Stochastic Protein Labeling Enables Long-Term Single Molecule Observation in vivo

To circumvent our dependence on photoactivation in single-molecule microscopy, we devise a universal genetic system to precisely control copy number of fluorescently labeled molecules in a cell. Combined with photostable labels, this system enables long-term single-particle tracking of densely-packed cellular organelles and proteins. Real-time imaging in neurons reveals that axon initial segment actively promotes synaptic vesicle anterograde transport by a "waterfall" mechanism. We also show that transcription factor Sox2 samples clustered binding sites in spatially-restricted regions, suggesting that topological structures in the nucleus shape gene activities by a sequestering mechanism. This strategy thus greatly expands spatiotemporal length scales of live-cell single-molecule measurements to quantitatively understand complex control of molecular dynamics in vivo.