Enhancing FRET through DNA-controlled Emitters and ENZ Metamaterials

Abstract: The ability to significantly enhance energy transfer processes at the nanoscale requires the simultaneous optimization of molecular scale orientation and macroscopic photonic enhancement between multiple quantum emitters. However, achieving this dual control has remained a significant experimental challenge, often limited by the stochastic arrangement of emitter assemblies and spatially non-uniform electromagnetic fields in conventional photonic platforms. In this work, we demonstrate a unified architecture that achieves this synergy by combining the structural precision of DNA nanotechnology with the unique field environment generated by epsilon-near-zero (ENZ) materials. Using DNA molecular beacons as programmable emitter scaffolds, we establish fixed donor-acceptor separations and emitter orientations (Atto425/Cy3.5) in two well-defined conformational states: closed hairpin (emitter separation 2 nm), and open extended (7.2 nm) configurations. These structures are then embedded in the near-field of a multilayer ENZ metamaterial substrate, which facilitates spatially uniform, enhanced electromagnetic field coupling. Time-resolved photoluminescence measurements demonstrate a significant increase in FRET efficiency for DNA-programmed emitter pairs in the ENZ environment, compared to those on a glass substrate, corresponding to increased donor quenching and shortened donor lifetime. These results establish a scalable experimental pathway for engineering light-matter interactions at molecular scales, enabled by the structural precision of DNA paired with ENZ mediated redistribution of the local density of optical states (LDOS) to amplify near-filed coupling between quantum emitters, with applications in next-generation bio-sensing and quantum photonic technologies.