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Enhancing FRET through DNA-controlled Emitters and ENZ Metamaterials

Akeshi Aththanayeke, Andrew Lininger, Anh Pham, Radu Malureanu, Divita Mathur, Giuseppe Strangi

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.

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.
Paper Structure (8 sections, 2 equations, 4 figures, 1 table)

This paper contains 8 sections, 2 equations, 4 figures, 1 table.

Table of Contents

  1. Introduction
  2. Experimental Methods
  3. Experimental Implementation
  4. System Description
  5. Results and Discussion
  6. Closed MB
  7. Opened MB
  8. Conclusion

Figures (4)

  • Figure 1: Experimental implementation and system description: a) Experimental layout for steady-state and time-resolved spectroscopy. b) Schematic of DNA beacon-based spatial locking of the donor-acceptor pair. Dye-labeled MBs are embedded in a thin PVA film on the ENZ multilayer, positioning fixed-distance FRET pairs within the ENZ near field.
  • Figure 2: ENZ and fluorophore selection: (a) Schematic cross-section of the Au/TiO$_2$ multilayer ENZ platform with the ellipsometry data for real and imaginary parts of the permittivity ($n$=periodicity for the layers). (b) Normalized donor emission and acceptor absorption spectra showing the donor-acceptor spectral overlap region. (c) Molecular structures of the donor (left) and acceptor (right), with the atomic model of the complete molecular beacon shown in the middle abramson2024accurate (closed MB configuration).
  • Figure 3: Closed MB system (a) Donor+Acceptor PL decay curves on glass and ENZ substrates (400 nm excitation and 532 emission) (b) Histogram showing the fastened decay on ENZ (c) Steady-state fluorescence emission intensity for the closed donor-MB and for the closed MB systems.
  • Figure 4: Opened MB system (a) Time-resolved photoluminescence (PL) decay curves for the unfolded beacon containing only the donor dye, measured on a 90 nm polymer film on glass and on the ENZ substrate. (b) PL decay curves for the unfolded beacon containing both donor and acceptor dyes under the same film and substrate conditions (c) Steady-state FL emission opened MB configurations (d) Hierarchical enhancement of energy transfer efficiency, the transition from the stochastic limit (blue dashed line) to the non-enhanced limit on glass (green bar) demonstrates the structural precision provided by DNA locked precision, which overcomes the geometric uncertainty typical of random fluorophore dispersions. The subsequent transition from glass to the ENZ substrate (yellow bar) represents the Photonic enhancement phase.