Nanomaterials are often functionalized with biological ligands to enable their use as sensors of biological activity. However, the intricacies of nano-bio interactions are poorly understood, which hampers our ability to design nanomaterial-based sensors. Current experimental tools have been unable to visualize interactions occurring on the nano-bio interface with the spatial and temporal resolution needed to quantify biological interactions at their fundamental length and time scales. To fill the need for concurrent visualization of nanoparticles and biomolecules, we have combined two common microscopy techniques, one being for the study of biomolecules and the other for the study of nanoparticles, into a single instrument that has the capacity to study both nanoparticles and biological molecules simultaneously with spatial and temporal resolution that is appropriate for nanoscale interactions. This novel instrument has been used for the characterization of high-sensitivity sensors by designing synthetic biological polymers to selectively encapsulate single-wall carbon nanotubes. The design of synthetic sensing tools based on nanoparticle-biomolecule hybrids is promising for areas in need of high-specificity sensors, such as label-free detection of molecules within a cell, nanoparticle-based diagnostic tools, and nanoscale therapeutics. We introduce three examples of high-sensitivity and high-selectivity synthetic sensors that have the ability to detect a variety of molecules on a single-molecule scale: riboflavin, L-thyroxine, and oestradiol. These sensors have been used to detect and quantify riboflavin levels within a live murine macrophage cell in real-time. The findings provided herein will enable the development of early-onset diagnostic tools at the level of a single cell.