A molecular sensor to quantify the localization of proteins, DNA and nanoparticles in cells

Intracellular trafficking governs receptor signaling, pathogenesis, immune responses and fate of nanomedicines. These processes are typically tracked by observing colocalization of fluorescent markers using confocal microscopy. However, this method is low throughput, limited by the resolution of microscopy, and can miss fleeting interactions. To address this, we developed a localization sensor composed of a quenched SNAP-tag substrate (SNAP_Switch) that can be conjugated to biomolecules using click chemistry. SNAP_Switch enables quantitative detection of trafficking to locations of interest within live cells using flow cytometry. Using SNAP_Switch, we followed the trafficking of DNA complexes from endosomes into the cytosol and nucleus. We show that antibodies against the transferrin or hyaluronan receptor are initially sorted into different compartments following endocytosis. In addition, we can resolve which side of the cellular membrane material was located. These results demonstrate SNAP_Switch is a high-throughput and broadly applicable tool to quantitatively track localization of materials in cells.