The proposed Universal Fingerprinting Chips (UFCs) are microarrays of thousands of oligonucleotide probes designed to interrogate the "sequence space" occupied by essentially any genome or transcriptome. The probe sequences are selected according to specific criteria tailored to the particular application. For example, the probe length will depend on the genetic complexity of the analyte nucleic acid and sequences are chosen to maximize the sequence diversity and avoid repetitive sequences and yield information-rich hybridization fingerprints. Major envisioned applications of the UFC include species, strain and individual identification, phylogenetic tree construction, DNA marker discovery, and gene expression profiling. One advantage of the UFC over traditional DNA fingerprinting methods is its greater information content, which is envisioned to increase the accuracy of species and strain identification. Another advantage of the UFC is that its use does not require any nucleotide sequence information, which enables genomic fingerprinting and gene expression profiling to be carried out in species that have not yet been sequenced. In the field of molecular systematics it is envisioned that phylogenetic relationships can be determined simply and rapidly using the UFC, as opposed to the current labor-intensive sequencing approach. In this Phase I SBIR we propose to demonstrate feasibility of the UFC for microbial identification and phylogenetic tree construction. The specific aims include (i) determine appropriate probe length for DNA samples of various genetic complexities; (ii) identify experimental protocols that yield reproducible UFC fingerprints; (iii) design and fabricate UFCs for species identification and phylogenetic tree construction in bacteria; (iv) build a UFC Reference Database containing both experimentally derived and in silico-predicted fingerprints and develop fingerprint analysis tools; and (v) demonstrate the utility of UFC in bacterial identification and phylogenetic tree construction. The UFCs will be designed using Amerigenics' UFCdesigner software and fabricated in the Invitrogen microfluidic XeoChip platform. UFCs will be tested using a variety of bacterial DNAs acquired from ATCC plus strains in the University of Tennessee Center for Environmental Biotechnology culture collection. Phylogenetic trees constructed using Amerigenics' UFCtree software will be compared with those obtained by the traditional sequence alignment method
