Single Molecule Oscillations of an RNA/DNA Duplex in a Plasmonic Nanocavity

We report the visualization of single molecule dynamics in epifluorescence mode through extraordinary plasmonic enhancement provided by silver grating with embedded nanocavities. Cy3/Cy5-labeled DNA/RNA hybrid duplexes were affixed to SiO2-capped silver gratings produced by soft lithography process. Tracking single-molecule fluorescence revealed damped sub-1 Hz periodic Cy3 intensity fluctuations with strong dependence on the bulk MgCl2 concentration. Extreme concentration of electric field at the nanocavity edge induces plasmonic heating, which sets up convection deep within the nanocavity. Local fluctuations in Mg2+ ion concentration promote a bent or unbent duplex conformational state, respectively, by varying degrees of negative charge screening along the duplex backbone. These oscillations continue until the duplex conformational state stabilizes or the dyes bleach. This unique molecular behavior in the nanocavity could be used to study duplex complementarity, structural polymorphisms, and protein-nucleic acid interactions at the single molecule level.