Techniques for synthesis integrity evaluation utilizing cycle fidelity probes

Abstract

Techniques for designing polymer probes to verify the integrity of the probe synthesis are provided. Multiple probes with identical sequences are designed so that the probes will be formed utilizing at least one different monomer addition cycle. Based on the probes affinity to a control target, variations (e.g., errors) in probe synthesis may be identified.

1 . A chip design file for synthesizing a substrate having polymer probes coupled thereto, comprising: 
 computer code specifying a plurality of regions on the substrate in which diverse polymer probes are coupled; and    computer code specifying a plurality of regions on the substrate in which polymer probes having the same desired sequence are coupled, wherein the polymer probes having the same desired sequence will bind with a control sequence of monomers but the polymer probes are formed with at least one different monomer addition cycle that adds a same monomer and at least one of the polymer probes does not have the same actual sequence as a result of a different monomer addition cycle from an error in probe synthesis.    
     
     
         2 . The chip design file of  claim 1 , wherein the plurality of regions are at the center of the substrate.  
     
     
         3 . The chip design file of  claim 1 , wherein the plurality of regions are in a checkerboard pattern on the substrate.  
     
     
         4 . A chip design file for synthesizing a substrate having nucleic acid probes coupled thereto, comprising: 
 computer code specifying a plurality of regions on the substrate in which diverse nucleic acid probes are coupled; and    computer code specifying a plurality of regions on the substrate in which nucleic acid probes having the same desired sequence are coupled, wherein the nucleic acid probes having the same desired sequence will bind with a control sequence of nucleotides but the nucleic acid probes are formed with at least one different nucleotide addition cycle that adds a same nucleotide and at least one of the nucleic acid probes does not have the same actual sequence as a result of a different nucleotide addition cycle from an error in probe synthesis.    
     
     
         5 . The chip design file of  claim 4 , wherein the plurality of regions are at the center of the substrate.  
     
     
         6 . The chip design file of  claim 4 , wherein the plurality of regions are in a checkerboard pattern on the substrate.