This method enables targeting of 100 spots per second. The enzyme Cleavase recognizes and cuts secondary structures formed in the single strands of a DNA fragment following denaturation. Presence of a mutation is indicated by a change in fragment pattern near the mutation region. Like bar codes, cleavage patterns are reproducible and can be archived electronically. Pirrung's group has developed a superior new photoremovable group for light-directed DNA array synthesis.
APEX uses analyte DNA as a template and synthesized DNA in an array as a primer.
These arrays can be used effectively for comparison sequencing with APEX and for analysis of gene expression with mRNA templates and reverse transcriptase. Substitution, deletion, and insertion mutations have been detected.