A Bright, Photostable, and Far-Red Dye That Enables Multicolor, Time-Lapse, and Super-Resolution Imaging of Acidic Organelles.

Lysosomes have long been known for their acidic lumens and efficient degradation of cellular byproducts. In recent years, it has become clear that their function is far more sophisticated, involving multiple cell signaling pathways and interactions with other organelles. Unfortunately, their acidic interior, fast dynamics, and small size make lysosomes difficult to image with fluorescence microscopy. Here we report a far-red small molecule, HMSiR-Me, that fluoresces only under acidic conditions, causing selective labeling of acidic organelles in live cells. HMSiR-Me can be used alongside other far-red dyes in multicolor imaging experiments and is superior to existing lysosome probes in terms of photostability and maintaining cell health and lysosome motility. We demonstrate that HMSiR-Me is compatible with overnight time-lapse experiments as well as time-lapse super-resolution microscopy with a frame rate of 1.5 fps for at least 1000 frames. HMSiR-Me can also be used alongside silicon rhodamine dyes in a multiplexed super-resolution microscopy experiment to visualize interactions between mitochondria and lysosomes with only a single excitation laser and simultaneous depletion. We envision this dye permitting a more detailed study of the role of lysosomes in dynamic cellular processes and disease.