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Zero-mode waveguides (ZMWs) are confining light into attoliter volumes, enabling single molecule fluorescence experiments at physiological micromolar concentrations. Among the fluorescence spectroscopy techniques that can be enhanced by ZMWs, F\"{o}rster resonance energy transfer (FRET) is one of the most widely used in life sciences. Combining zero-mode waveguides with FRET provides new opportunities to investigate biochemical structures or follow interaction dynamics at micromolar concentration with single molecule resolution. However, prior to any quantitative FRET analysis on biological samples, it is crucial to establish first the influence of the ZMW on the FRET process. Here, we quantify the FRET rates and efficiencies between individual donor-acceptor fluorophore pairs diffusing in aluminum zero-mode waveguides. Aluminum ZMWs are important structures thanks to their commercial availability and the large literature describing their use for single molecule fluorescence spectroscopy. We also compare the results between ZMWs milled in gold and aluminum, and find that while gold has a stronger influence on the decay rates, the lower losses of aluminum in the green spectral region provide larger fluorescence brightness enhancement factors. For both aluminum and gold ZMWs, we observe that the FRET rate scales linearly with the isolated donor decay rate and the local density of optical states (LDOS). Detailed information about FRET in ZMWs unlocks their application as new devices for enhanced single molecule FRET at physiological concentrations.

Nanophotonics achieves accurate control over the luminescence properties of a single quantum emitter by tailoring the light-matter interaction at the nanoscale and modifying the local density of optical states (LDOS). This paradigm could also benefit to F\"orster resonance energy transfer (FRET) by enhancing the near-field electromagnetic interaction between two fluorescent emitters. Despite the wide applications of FRET in nanosciences, using nanophotonics to enhance FRET remains a debated and complex challenge. Here, we demonstrate enhanced energy transfer within single donor-acceptor fluorophore pairs confined in gold nanoapertures. Experiments monitoring both the donor and the acceptor emission photodynamics at the single molecule level clearly establish a linear dependence of the FRET rate on the LDOS in nanoapertures. These findings are applied to enhance the FRET rate in nanoapertures up to six times, demonstrating that nanophotonics can be used to intensify the near-field energy transfer and improve the biophotonic applications of FRET.

Single-molecule approaches to biology offer a powerful new vision to elucidate the mechanisms that underpin the functioning of living cells. However, conventional optical single molecule spectroscopy techniques such as F\"orster fluorescence resonance energy transfer (FRET) or fluorescence correlation spectroscopy (FCS) are limited by diffraction to the nanomolar concentration range, far below the physiological micromolar concentration range where most biological reaction occur. To breach the diffraction limit, zero mode waveguides and plasmonic antennas exploit the surface plasmon resonances to confine and enhance light down to the nanometre scale. The ability of plasmonics to achieve extreme light concentration unlocks an enormous potential to enhance fluorescence detection, FRET and FCS. Single molecule spectroscopy techniques greatly benefit from zero mode waveguides and plasmonic antennas to enter a new dimension of molecular concentration reaching physiological conditions. The application of nano-optics to biological problems with FRET and FCS is an emerging and exciting field, and is promising to reveal new insights on biological functions and dynamics., Comment: WIREs Nanomed Nanobiotechnol 2014