Lysosomes are the “waste-disposal” system of the cell digesting unwanted materials and cellular debris in the cytoplasm. They are membrane-enclosed organelles that have an acidic interior (pH ∼4.8) and can vary in size from 0.1 to 1.2 µm. Lysosomes house various hydrolytic enzymes responsible for digesting biopolymers such as proteins, peptides, nucleic acids, carbohydrates and lipids. The synthesis of lysosomal hydrolases are controlled by nuclear genes, and mutations in these genes can cause an array of inherited metabolic disorders due to defects in lysosomal enzyme functionality. These metabolic disorders are collectively known as lysosomal storage diseases. Defects to lysosomal hydrolytic enzymes result in the accumulation of macromolecules or monomeric compounds contributing to abnormal signaling pathways which ultimately lead to pathogenic disorders. In addition to breaking down polymers, lysosomes can fuse with other organelles to allow lysosomal hydrolytic enzymes to digest the organelle’s contents and to clear out damaged structures, a mechanism known as autophagy.

Lysosomal Labeling Dyes and Kits

LysoBrite™ dyes are a series of cell-permeable fluorecent dyes for imaging lysosomal morphology and localization, and to investigate the biosynthesis and pathogenesis of lysosomes in live cells. At nanomolar concentrations, LysoBrite™ dyes selectively target and accumulate within lysosomes and other acidic organelles via the lysosomal pH gradient. Upon entering lysosomes, the pH-sensitive fluorescence of LysoBrite™ dyes significantly enhances. The resulting signal can be measured using either fluorescence imaging, high-content imaging, microplate fluorometry, or flow cytometry. LysoBrite™ Orange, LysoBrite™ Red, LysoBrite™ Deep Red, and LysoBrite™ NIR dyes have extremely high photostability as well as excellent cellular retention make them useful for a variety of studies, including cell adhesion, chemotaxis, multidrug resistance, cell viability, apoptosis and cytotoxicity.


LysoBrite™ Dyes for Live Cell Lysosomal Imaging

LysoBrite™ dyes are available in spectral characteristics ranging from blue to near-infrared to accommodate multiplexing with other fluorescent probes or after fixation for co-localization studies if using fixable dye LysoBrite™ Red DND-99 (Cat No. 22647). LysoBrite™ dyes are key components of Cell Navigator™ Lysosome Staining Kits made available separately here. Each kit provides sufficient materials for 500 tests.

Features of LysoBrite™ dyes:

  • Selectively accumulates inside lysosomes and other acidic organelles via the lysosomal pH gradient
  • pH-sensitive fluoresence for a more specific lysosomal staining
  • Photostable signal generation for extended imaging windows
  • Minimal cytotoxicity
  • Can be imaged without washing
  • Multiple wavelength options for multiplex analysis with other fluorescent probes
  • Suitable for both proliferating and non-proliferating cells, as well as, cell in suspension and adherent cells

LysoBrite™ Green vs LysoTracker® Green

Figure 1. Images of HeLa cells stained with AAT Bioquest’s LysoBrite™ Green (Cat No. 22643) and ThermoFisher’s LysoTracker® Green DND-26 in a Costar black wall/clear bottom 96-well microplate. Samples were continuously illuminated for 120 seconds and the signals were compared before and after exposure using a Keyence fluorescence microscope.

Table 1. Available LysoBrite™ dyes for labeling lysosomes in live cells.

Product name Sample Type Fixable Ex (nm) Em (nm) Filter Set Unit Size Cat No. Assay Kit No.
LysoBrite™ Blue Live Cells No 434 480 DAPI 500 Tests 22642 22655
LysoBrite™ VLG26 Live Cells No 405 480 Violet 500 Tests 22651
LysoBrite™ Green Live Cells No 501 510 FITC 500 Tests 22643 22656
LysoBrite™ Orange Live Cells No 543 565 TRITC 500 Tests 22644 22657
LysoBrite™ Red DND-99 Live Cells Yes 573 592 TRITC 500 Tests 22647
LysoBrite™ Red Live Cells No 576 596 TRITC 500 Tests 22645 22658
LysoBrite™ Deep Red Live Cells No 597 619 Texas Red 500 Tests 22646 22659
LysoBrite™ NIR Live Cells No 636 651 Cy5 500 Tests 22641 22652

CytoFix™ Red Fixable Lysosomal Stain

The enhanced cellular retention of CytoFix™ Red lysosomal stain preserves its lysosomal localized fluorescence even after the pH gradient is lost during fixation. The fluorescence signal generated by this dye is well-retained in the lyososme for at least 1 week, making it well-suited for long-term lysosomal tracking. CytoFix™ Red can be used with GFP expressed cells, other fluorescent conjugates or other organelle stains for multicolor analysis. It can be used for both suspension and adherent cells and readily adapted for a wide variety of fluorescence platforms.

