A DNA-Based Plasmonic Nano-Ruler

DNA is an exceptional building block for the fabrication of dynamic supramolecular systems with chemically switchable geometries. Here, a self-assembled, fine-tunable plas-monic-fluorescent ruler was developed. A precise sliding motion mechanism was operated through the strict control of strand displacement reactions, shifting two ssDNA rails over a ssDNA quasi-ring structure. The DNA ruler, reconfigured as a nano-mechanical slider, and gen-erated six discrete configurations, setting specific distances between a tethered gold nanoparticle (AuNPs), and a fluorophore unit (Cy3), placed at two different distinct sites on the rigid nano-structure. In order to optimize the system, the reversible distance-dependent fluorescence quenching or enhancement phenomena were investigated by testing gold nanoparticles with diameters 5, 10 and 15 nm AuNPs. The best performances in terms of Cy3 fluorescence mod-ulation were yielded by 10 nm AuNPs , as experimentally demonstrated by fluorescence emis-sion kinetics during the strand-displacement operated reconfigurations. Furthermore, a geomet-ric model of the system was produced, confirming the observed results. The fluoro-phore-plasmonic surface positioning, conferred by the DNA ruler, led to an overall finite state nano-machine with six alternative signal outputs. This mechanism, working as a fluorescent re-porter, could find application in multiple responsive detection of single-strand nucleic acid, such as virus or miRNA.