials to be deposited, wherein there is one reservoir for each different monomer to be deposited; and a conduit for each reservoir of the plurality of reservoirs for carrying a respective monomer to a respective deposition tool.  
     
     
         38 . A system for hybridizing biological materials in an annular array pattern comprising: a holder for holding a substrate, the substrate having an array of first biological material bound to an annular region on a surface of the substrate; a spinner assembly for rotating the holder at a plurality of rotational speeds, the holder being connected to the assembly; a deposition tool for providing a second biological material onto the surface of the substrate; and a dispenser tool for dispensing ancillary materials into the chamber, wherein the spinner assembly rotates the holder and the substrate at least one of the plurality of rotational speeds after the second biological material is provided and at least another one of the plurality of rotational speeds after the ancillary materials are dispensed.  
     
     
         39 . The hybridization system of  claim 38 , wherein the plurality of rotational speeds comprises: a first rotational speed sufficient to spread the second biological material into contact with the first biological material for hybridization, and a second rotational speed sufficient to remove unhybridized second biological material from the substrate surface after hybridization, wherein the first rotational speed is sufficient to spread the ancillary materials into contact with hybridized biological materials and the second rotational speed is sufficient to remove the ancillary materials from the substrate surface.  
     
     
         40 . The hybridization system of  claim 38 , wherein the substrate is enclosed in a housing and the holder is adapted to hold the housed substrate.  
     
     
         41 . The hybridization system of  claim 40 , wherein the housing comprises: a cavity adjacent to the first biological material on the substrate, a port for receiving the second biological material into the cavity; and an exit valve assembly in communication with the cavity and in communication with an exterior of the housing, wherein the second biological material is deposited by the deposition tool through the port and into the cavity, and wherein the ancillary materials are dispensed by the dispenser assembly through the port and into the cavity, and wherein the valve assembly receives unhybridized second biological material and the ancillary materials when sufficient centrifugal force is created by one of the plurality of rotational speeds.  
     
     
         42 . A system for optically interrogating an annular array of hybridized biological material comprising: a light source for emitting a light beam; a first optics subsystem for directing the light beam onto the array; a scanning subsystem for providing rotational movement to the array during an optical scan; a detector subsystem for detecting a signal from the array in response to the light beam; and an analysis subsystem for analyzing the detected signals gathered by the detection subsystem and for automatically controlling the light source, the scanning subsystem and the detector subsystem.  
     
     
         43 . The optical interrogation system of  claim 42 , wherein the scanning subsystem comprises: a holder for holding the hybridized annular array; and an annular subassembly for providing rotational movement to the holder and the array.  
     
     
         44 . The optical interrogation system of  claim 43 , wherein the annular subassembly comprises: a motor having incremental and variable rotational speeds; and a spindle which is connected to the motor at one end, the holder being connected to the spindle at another end opposite to the one end.  
     
     
         45 . The optical interrogation system of  claim 43 , wherein the scanning subsystem further comprises a linear movement subassembly for further providing linear movement during the optical scan.  
     
     
         46 . The optical interrogation system of  claim 45 , wherein the linear movement subassembly provides linear movement to the annular subassembly during the optical scan.  
     
     
         47 . The optical interrogation system of  claim 45 , wherein the linear movement subassembly provides linear movement to the optics subsystem during the optical scan.  
     
     
         48 . A method of assaying biological material in an annular array comprising the steps of: providing a plurality of discrete features comprising a first biological material in an annular region on a surface of a substrate; hybridizing a second biological material with the first biological material on the substrate, the hybridized discrete feature having a signal producing system; optically interrogating the hybridized discrete features on the substrate; and determining characteristics about the first biological material and the second biological material from the optical interrogation.  
     
     
         49 . The method of  claim 48 , wherein the step of providing a first biological material comprises the steps of: a plurality of steps of depositing monomers of the first biological material; rotating the substrate incrementally to each discrete feature location between each deposition step of the plurality of steps of depositing to deposit the monomers in the annular region; and dispensing ancillary materials on the substrate after each different monomer is deposited in the annular region; and spinning the substrate at a speed high enough to remove the ancillary materials from the substrate after each step of dispensing.  
     
     
         50 . The method of  claim 48 , wherein the step of hybridizing comprises the steps of: depositing the second biological material on the substrate; spinning the substrate at a first speed sufficient to spread the second biological material into contact with the first biological material; providing an environment for hybridization to occur; spinning the substrate at a second speed high enough to remove any unhybridized second biological material from the substrate; and dispensing ancillary materials on the substrate after the step of spinning at the second speed to wash the substrate; and spinning the substrate at the second speed to remove the ancillary materials from the substrate.  
     
     
         51 . The method of  claim 50 , further comprising the step of enclosing the substrate in a housing before the step of depositing, wherein the step of enclosing comprises the steps of: providing a base plate with a central recess, a first annular recess and a second annular recess on a first side thereof, the central recess having a port providing communication between the first side and a second side of the plate; assembling a valve assembly in a radially extending recess in the base plate, wherein the step of assembling comprises the step of attaching a cover over one opening in the radial recess adjacent to an outer edge of the base plate to enclose the valve assembly and form a valve chamber, wherein the valve chamber is in communication with an exterior of the base plate; attaching a cover over the port, the port having a septum, the port for receiving biological material and ancillary materials, the septum for preventing the materials from escaping from the port; and attaching the substrate to the second annular recess in the base plate, wherein the substrate surface is adjacent to the first annular recess and wherein the substrate, the central recess and the first annular recess form a chamber for receiving the materials through the port, wherein the chamber is in communication with the valve chamber.  
     
     
         52 . The method of  claim 51 , wherein the step of depositing comprises the step of depositing the second biological material into the chamber of the housing through the port, and the step of dispensing comprises the step of dispensing the ancillary materials into the chamber through the port, and wherein the method further comprises the step of spinning the enclosed substrate at the second speed to generate sufficient centrifugal force to activate the valve assembly to release the unhybridized second biological material and the ancillary materials into the valve chamber.  
     
     
         53 . The method of  claim 48 , wherein the step of optical interrogation comprises the steps of: mounting the hybridized array substrate into a rotating holder; impinging a light beam on the array substrate in a scan line; and rotating the substrate at speed sufficient for the beam to impinge on the discrete features on the array, such that the hybridized discrete features emit a signal; moving the scan line incrementally in a radial direction after each step of rotating until the beam impinges on all of the discrete features on the array; detecting the signal from the hybridized discrete features; and analyzing the signals that were detected to determine information about the first biological material and the second biological material.  
     
     
         54 . The method of  claim 48  further comprising the step of controlling each of the steps of providing, hybridizing, interrogating and determining with a computer subsystem to automate the method of assaying.