Method and apparatus for performing biological reactions on a substrate surface

Abstract

The present invention provides an apparatus for performing biological reactions on a substrate layer having a multiplicity of oligonucleotide binding sites disposed thereon. The invention provides a hybridization chamber wherein nucleic acid hybridization is performed by reacting biological material on a biochip comprising a substrate having an array of oligonucleotide binding sites. The binding sites are associated with an array of 3-dimensional polyacrylamide pads for anchoring the reactants. The arrays are covered with a flexible layer that permits mixing of the hybridization solution on the biochip and detection of hybridization in situ. Fluid inlet and outlet ports in the chamber provide for control of fluid flow into and out of the chamber.

What we claim is:  
     
         1 . An apparatus for performing biological reactions, comprising: 
 (a) a substrate having a first surface and a second surface opposite thereto,    (b) an array of biomolecules positioned on the first surface of the substrate,    (c) a flexible layer affixed to the first surface of the substrate by an adhesive layer, wherein the adhesive layer is deposited on the first surface of the substrate and encloses an area thereupon;    (d) a port extending through the substrate from the first surface to the second surface thereof and having a first opening and a second opening, wherein the first opening of the port is provided within the area bounded by the adhesive and covered by the flexible layer and the second opening of the port is provided on the second surface of the substrate;    (e) a removable cover positioned over the second opening of the port; and    (f) a layer of a water-soluble compound that is a solid at a first temperature and a liquid at a second, higher temperature, the layer being positioned between the first surface of the substrate and the flexible layer.    
     
     
         2 . The apparatus of  claim 1  wherein the substrate is made of glass, silicon, ceramic or plastic.  
     
     
         3 . The apparatus of  claim 1  wherein the array further comprises a gel pad.  
     
     
         4 . The apparatus of  claim 3  wherein the gel pad is made of polyacrylamide.  
     
     
         5 . The apparatus of  claim 1  wherein the flexible layer is made of plastic, rubber, polyester, or Teflon.  
     
     
         6 . The apparatus of  claim 5  wherein the flexible layer is made of polypropylene, polyethylene or polyvinylidene chloride.  
     
     
         7 . The apparatus of  claim 1  wherein the flexible layer is a translucent plastic.  
     
     
         8 . The apparatus of  claim 1  wherein the flexible layer is a gas permeable membrane.  
     
     
         9 . The apparatus of  claim 1  wherein the removable cover is a foil tape.  
     
     
         10 . The apparatus of  claim 1  wherein the water-soluble compound is polyethylene glycol.  
     
     
         11 . The apparatus of  claim 7  wherein the water-soluble compound is polyethylene glycol 600.  
     
     
         12 . The apparatus of  claim 1  wherein the port is in the shape of a truncated cone having a small-diameter end and a large diameter end, and wherein the small diameter end is provided in the area on the first substrate surface bounded by the adhesive layer and the large diameter end is provided on the second substrate surface.  
     
     
         13 . The apparatus of  claim 12  wherein the port further comprises walls that form an angle of less than 90° with the second substrate surface.  
     
     
         14 . The apparatus of  claim 13  wherein the port contains a sample fluid having a contact angle, and the angle formed between the second substrate surface and the port walls is less than or equal to the contact angle of the sample fluid.  
     
     
         15 . The apparatus of  claim 1  further comprising a second port extending through the substrate from the first surface to the second surface thereof and having a first opening and a second opening, wherein the first opening of the outlet port is provided on the first substrate surface within the area bounded by the adhesive and covered by the flexible layer, and the second opening of the outlet port is provided on the second substrate surface and is covered by a removable cover.  
     
     
         16 . The apparatus of  claim 15  wherein the second port further comprises walls that form an angle of less than 90° with the second substrate surface.  
     
     
         17 . The apparatus of  claim 16  wherein the second port contains a sample fluid having a contact angle, and the angle formed between the second substrate surface and the port walls is less than or equal to the contact angle of the sample fluid.  
     
     
         18 . The apparatus of  claim 1  further comprising a reflective layer positioned -between the array and the first substrate surface.  
     
     
         19 . The apparatus of  claim 1  further comprising a resistive heater.  
     
     
         20 . The apparatus of  claim 1  wherein the resistive heater comprises a reflective layer positioned between the array and the first substrate surface.  
     
     
         21 . The apparatus of  claim 1  further comprising a passivation layer.  
     
     
         22 . The apparatus of  claim 21  wherein the passivation layer is made of parylene.  
     
