A Review of Reagents for Fluorescence Microscopy of Cellular Compartments and Structures, Part II: Reagents for Non‐Vesicular Organelles

Abstract

A wide range of fluorescent dyes and reagents exist for labeling organelles in live and fixed cells. Choosing between them can lead to confusion, and optimization for many of them can be challenging. Presented here is a discussion on the commercially available reagents that have shown the most promise for each organelle of interest, including endoplasmic reticulum/nuclear membrane, Golgi apparatus, mitochondria, nucleoli, and nuclei, with an emphasis on localization of these structures for microscopy. Included is a featured reagent for each structure with a recommended protocol, troubleshooting guide, and example image.

Innovative Cyanine-Based Fluorescent Dye for Targeted Mitochondrial Imaging and Its Utility in Whole-Brain Visualization

“…Additionally, imaging deep brain regions can be challenging due to light scattering, absorption, and tissue autofluorescence, which can disrupt clear and specific labeling with MitoTracker dyes. Lastly, MitoTracker dyes can sometimes accumulate in other cellular compartments or structures, leading to potential false signals or confusion in interpretation . To overcome these limitations, we aim to find new fluorescent dyes that target mitochondria and aid in studying these organelles, particularly for in vivo brain imaging.…”

“…Lastly, MitoTracker dyes can sometimes accumulate in other cellular compartments or structures, leading to potential false signals or confusion in interpretation. 11 To overcome these limitations, we aim to find new fluorescent dyes that target mitochondria and aid in studying these organelles, particularly for in vivo brain imaging.…”

Comparing Mitochondrial Activity, Oxidative Stress Tolerance, and Longevity of Thirteen Ascomycota Yeast Species

“…A chloromethyl moiety on the structure allows the dye binding to thiol groups on proteins through this chloromethyl group, which enhances the dye's retention. The charge-related accumulation of MitoTracker Red CMXRos is what gives the dye its usefulness as an indicator of mitochondrial membrane potential: the fluorescent intensity diminishes upon mitochondrial depolarization (for a recent review, see [34]). As shown in Figure 4 by fluorescence microscopy, the dye heavily stained the mitochondria of 7 strains, and barely incorporated into the mitochondria of S. cerevisiae, S. kudriavzevii and S. castellii (Figures 4 and S4).…”