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Biotium offers a wide selection of synaptic vesicle dyes, neuronal tracers, dyes for amyloid and neurotoxicity, fluorescent indicators for calcium, other ions, membrane potential, and more. Jump to a section below:

Neurotoxins & Fluorescent Toxin-Based Receptor Probes

α-Bungarotoxin (BTX) & Bungarotoxin Conjugates

α-Bungarotoxin is a potent inhibitor for the nicotinic acetylcholine receptor with sub-nanomolar affinity. Fluorescent conjugates of α-bungarotoxin can be used for labeling motor endplates in tissue sections. We offer pure α-bungarotoxin as well as conjugates with a selection of our CF® dyes and other labels. CF® dyes offer advantages in brightness and photostability compared to Alexa Fluor® dyes and other next generation fluorescent dyes. Learn more about CF® Dyes, or download the CF® Dye Selection Guide.

Figure 1. Neuromuscular junction endplate in a rat skeletal muscle cryosection stained with CF®594 α-bungarotoxin (red). Nuclei are stained with DAPI (blue).

Tetrodotoxin (TTX)

Tetrodotoxin (TTX) reversibly blocks excitable sodium channels and has been a widely used tool for studies of excitable membranes of nerve and muscle cells. Available lyophilized in citrate buffer, or citrate-free.

TTX, With or Without Citrate

Catalog numberSizeProduct
000601 mgTetrodotoxin, Citrate-Free
000611 mgTetrodotoxin, with Citrate

Cholera Toxin Subunit B

Cholera toxin is the symptom-causing toxin produced by the bacteria Vibrio cholerae during cholera infection. The toxin is composed of two subunits, A and B. Subunit A is the toxic enzymatic subunit present in one copy per toxin. Cholera toxin subunit B (CT-B) is the receptor binding subunit that is found as a pentamer in each toxin and is relatively non-toxic, making it useful for cell biological studies.

CT-B has been used as a neuronal tracer and has also been shown to bind to GM1 gangliosides that are found in lipid rafts on the surface of mammalian cells. Therefore, fluorescently labeled conjugates of CT-B have been used as lipid raft markers and endocytic tracers for live imaging or on fixed cells. Cholera Toxin Subunit B is available with a wide selection of our bright and photostable CF® dyes.

α-Bungarotoxin & Conjugates

ProductEx/Em Catalog numberSize
α-BungarotoxinN/A00010-11 mg
CF®405S α-Bungarotoxin404/431 nm00002100 ug or 0.5 mg
CF®488A α-Bungarotoxin490/515 nm00005
CF®543 α-Bungarotoxin541/560 nm00026
CF®555 α-Bungarotoxin555/565 nm00018
CF®568 α-Bungarotoxin562/583 nm00006
CF®594 α-Bungarotoxin596/614 nm00007
CF®633 α-Bungarotoxin630/650 nm00009
CF®640R α-Bungarotoxin642/662 nm00004
CF®680R α-Bungarotoxin680/701 nm00003
Biotin-XX-α-BungarotoxinN/A000170.5 mg
FITC α-Bungarotoxin494/518 nm00011
10×50 ug or
0.5 mg
Tetramethylrhodamine α-Bungarotoxin553/577 nm00012
Sulforhodamine-101 (Texas Red®) α-Bungarotoxin593/613 nm00015
Texas Red is a registered trademark of Thermo Fisher Scientific.

CF® Dye Cholera Toxin Conjugates

ConjugationEx/EmSizeCatalog No.Dye Features
CF®405M408/452 nm100 ug00068CF®405M Features
CF®488A490/515 nm100 ug00070CF®488A Features
CF®532527/558 nm100 ug00074CF®532 Features
CF®543541/560 nm100 ug00075CF®543 Features
CF®568562/583 nm100 ug00071CF®568 Features
CF®594593/614 nm100 ug00072CF®594 Features
CF®633630/650 nm100 ug00077CF®633 Features
CF®640R642/662 nm100 ug00073CF®640R Features
CF®647650/665 nm100 ug00069CF®647 Features
CF®660R663/682 nm100 ug00078CF®660R Features
CF®680R680/701 nm100 ug00079CF®680R Features

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Nerve Terminal Dyes

SynaptoRed™ & SynaptoGreen™

SynaptoGreen™ and SynaptoRed™ nerve terminal probes (originally called FM® dyes) are membrane dyes used to trace endocytic vesicles. They are a series of fluorescent cationic styryl dyes developed to follow synaptic activity at neuromuscular junctions or synapses. The dyes label synaptic vesicles in neuronal tissues and cultured neurons in an activity-depending fashion. They also can be used to label endocytic vesicles in other cell types.

