Fluorescence resonance energy transfer (FRET) has been instrumental to determine the structure and dynamics of biomolecules but distances above 8 nanometer are not accessible. However, with the advent and rapid development of super-resolution (SR) microscopy, distances between two fluorescent dyes below 20 nanometer can be resolved, which hitherto has been inaccessible for fluorescence microscopy approaches. Therefore, the question arises whether SR microscopy can ultimately close the resolution gap between FRET and the diffraction limit and whether SR microscopy can be employed for the structural interrogation of proteins in the sub-20 nm range? Here, we show that the marriage of DNA nanotechnology and single-molecule biochemistry allows the first steps towards the investigation of the structural organization of a protein via SR microscopy. Limiting factors and possible future directions for the full implementation of SR microscopy as structural tool are discussed.