  Plasmonically enhanced fluorescence is a widely studied and applied
phenomenon, however only a comparative theoretical and experimental analyses of
coupled fluorophores and plasmonic nanoresonators makes it possible to uncover,
how this phenomenon can be controlled. A numerical optimization method was
applied to design configurations that are capable of resulting in an
enhancement of excitation and emission, moreover of both phenomena
simultaneously in coupled Cy5 dye molecule and gold nanorod systems. Parametric
sensitivity studies revealed, how the fluorescence enhancement depends on the
molecule's location, distance and orientation. Coupled systems designed for
simultaneous improvement exhibited the highest (intermediate directional) total
fluorescence enhancement, which is accompanied by intermediate sensitivity to
the molecule's parameters, except the location and orientation sensitivity at
the excitation wavelength. Gold nanorods with a geometry corresponding to the
predicted optimal configurations were synthesized, and DNA strands were used to
control the Cy5 dye molecule distance from the nanorod surface via
hybridization of the Cy5-labelled oligonucleotide. State-of-the-art dSTORM
microscopy was used to accomplish a proof-of-concept experimental demonstration
of the theoretically predicted (directional) total fluorescence enhancement.
The measured fluorescence enhancement was in good agreement with theoretical
predictions, thus providing a complete kit to design and prepare coupled
nanosystems exhibiting plasmonically enhanced fluorescence.