Nerve terminal dyes have highly hydrophilic, cationically charged head group at one end with lipophilic tails at the other end. They are virtually non-fluorescent in aqueous solution, but become intensely fluorescent in membranes. Following nerve stimulation, the dye molecules are internalized in newly formed endocytic vesicles. During exocytosis, the dyes are released from the vesicles along with neurotransmitters, causing a decrease in fluorescence signal. As a result, the change in fluorescent intensity reflects the amount of endocytosis/exocytosis or synaptic activity. The rate of fluorescence increase during endocytosis (on-rate), and the rate of fluorescence decrease during exocytosis (off-rate) vary from dye to dye. AM dyes and HM dyes are fixable nerve terminal dyes. After staining with these dyes, cells can be fixed and permeabilized for subsequent immunostaining. See the table below for a list of nerve terminal dyes and their properties.

Figure 2. General structure of SynaptoGreen™ and SynaptoRed™ dyes.
Figure 3. General structure of AM fixable nerve terminal dyes.

Background Reducers & Nerve Terminal Staining Kits

A common problem encountered with nerve terminal dyes is background fluorescence due to residual membrane staining, even after extensive washing. To reduce this background fluorescence, we offer three quencher or dye-clearing agents. ADVASEP-7, a sulfonated β-cyclodextrin, forms a water soluble inclusion complex with SynaptoGreen™ C4 that can be removed more effectively by washing. Biotium’s unique quencher, SCAS, reduces background fluorescence as soon as it is added to the preparation without the need for washing. Sulforhodamine 101 quenches SynaptoGreen™ background staining via fluorescent resonance energy transfer (FRET). We offer these reagents as individual products and in kits with dyes and the quencher/dye-clearing agents.

Figure 4. Neurons in mouse dorsal root ganglia (DRG) labeled with AM1-43. Image courtesy of Dr. David Corey, Harvard Medical School. Also see Figure 6.

Properties of Nerve Terminal Dyes

Nerve Terminal Dyem*n*Fixable?SizeCatalog numberFeatures
SynaptGreen™ Dyes (Ex/Em ~480/660 nm in membranes)
SynaptoGreen™ C101No5 mg, 5 x 1 mg70042, 70043• Green nerve terminal probe
• Shortest tail for slowest on-rate & fastest off-rate
SynaptoGreen™ C2 (equivalent to FM®2-10)11No70044, 70045• Equivalent to FM®2-10
SynaptoGreen™ C321No70023, 70026• Green nerve terminal probe
SynaptoGreen™ C4 (equivalent to FM®1-43)31No70020, 70022• Equivalent to FM®1-43
SynaptoGreen™ C5 (equivalent to FM®1-84)41No70046, 70047• Equivalent to FM®1-84
SynaptoGreen™ C18 (equivalent to FM®3-25)171No70048, 70049• Equivalent to FM®3-25
AM1-4331Yes1 mg70024• Fixable version of SynaptoGreen C4
• Equivalent to FM®1-43FX
AM1-4441Yes70038• Improved fixability over AM1-43
AM2-1011Yes70036• Fixable analog of SynaptoGreen™ C2
AM3-25171Yes70051• Fixable far-red nerve terminal probe
HM1-4331Yes70053• Fixable red nerve terminal probe
SynaptoRed Dyes™ (Ex/Em ~510/750 nm in membranes)
SynaptoRed™ C103No5 mg, 5 x 1 mg70040, 70041• One carbon shorter than SynaptoRed™ C2
SynaptoRed™ C2 (equivalent to FM®4-64)13No70021, 70027• Equivalent to FM®4-64
SynaptoRed™ C2M** (equivalent to FM®5-95)13No70019, 70028• More water soluble than SynaptoRed™ C2
• Equivalent to FM®5-95
AM4-6413Yes1 mg70025• Fixable version of SynaptoRed™ C2
AM4-6533Yes70039• Fixable version of SynaptoRed™ C2
AM4-6643Yes70050• Fixable and spectrally identical to SynaptoRed™ C2
*m is the number of carbons in the lipophilic tail and n is the number of double bonds linking the two aromatic rings in the dye.
**The positively-charged end of SynaptoRed C2M is a trimethylammonium group.
FM is a registered trademark of Thermo Fisher Scientific.

Nerve Terminal Staining Kits

Nerve Terminal Staining KitNerve Terminal DyeBackground ReducerCatalog number
Nerve Terminal Staining Kit ISynaptoGreen™ C4 (5 x 1 mg )ADVASEP-7 (250 mg)70030
Nerve Terminal Staining Kit II (A)AM1-43 (1 mg)ADVASEP-7 (100 mg)70031
Nerve Terminal Staining Kit II (B)AM1-43 (1 mg)SCAS (100 mg)70031-1
Nerve Terminal Staining Kit IIISynaptoGreen™ C4 (5 x 1 mg)Sulforhodamine 101 (100 mg)70032
Nerve Terminal Staining Kit VSynaptoRed™ C2 (5 x 1 mg)ADVASEP-7 (250 mg)70034

Also see our selection of fast- and slow-responding potentiometric membrane potential dyes.