     
         23 . The apparatus of  claim 1  further comprising a scanner, wherein the scanner is in contact with the flexible layer at a position over the array.  
     
     
         24 . The apparatus of  claim 12 , wherein the scanner is a light pipe and covers the entirety of the area bounded by the adhesive and comprising the array.  
     
     
         25 . The apparatus of  claim 12 , wherein the scanner is a movable scanner and moves longitudinally across the area bounded by the adhesive and comprising the array.  
     
     
         26 . The apparatus of  claim 1  further comprising a sample preparation chip in contact with the second substrate surface, wherein the sample preparation chip has a port that is aligned with the first port of the apparatus.  
     
     
         27 . The apparatus of  claim 1  further comprising a roller, wherein the roller is in contact with the flexible layer at a position over the array.  
     
     
         28 . The apparatus of  claim 16 , wherein the roller moves longitudinally across the area bounded by the adhesive and comprising the array.  
     
     
         29 . The apparatus of  claim 1  further comprising: 
 (a) a case having a lid and a base,  
 (b) a cavity disposed in the base, and  
 (c) a carriage comprising a scanner and a roller, wherein the carriage is provided in the cavity, wherein the substrate is removably positioned above the carriage such that the first substrate surface is in operative contact with the carriage.  
 
     
     
         30 . The apparatus of  claim 29  wherein the lid further comprises a display unit.  
     
     
         31 . The apparatus of  claim 29  wherein the carriage further comprises a pivot point provided between the scanner and the roller.  
     
     
         32 . The apparatus of  claim 31  and wherein the motion of the carriage about the pivot point is controlled by a solenoid.  
     
     
         33 . An apparatus for performing biological reactions comprising: 
 (a) a glass microscope slide having a first surface and a second surface opposite thereto;    (b) an array of biomolecules positioned on the first surface of the slide, wherein each biomolecule within the array is anchored to the first surface by a polyacrylamide gel pad;    (c) a layer of polyvinylidene chloride affixed to the first surface of the slide by a layer of double-sided adhesive, wherein the adhesive layer is deposited on the first surface of the slide and encloses an area thereupon;    (d) a first and second port extending through the slide from the first surface to the second surface thereof each having a first opening and a second opening, wherein the first opening of each port is provided within the area on the first surface of the slide bounded by the adhesive and covered by the flexible layer and the second opening of each port is provided on the second surface of the slide, and wherein each port is in the shape of a truncated cone having a small-diameter end and a large diameter end, and wherein the small diameter end is the first opening and the large diameter end is the second opening;    (e) a layer of foil tape positioned over the second opening of each port;    (f) a layer of a polyethylene glycol positioned between the first surface of the slide and the layer of polyvinylidene chloride;    (g) a reflective layer positioned between the array and the first substrate surface;    (h) a layer of parylene positioned between the reflective layer and the and the layer of polyvinylidene chloride; and    (i) a resistive heater.    
     
     
         34 . An apparatus for performing biological reactions, comprising: 
 (a) a glass microscope slide having a first surface and a second surface opposite thereto,    (b) an array of biomolecules positioned on the first surface of the slide, wherein each biomolecule within the array is anchored to the first surface by a polyacrylamide gel pad;    (c) a layer of polyvinylidene chloride affixed to the first surface of the slide by a layer of double-sided adhesive, wherein the adhesive layer is deposited on the first surface of the slide and encloses an area thereupon;    (d) a first and second port extending through the slide from the first surface to the second surface thereof each having a first opening and a second opening, wherein the first opening of each port is provided within the area on the first surface of the slide bounded by the adhesive and covered by the flexible layer and the second opening of each port is provided on the second surface of the slide, and wherein each port is in the shape of a truncated cone having a small-diameter end and a large diameter end, and wherein the small diameter end is the first opening and the large diameter end is the second opening;    (e) a layer of foil tape positioned over the second opening of each port;    (f) a layer of a polyethylene glycol positioned between the first surface of the slide and the layer of polyvinylidene chloride;    (g) a reflective layer positioned between the array and the first substrate surface;    (h) a layer of parylene positioned between the reflective layer and the and the layer of polyvinylidene chloride;    (i) a resistive heater;    (j) a case having a lid and a base; wherein the lid further-comprises a display unit;    (k) a cavity disposed in the base; and    (l) a carriage comprising a scanner and a roller, wherein the carriage is provided in the cavity, and wherein the slide is removably positioned above the carriage such that the first slide surface is in operative contact with the carriage.