Development of Array-Based Universal Biosensing Devices Based Upon Intelligent Oligonucleotide Probe Sets

"The present proposal describes strategies leading to the development of an array-based universal biosensor for detecting and differentiating microbial species, or differentiating at the DNA or RNA level between cell types of the same species. The proposed strategy relies on the differential hybridization of genomic DNA, extrachromosomal DNA, mRNA, or ribosomal RNA from different sources to a common, intelligently designed oligonucleotide probe set to produce a useful or diagnostic pattern or fingerprint.The rational design of the probe sets may be accomplished without a prior knowledge of specific sequence information, but will account for principles governing nucleic acid hybridization with regard to genome complexity and base content. Furthermore, thedescribed approach 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 such common arrays allowsfor the design of universal-type 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. Successfulimplementation of the principles outlind in this proposal may lead to the development of an array-based universal biosensor for detecting and differentiating microbial species without