Sparse sensing DNA microarray-based biosensor: Is it feasible?

Conventional microarray-based biosensors can only detect a limited number of organisms, and adding sensor capabilities requires re-engineering of reagents and devices to detect the presence of a novel microbial organism. To overcome these limitations, the size of the microarray may need to be prohibitively large, an impractical proposition, cost-wise, using current technology. We hypothesized that a relatively small number of oligomers is sufficient to design a microarray capable of differentiating between the genomic signatures of multiple organisms. To test this hypothesis, we designed a sparse, pseudo-random prototype microarray-based biosensor by generating 12,600 25 bp oligomer probes derived from a mathematical model based on random selection of DNA sequences from seven pathogenic prokaryotic genomes. To enable identification of novel organisms, a reference library of pure genomic DNA was generated from three simulant organisms that are known to be phylogenetically distant from the seven base species used to generate the probes. These simulants were combined to produce complex DNA samples meant to mimic the uncertainty and complexity of an unknown environmental genomic background. A mathematical model was then developed to capture the signature of each simulant organism. The model detected the presence of all three simulant organisms in the mixed DNA samples with high accuracy.