JC-1 (CBIC2) is a fluorescent lipophilic carbonyl cyanine dye. JC-1 is used to measure mitochondrial membrane potential. When the mitochondrial membrane potential is relatively high, JC-1 converges in the matrix to form a polymer, which can produce red fluorescence (λex=585 nm, λem=590 nm). When the mitochondrial membrane potential is low, JC-1 cannot accumulate in the mitochondrial matrix and exists in the form of monomers to produce green fluorescence (λex=510 nm, λem=527 nm).

MitoSOX Red TFA (Mito-hydroethidine TFA) is a fluorescent probe that specifically targets mitochondria in living cells.MitoSOX Red is susceptible to oxidation by superoxide, but is not easily oxidized by other ROS or RNS-generating systems.MitoSOX Red acts as a fluorescent indicator and can be used for live cell imaging.

MitoBADY is a mitochondria-selective Raman probe composed of bis(phenylbutadiene) with triphenylphosphine for live cell imaging of mitochondria.

DiSC3(5) is a lipophilic cationic fluorescent probe sensitive to changes in membrane potential. 3,3'-Dipropylthiadicarbocyanine iodide accumulates in hyperpolarized cell membranes, leading to fluorescence quenching; when the membranes are depolarized, the dye is released from the cells and the fluorescence intensity is enhanced, which is used for real-time monitoring of mitochondrial membrane potential changes and membrane hyperpolarization. The maximum excitation/emission wavelength was 622/670 nm.

TMRM Perchlorate (T668) is a cell-permeant cationic lipophilic red fluorescent dye (λex=530 nm, λem=592 nm).

JC-10 is a potent inhibitor of metalloproteinases and is often used as a probe.

MitoTracker Orange CMTMRos is a live cell fluorescent dye that labels mitochondria in living cells by mitochondrial membrane potential accumulation and is suitable for live cell imaging and apoptosis studies.

4-Di-1-ASP is a positively charged fluorescent dye used to label glioma cells in live brain tissue and can also be used to observe mitochondria in live cells, with λex/λem = 475/606 nm.

10-Octadecylacridine orange (bromide) serves as a versatile dye, instrumental in both scientific and industrial applications. Within the realm of biological experiments, this dye facilitates the observation and analysis of cell structures, enables tracking of biomolecules, assists in cell function evaluation, aids in distinguishing cell types, detects biomolecules, supports tissue pathology studies, and monitors microorganisms. Its use extends beyond basic research into a broad spectrum of clinical diagnostics. Additionally, the dye is prevalent in traditional sectors like textile dyeing and in innovative areas including functional textile processing, food pigments, and dye-sensitized solar cells.

Mito-CCY, a mitochondria-targeted NIR-absorbing cryptocyanine probe, exhibits high photothermal conversion efficiency and good biological compatibility in vitro. Additionally, it demonstrates photoinduced cytotoxicity in HeLa cells [1].

Oxonol Blue is a staining dye that can be used as a monitor of membrane potential [1].

DMANI is a mitochondria-targeted ratiometric fluorescent probe based on intramolecular charge transfer (ICT). It is useful for monitoring mitochondrial peroxynitrite (ONOO−) within living cells.

HKOCl-4m is a rhodol-based fluorescent probe designed for the specific and deliberate targeting of mitochondria, enabling the monitoring of mitochondrial hypochlorous acid (HOCl).

DASPEI, a cationic styrenyl mitochondrial dye, is characterized by a large Stokes shift and excitation/emission wavelengths at 550/573 nm, yielding robust chromogenic properties. It effectively stains mitochondria in live cells and labels presynaptic nerve endings regardless of neuronal activity [1].

Rhodamine 6G hydrazide (R6GH), a fluorescent dye, is employed for selective colorimetric and fluorescent sensing [1].

MitoTracker Deep Red FM is a deep red fluorescent dye for mitochondria that selectively accumulates within the mitochondrial matrix dependent on the mitochondrial membrane potential (Δψ). It covalently binds to mitochondrial proteins by reacting with free thiol groups on cysteine residues. Following covalent binding, sensitivity to Δψ changes diminishes, though initial staining remains Δψ-dependent. The MitoTracker Deep Red FM probe is suitable for staining live cells or tissues, serving to label mitochondria and indirectly detect mitochondrial membrane potential alterations. Its maximum excitation/emission wavelengths are 644/665 nm (Storage: Protect from light).

3,3′-Diheptylthiacarbocyanine iodide, a cyanine dye used for measuring membrane potential (λ ex = 562 nm, λ em = 575 nm) [1].

Janus blue is a basic dye.

HBmito Crimson is a cell-permeable red fluorescent probe specifically targeting the inner mitochondrial membrane (IMM). It exhibits high selectivity for the IMM, making it useful for specific fluorescent staining of live cell mitochondria.

4-Di-2-ASP, a styryl pyridinium fluorescent dye, serves as an essential mitochondrial marker. It effectively and specifically labels pulmonary NEBs (neuroepithelial bodies) [1].

Mito Flipper-TR 27, a fluorescent probe, accumulates in mitochondria to measure membrane tension in living cells. Its accumulation is driven by the strong internal negative membrane potential, which propels the permanently hydrophobic triphenylphosphine cation across the inner membrane and prevents its release, thereby facilitating mitochondrial tracking [1].

Mito Red is a multifunctional dye used extensively in biological experiments to observe and analyze cell structures, track biomolecules, assess cell functions, distinguish cell types, detect biomolecules, study tissue pathology, and monitor microorganisms. Its applications range from basic scientific research to clinical diagnostics. Additionally, dyes are widely utilized in traditional fields like textile dyeing, as well as emerging areas such as functional textile processing, food pigments, and dye-sensitized solar cells.

Tetramethylrhodamine B isothiocyanate (Rhodamine B, tetramethyl-, isothiocyanate) is a fluorescent dye with a strong two-photon absorption at approximately 830 nm [1].

Rhodamine B hexyl ester (perchlorate) is a cell-permeant, orange-fluorescent dye specifically targeting mitochondria.