Method and apparatus for performing biological reactions on a substrate surface

Abstract

The present invention provides methods and apparatus for performing biological reactions on a substrate surface that use a low volume of sample fluid, accommodate substrates as large as or larger than a conventional microscope slide, accommodate a plurality of independent reactions, and accommodate a substrate surface having one or more hydrogel-based microarrays attached thereto. The invention further provides an apparatus that allows introduction of fluids in addition to sample fluid into each reaction chamber via standard pipet tips and associated pipettor apparatus. The invention further an apparatus that increases reaction reproducibility, increases reaction efficiency, and reduces reaction duration. The preferred embodiment of the invention is configured to accommodate a standard microscope slide substrate having four hydrogel-based microarrays attached thereto and comprises a base plate having a well structure corresponding to each microarray and two fluid ports extending through the base plate into each well structure, a means for temporarily clamping the substrate against the base plate such that the microarrays face into the well structures, a means for sealing the perimeter around each microarray and well structure, and a means for sealing the fluid ports from the environment.

What is claimed is:  
     
         1 . An apparatus for performing biological reactions on a substrate surface, the apparatus comprising: 
 a biochip comprising: 
 a substrate; and  
 a plurality of arrays of biologically reactive sites on said substrate;  
   a base plate; and    a gasket affixed between the biochip and the base plate, the gasket defining a plurality of reaction chambers, each reaction chamber corresponding to one of the arrays.    
     
     
         2 . An apparatus according to  claim 1 , wherein the base plate defines at least one well structure, at least one reaction chamber being positioned to include the well structure.  
     
     
         3 . An apparatus according to  claim 1 , further comprising: 
 a first port extending from at least one of said reaction chambers through the base plate.    
     
     
         4 . An apparatus according to  claim 3 , further comprising a second port extending from at least one said reaction chambers through the base plate.  
     
     
         5 . An apparatus according to  claim 1 , wherein at least one of the plurality of arrays of biologically reactive sites comprises oligonucleotide probes.  
     
     
         6 . An apparatus according to  claim 1 , further comprising a heating element positioned to heat at least one reaction chamber.  
     
     
         7 . An apparatus for performing biological reactions on a substrate layer comprising: 
 a substrate having a first surface containing a plurality of biologically reactive sites disposed thereon;    a base plate having a first surface and a second surface, wherein the first surface further comprises a cavity comprising one or a plurality of well structures;    a sealing member disposed in each well structure, wherein each sealing member defines a reaction chamber between the surface of the substrate layer containing the biologically reactive sites and the first surface of the base plate; and    a fluid port connected to at least one reaction chamber.    
     
     
         8 . An apparatus according to  claim 7 , further comprising a second port extending from at least one said reaction chambers through the base plate.  
     
     
         9 . An apparatus according to  claim 7 , wherein at least one of the biologically reactive sites comprise oligonucleotide probes.  
     
     
         10 . An apparatus according to  claim 7 , further comprising a heating element positioned to heat at least one reaction chamber.