Features of CytoFix™ Red:

  • High lysosomal staining efficiency
  • Long retention after fixation (1 week or longer)
  • Labeling protocol with minimal hands on time

CytoFix™ Red

Figure 2. The fluorescence images of HeLa cells stained with CytoFix™ LysoRed in a 96-well black-wall clear-bottom plate. Image was acquired before (Left) and after (Right) fixation with 4% formaldehyde solution for 20 minutes at RT. The cells were imaged using fluorescence microscope with a Cy3/TRITC filter.

Table 2. CytoFix™ Red fixable lysosomal stain

Product name Sample Type Fixable Ex (nm) Em (nm) Filter Set Unit Size Cat No.
CytoFix™ Red Lysosomal Stain Live Cells Yes 540 590 Cy3/TRITC 500 Tests 23210

Autophagy – Lysosomal Degradation Pathway

Autophagy is a natural and regulated lysosomal degradation pathway essential for cell viability, development and homeostasis. It is the destructive mechanism of cells that degrades and recycles unnecessary or dysfunctional cellular components. It achieves this through the sequestration of targeted cytoplasmic materials into double-membrane bound organelles known as autophagosomes. These autophagosomes later fuse with lysosomal organelles to have their contents digested and recycled by lysosomal enzymes. Autophagy serves as an adaptive mechanism to protect organisms against various pathologies. To investigate the role autophagy plays in cell homeostasis, imaging tools and assays have been developed to monitor autophagy functionality in response to cellular stress, microbial infection and disease. Cell Meter™ Autophagy Fluorescence Imaging Kits utilizes our proprietary Autophagy Super Blue™ probe, to selectively target and analyze autophagy activity.

Control Autophagy Treatment
(DMEM Medium)
Autophagy Treatment
(1X HBSS buffer with 5% serum)
Figure 3. Autophagy Green™ labeled vesicles are induced by starvation in HeLa cells. HeLa cells were incubated in a regular DMEM medium (Control) or in 1X HBSS buffer with 5% serum (Autophagy Treatment) for 16 hours. Both control cells and starved cells were incubated with Autophagy Green™ working solution for 20 minutes in a 37 °C, 5% CO2 incubator, and then washed 3 times with wash buffer. Cells were imaged immediately under a fluorescence microscope with a FITC channel (green). Cell nuclei were stained with Hoechst 33342 (Cat No. 17530).


Table 3. Cell Meter™ assay kits for measuring autophagy activity.

Product name Sample Type Ex (nm) Em (nm) Filter Set Unit Size Cat No.
Cell Meter™ Autophagy Fluorescence Imaging Kit Live Cells 360 445 DAPI 200 Tests 23001
Cell Meter™ Autophagy Assay Kit *Blue Fluorescence* Live Cells 360 445 DAPI 200 Tests 23000
Cell Meter™ Autophagy Assay Kit *Green Fluorescence* Live Cells 485 525 FITC 200 Tests 23002
Cell Meter™ Mitochondrial Autophagy Imaging Kit *Red Fluorescence* Live Cells 540 590 Cy3/TRITC 100 Tests 22998

Product Ordering Information


Table 4. Ordering Info for Lysosome Products

Cat# Product Name Unit Size
22641 LysoBrite™ NIR 500 Tests
22642 LysoBrite™ Blue 500 Tests
22643 LysoBrite™ Green 500 Tests
22644 LysoBrite™ Orange 500 Tests
22645 LysoBrite™ Red 500 Tests
22646 LysoBrite™ Deep Red 500 Tests
22647 LysoBrite™ Red DND-99 500 Tests
22651 Cell Navigator™ Lysosome Staining Kit *Green Fluorescence with 405 nm Excitation* 500 Tests
22652 Cell Navigator™ Lysosome Staining Kit *NIR Fluorescence* 500 Tests
22655 Cell Navigator™ Lysosome Staining Kit *Blue Fluorescence* 500 Tests
22656 Cell Navigator™ Lysosome Staining Kit *Green Fluorescence* 500 Tests
22657 Cell Navigator™ Lysosome Staining Kit *Orange Fluorescence* 500 Tests
22658 Cell Navigator™ Lysosome Staining Kit *Red Fluorescence* 500 Tests
22659 Cell Navigator™ Lysosome Staining Kit *Deep Red Fluorescence* 500 Tests
23000 Cell Meter™ Autophagy Assay Kit *Blue Fluorescence* 200 Tests
23001 Cell Meter™ Autophagy Fluorescence Imaging Kit 200 Tests
23002 Cell Meter™ Autophagy Assay Kit *Green Fluorescence* 200 Tests


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