Gels, methods and apparatus for identification and characterization of biomolecules

Abstract

The present invention is directed to efficient, computer-assisted methods and apparatus for identifying, selecting and characterizing biomolecules in a biological sample. According to the invention, a biological sample is first treated to isolate biomolecules of interest, and a two-dimensional array is then generated by separating the biomolecules present in a complex mixture. The invention provides a computer-generated digital profile representing the identity and relative abundance of a plurality of biomolecules detected in the two-dimensional array, thereby permitting computer-mediated comparison of profiles from multiple biological samples. This automatable technology for screening biological samples and comparing their profiles permits rapid and efficient identification of individual biomolecules whose presence, absence or altered expression is associated with a disease or condition of interest.

1 . A computer-assisted method for selecting and directing the isolation of one or more biomolecules present in a two-dimensional array, comprising: 
 a purification step, wherein a plurality of biomolecules of interest are substantially isolated from a first biological sample;    a first separation step, wherein said biomolecules are separated according to a first physical or chemical property to form a one-dimensional array of biomolecules;    a second separation step, wherein said one-dimensional array of biomolecules is separated according to a second physical or chemical property to form said two-dimensional array;    imaging said two-dimensional array or a replica thereof to generate a computer-readable output comprising, for each of a plurality of biomolecules detected in said two-dimensional array, a pair of x,y coordinates and a signal value;    processing said output in at least one computer to select one or more of said detected biomolecules in accordance with previously ordained or operator-specified criteria; and optionally    generating machine-readable instructions that direct a robotic device to isolate at least one of said selected biomolecules from said two-dimensional array.    
     
     
         2 . The method according to  claim 1 , further comprising: 
 isolating at least one of said selected biomolecules from said two-dimensional array by means of said robotic device in accordance with said machine-readable instructions.    
     
     
         3 . The method according to  claim 1  or  claim 2 , in which said biomolecules are oligosaccharides.  
     
     
         4 . The method according to  claim 1  or  claim 2 , in which said biomolecules are proteins.  
     
     
         5 . The method according to  claim 4 , in which said proteins are glycoproteins.  
     
     
         6 . The method according to any preceding claim, in which said two-dimensional array is contained in a polyacrylamide gel.  
     
     
         7 . The method according to  claim 6 , in which said biomolecules have been separated by isoelectric focusing, followed by electrophoresis in the presence of sodium dodecyl sulfate.  
     
     
         8 . The method according to  claim 6  or  claim 7 , in which said polyacrylamide gel is bonded to a generally planar solid support such that the gel has two-dimensional spatial stability, and the support is substantially non-interfering with respect to detection of a detectable label carried by the proteins.  
     
     
         9 . The method according to  claim 8 , in which said polyacrylamide gel is covalently bonded to said solid support.  
     
     
         10 . The method according to  claim 8  or  claim 9 , in which said detectable label is a fluorescent label.  
     
     
         11 . The method according to any of  claims 8  to  10 , in which said solid support is glass.  
     
     
         12 . The method according to any preceding claim, wherein the purification step is carried out using FPLC.