Sequence-specific nucleic acid detection has become a pervasive theme in a variety of biomedical disciplines, such as disease diagnosis and treatment, forensic analysis and biodefence strategy. Driven by the need to analyze an ever-increasing number of target sequences in a complex mixture, our current efforts have been focused on the development of addressable DNA nanosensors capable of measuring multiple targets (Bacillus anthracis [anthrax] and Escherichia coli) in parallel. In this paper, we report a gold-nanoparticle-based miniaturized, inexpensive and battery-operated ultra-sensitive fluorescence resonance energy transfer probe for screening bioagent’s DNA, with excellent sensitivity (600 fM) and selectivity. We have demonstrated a multiplexed hybridization detection method in a homogeneous, separation-free format based on multicolor oligonucleotide-functionalized dyes with gold nanoprobes.

Our experimental observation paradigm for the design of optical-based molecular-ruler strategies more than triples the distances achieved using traditional dipole–dipole Columbic energy-transfer-based methods. Given the simplicity, speed and sensitivity of this approach, the described methodology could easily be extended to a high-throughput format and become a new method of choice in all applications that require an assay for bioagent DNA detection. Our observations also point toward an exciting possibility to perform spatially confined detection on array formats of biological recognition.