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A miniaturized, inexpensive and battery operated ultra-sensitive nanomaterial-based fluorescence resonance energy transfer (NSET) probe has been developed and evaluated for screening microbial pathogens DNA and chemical toxins at high sensitivity and selectivity. This paper illustrates application of the NSET portable device to detect microbial pathogens, e.g., Campylobacter, C. perfringens, and S. aureus DNA based on quenching of the NSET signal by gold nanoparticles to detect single base-mismatch DNA with high sensitivity (600 fM). Presence of the fluorescence signal indicates that the target DNA has been detected. We also report that the NSET probe is capable of screening chemical toxins like mercury from contaminated water with excellent sensitivity (2 parts-per-trillion) and selectivity for over competing analytes.