Single molecule Förster resonance energy transfer (smFRET) is widely used to monitor conformations and interactions dynamics at the molecular level. However, conventional smFRET measurements are ineffective at donor-acceptor distances exceeding 10 nm, impeding the studies on biomolecules of larger size. Here, we show that zero-mode waveguide (ZMW) apertures can be used to overcome the 10 nm barrier in smFRET. Using an optimized ZMW structure, we demonstrate smFRET between standard commercial fluorophores up to 13.6 nm distance with a significantly improved FRET efficiency. To further break into the classical FRET range limit, ZMWs are combined with molecular constructs featuring multiple acceptor dyes to achieve high FRET efficiencies together with high fluorescence count rates. As we discuss general guidelines for quantitative smFRET measurements inside ZMWs, the technique can be readily applied for monitoring conformations and interactions on large molecular complexes with enhanced brightness.

Plasmonic nanoapertures generate strong field gradients enabling efficient optical trapping of nanoobjects. However, because the infrared laser used for trapping is also partly absorbed into the metal leading to Joule heating, plasmonic nano-optical tweezers face the issue of local temperature increase.Here, we develop three independent methods based on molecular fluorescence to quantify the temperature increase induced by a 1064 nm trapping beam focused on single and double nanoholes milled in gold films. We show that the temperature in the nanohole can be increased by 10°C even at the moderate intensities of 2 mW/µm² used for nano-optical trapping. The temperature gain is found to be largely governed by the Ohmic losses into the metal layer, independently of the aperture size, double-nanohole gap or laser polarization. The techniques developed therein can be readily extended to other structures to improve our understanding of nano-optical tweezers and explore heatcontrolled chemical reactions in nanoapertures.