The development of super-resolution microscopy has been one of the most important advances in order to image tissue structures or cellular dynamics and interactions at the nanoscale. Because of the biological targets, super-resolution experiments are typically performed in aqueous solution. However, water is known to be a fluorescence quencher of organic dyes and the replacement of H2O by D2O can drastically increase the fluorescence quantum yield and the localization precision. Recently, the quenching of 40 dyes was investigated leading to the conclusion of a FRET mechanism between red-emitting fluorophores and vibrational overtones and combination bands of -OH groups of the solvent in direct contact with the dyes. Since fluorophores in biological samples are mostly surrounded by water, one way to prevent quenching from occurring would be to isolate them from the solvent using macrocyclic cavities such as cyclodextrins and cucurbiturils. The goal of this thesis work was therefore to investigate encapsulation strategies for red-emitting fluorophores compatible with the stringent requirement of single-molecule and super-resolution imaging, that either enable to efficiently shield fluorophores from water, thereby enhancing their brightness, or to modulate their photophysics in other useful ways.