Lithographic mask design and synthesis of diverse probes on a substrate

Abstract

Systems and methods of synthesizing probes on a substrate are provided. One or more shift reticles are utilized to uniformly add monomers to the substrate at specified locations. The shift reticles are shifted relative to the substrate between monomer addition steps. Additionally, characteristics of the desired probes may be specified at synthesis time.

1 . A method of synthesizing rows of probes including an interrogation position on a substrate, comprising the steps of 
 coupling non-interrogation position monomers on the substrate in a first region having a first width, and    coupling rows of interrogation position monomers on the substrate in a second region having a second width, the second region being within the first region and the second width being less than the first width.    
     
     
         2 . The method of  claim 1 , wherein each row of probes includes a different monomer at the interrogation position.  
     
     
         3 . The method of  claim 2 , wherein the interrogation position monomers include A, C, G, and T(U).  
     
     
         4 . The method of  claim 1 , the probes that are within the first region and not the second region do not include interrogation position monomers.  
     
     
         5 . The method of  claim 1 , wherein coupling the non-interrogation position monomers on the substrate, comprises 
 coupling monomers on the substrate at locations specified by at least one shift reticle,    shifting the at least one shift reticle relative to the substrate, and    after shifting the at least one shift reticle, coupling monomers on the substrate at locations specified by the at least one shift reticle.    
     
     
         6 . The method of  claim 5 , wherein the probes synthesized on the substrate include multiple monomers that were coupled to the substrate utilizing the at least one shift reticle.  
     
     
         7 . The method of  claim 1 , wherein coupling the interrogation position monomers on the substrate, comprises 
 coupling monomers on the substrate at locations specified by an interrogation position reticle,    shifting the interrogation position relative to the substrate, and    after shifting the interrogation position reticle, coupling monomers on the substrate at locations specified by the interrogation position reticle.    
     
     
         8 . The method of  claim 7 , wherein the interrogation position reticle is shifted in a direction perpendicular to a direction that the at least one shift reticle is shifted.  
     
     
         9 . A substrate, comprising 
 multiple rows of probes including an interrogation position monomer coupled to the substrate, and    at least one row of probes that do not include an interrogation position monomer coupled to the substrate between two rows of probes the do include an interrogation position monomer.    
     
     
         10 . The substrate of  claim 9 , wherein the multiple rows of probes including an interrogation position monomer include four rows of probes wherein each rows of probes includes a different monomer at the interrogation position.  
     
     
         11 . The substrate of  claim 10 , wherein the interrogation position monomers include A, C, G, and T(U).  
     
     
         12 . The substrate of  claim 8 , further comprising the step of shifting the shift reticle relative to the substrate in order to couple a second layer of different types of monomers on the substrate at the specified locations.  
     
     
         13 . A method of synthesizing probes on a substrate, comprising 
 coupling monomers on the substrate at locations specified by a plurality of shift reticles, each shift reticle being for coupling a specific monomer on the substrate and including a monomer addition region for coupling an interrogation position monomer,    shifting the plurality of shift reticles relative to the substrate in a first direction, and    after shifting the plurality of shift reticles, coupling monomers on the substrate at locations specified by the plurality of shift reticles so that probes are synthesized on the substrate including different interrogation positions.    
     
     
         14 . The method of  claim 13 , wherein each shift reticle includes rectangular monomer addition regions that are longer in a second direction that is perpendicular to the first direction.  
     
     
         15 . The method of  claim 14 , wherein each shift reticle includes an interrogation position monomer addition region that are at a different location in the second direction.  
     
     
         16 . The method of  claim 13 , wherein the plurality of shift reticles include at least one region in a same location that does not couple monomers on the substrate so that probes of varying lengths may be synthesized at the same time.