Photolithographic method and system for efficient mask usage in manufacturing DNA arrays

Abstract

Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle. The monomers may be, for example, nucleotides, amino acids or saccharides.

1 - 28 . (canceled)  
     
     
         29 . A method for synthesizing probe arrays of polymers on a substrate using a mask having a plurality of reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate, the method comprising the steps of: 
 (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate;    (b) coupling monomers on the first synthesis area at locations determined by the first reticle;    (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and    (d) coupling monomers on the first synthesis area at locations determined by the second reticle.    
     
     
         30 . The method of  claim 29 , wherein: 
 when the first reticle is aligned with the first synthesis area, every reticle of the first reticle area other than the first reticle is aligned with a discard area on the substrate.    
     
     
         31 . The method of  claim 29 , further comprising the step of: 
 dicing the substrate at least partially within the first discard area.    
     
     
         32 . The method of  claim 31 , wherein: 
 the dicing physically separates a probe array, including the first synthesis area on the substrate, from at least one other synthesis area on the substrate.    
     
     
         33 . The method of  claim 31 , wherein: 
 the plurality of reticles in each reticle area are arranged in a same pattern.    
     
     
         34 . The method of  claim 33 , wherein: 
 the pattern comprises rows and columns of reticles.    
     
     
         35 . The method of  claim 34 , wherein: 
 the dicing of the substrate is done in a straight line lying entirely within one or more discard areas including the first discard area.    
     
     
         36 . The method of  claim 29 , wherein: 
 the monomers are selected from the group consisting of nucleotides, amino acids or saccharides.    
     
     
         37 . The method of  claim 29 , wherein: 
 step (b) further comprises coupling a first monomer and step (d) further comprises coupling the first monomer or a second monomer.    
     
     
         38 . The method of  claim 29 , wherein: 
 steps (b) and (d) each further comprise directing light through the aligned reticles to de-protect the locations for coupling.    
     
     
         39 . A system for synthesizing probe arrays of polymers on a substrate, comprising: 
 (a) a mask having a plurality of reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate;    (b) an aligner constructed and arranged to 
 (i) align the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate, and  
 (ii) re-align the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and  
   (c) a synthesizer constructed and arranged to 
 (i) couple monomers on the first synthesis area at locations determined by the first reticle when the first reticle is aligned with the first synthesis area, and  
 (ii) couple monomers on the first synthesis area at locations determined by the second reticle when the second reticle is aligned with the first synthesis area.  
   
     
     
         40 . The system of  claim 39 , wherein: 
 the monomers are selected from the group consisting of nucleotides, amino acids or saccharides.    
     
     
         41 . The system of  claim 39 , wherein: 
 the synthesizer further is constructed and arranged to direct light through the aligned reticles to de-protect the locations for coupling.    
     
     
         42 - 48 . (canceled)  
     
     
         49 . A computer program product for synthesizing polymers on a substrate using a mask having a plurality of reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate, the product comprising a computer usable medium storing control logic that, when executed on a computer system, performs a method comprising the steps of: 
 (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate;    (b) coupling monomers on the first synthesis area at locations determined by the first reticle;    (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and    (d) coupling monomers on the first synthesis area at locations determined by the second reticle.    
     
     
         50 . The computer program product of  claim 49 , wherein the method further comprises the step of: 
 (e) dicing the substrate at least partially within the first discard area.    
     
     
         51 . The computer program product of  claim 49 , wherein: 
 the monomers are selected from the group consisting of nucleotides, amino acids or saccharides.