Probe Design for Compressive Sensing DNA Microarrays

Compressive sensing microarrays (CSM) are DNA-based sensors that operate using the principle of compressive sensing (CS). In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM each sensor responds to a group of targets. We study the problem of designing CS probes that simultaneously account for both the constraints from group testing theory and the biochemistry of probe-target DNA hybridization. Our results show that, in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, experiments show that out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications for which only short hybridization times are allowed.