The present invention provides a new nucleic acid hybridization-based biosensing device wherein the same can be utilized for detecting and differentiating microorganisms, or differentiating at the DNA or RNA level between cell types of the same species. The implementation of the invention relies on the differential hybridization of genomic DNA, extrachromosomal DNA, mRNA, or ribosomal RNA from different sources to a single or small number of intelligently designed oligonucleotide probes. The design of the probes not only accounts for principles governing nucleic acid hybridization on solid supports, but also allows for and, in fact, exploits deviations from predicted ideal hybridization behavior for individual probes. Interrogation of multiple species or sources of complex nucleic acid populations as systems using common arrays allows for the design of array-based universal biosensors or other bioanalytical devices without explicit prior knowledge of sequence content and without the use of cumbersome and, in some instances, unreliable bioinformatic tools for individual probe design.
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