LysoTracker Red DND-99 | CAS 231946-72-8

LysoTracker Red DND-99 is a red-fluorescent lysosome-selective staining reagent widely used to visualize acidic organelles in fixed and live-cell fluorescence workflows. The dye accumulates in acidic compartments, enabling strong contrast for monitoring lysosomal distribution and trafficking by fluorescence microscopy and related imaging platforms.

1. Lysosome Fluorescence Imaging

LysoTracker Red DND-99 is routinely used by cell biologists and imaging core facilities to label lysosomes and quantify changes in lysosomal abundance, morphology, and subcellular localization. Researchers commonly apply it in confocal and widefield fluorescence microscopy to follow lysosome dynamics during endocytic transport, autophagy-related workflows, and stimulus-driven trafficking studies. Because the staining readout is driven by lysosomal acidity, the reagent is frequently selected when the experimental goal is to track acidic organelles rather than to label a specific lysosomal protein.

2. Flow Cytometry Lysosomal Staining

LysoTracker Red DND-99 supports fluorescence-based population analysis for assays that compare lysosomal content or acidity across experimental conditions. In flow cytometry workflows, investigators use the dye to generate lysosome-associated fluorescence signals for cell-state comparisons, screening-style experiments, and method development for fluorescent readouts tied to acidic compartments. The reagent is also used to evaluate treatment-dependent shifts in lysosomal staining intensity in adherent or suspension cell models, where lysosome-associated signal can be measured alongside other fluorescence channels.

3. Autophagy And Trafficking Studies

LysoTracker Red DND-99 is commonly incorporated into experimental designs that probe endolysosomal trafficking and autophagy-related processes, where lysosome acidification and compartment remodeling are key observables. Researchers use the dye to visualize how lysosomes redistribute in response to nutrient or stress conditions, and to assess whether perturbations alter lysosomal compartment organization over time. This makes the reagent a practical choice for mechanistic cell biology studies that require a compartment-level fluorescence marker compatible with standard fluorescence imaging and quantitative analysis.

4. Multi-Channel Cellular Assays

LysoTracker Red DND-99 is frequently selected as a lysosome channel in multi-stain experiments that include additional fluorescent markers for membranes, nuclei, cytoskeleton, or endocytic pathway components. Imaging groups use it to contextualize lysosomal localization relative to other cellular structures, improving interpretability in colocalization studies and phenotypic imaging assays. Its red emission profile is often leveraged to reduce spectral overlap when designing multi-color panels for microscopy and imaging-based quantification.