Enhancing FRET through DNA-Controlled Emitters and ENZ Metamaterials

Abstract Simultaneous nanoscale spatial control and macroscopic electromagnetic enhancement are critical for maximizing resonance energy transfer. However, conventional systems with photonic platforms suffer from stochastic emitter distributions and steep field gradients. Here we demonstrate a unified architecture combining programmable DNA molecular beacons with an epsilon-near-zero (ENZ) multilayer metamaterial. Using DNA scaffolds, donor–acceptor pairs (Atto425/Cy3.5) are structurally locked into closed (2 nm) and extended (8.16 nm) conformations within the ENZ near field. Time-resolved photoluminescence reveals accelerated donor decay and an increase in extended state energy transfer efficiency from 56.7% on glass to 79.4% on ENZ, corresponding to a 5.8-fold transfer rate acceleration. Electromagnetic Green tensor modeling confirms that ENZ boundary conditions strongly amplify dipole coupling within the first few nanometers of the interface, exhibiting pronounced orientation selectivity. This hybrid platform provides a deterministic orientational and spatial control for sculpting molecular-scale light–matter interactions.