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Anterograde & Retrograde Axonal Tracers

Retrograde Tracers

Hydroxystilbamidine (also called Fluoro-Gold™) has been used extensively as a retrograde tracer for neurons and also a histochemical stain. Fluoro-Gold™ is used for retrograde tracing and dendrite filling.

Cholera toxin subunit B binds GM1 ganglioside in lipid rafts, and is used as a retrograde neuronal tracer. Available with a wide selection of bright and photostable CF® dyes. See Cholera Toxin Conjugates.

Retrograde & Anterograde Tracers

WGA is a glycoprotein-binding lectin that has been used for retrograde and anterograde neuronal tracing. We offer WGA CF® dye conjugates with fluorescence from UV to near-IR, plus HRP. See WGA Conjugates.

Labeled dextran amine can be used for both retrograde and anterograde tracing. CF® dye dextrans are anionic with an aldehyde-fixable free amine group, and are available with a wide selection of colors and a range of molecular weights. See Dextran Conjugates.

Biotin ethylenediamine is equivalent to Neurobiotin™, a useful anterograde and transneuronal tracer.

Anterograde & Retrograde Tracers

ProductEx/EmCatalog number
Hydroxystilbamidine (Fluoro-Gold™)361/536 nm80014
Hydroxystilbamidine (Fluoro-Gold™), 4% in H2O361/536 nm80023
Biotin ethylenediamine, hydrobromide (Neurobiotin™)N/A90057
Biotin ethylenediamine, hydrochlorideN/A90075
Cholera Toxin ConjugatesChoice of 10 colors
Wheat Germ Agglutinin ConjugatesChoice of 13 colors, plus HRP
Dextran ConjugatesChoice of 11 colors & 5 molecular weights

Cytosolic Tracers for Cell Morphology & Gap Junctions

Biotin derivatives

Formaldehyde-fixable biocytin and biocytin hydrazide are widely used microinjectable polar tracers. Biocytin has been used as an anterograde tracer and gap junction probe. Biotin derivatives can be detected with labeled streptavidin or anti-biotin antibodies. Biotin ethylenediamine is equivalent to Neurobiotin™, a useful anterograde and transneuronal tracer. We also offer fluorescent CF® dye biotin and biocytin conjugates.

Lucifer Yellow and Related Dyes

Lucifer Yellow is a classic cell-impermeant cytosolic and gap junction dye. We also offer Lucifer Yellow Cadaverine and Lucifer Yellow CH with aldehyde-fixable groups.

Membrane-Permeant Cytosolic Stains

Calcein-AM is a membrane-permeant, non-fluorescent compound that can be loaded into cultured cells by incubation. Once inside the cytoplasm, it is hydrolyzed inside viable cells to release the green fluorescent, membrane impermeant dye calcein, which fills the entire cell. Calcein-AM can be used to assess cell viability, and for short term cytoplasmic labeling.

ViaFluor® SE Cell Proliferation Dyes are membrane-permeant compounds that are hydrolyzed in the cytoplasm to release amine-reactive fluorescent dyes. The staining fills the entire cell, is stable for several days to weeks, and can withstand fixation and permeabilization. Available with blue and green fluorescence.

CF® Dye Hydrazides

Hydrazides are non-toxic, highly water soluble membrane-impermeant tracers that can be used to fill cells by microinjection. See our large selection of bright, photostable CF® dye hydrazides.

Figure 6. Cultured rat hippocampal neurons microinjected with CF®647 hydrazide (red) and stained with SynaptoGreen™ C4 (green). Image courtesy of Professor Guosong Liu, Tsinghua University.

Cytosolic Tracers & Fluid Phase Markers

CF® Hydrazides• Microinjectable, fixable fluorescent tracers
• Wide selection of bright & photostable CF® dyes
Calcein • Water soluble green fluorescent tracer for microinjection
Calcein AM• Membrane-permeable compound is hydrolyzed in live cells to release water soluble green fluorescent dye
• Uniform intracellular labeling
• Dead cells don’t retain dye, for true endpoint viability assay
ViaFluor® SE Dyes• Membrane-permeable compound is hydrolyzed in live cells to release amine-reactive dye
• Covalent, fixable intracellular labeling
• Choice of blue or green fluorescence
Lucifer Yellow Derivatives• Widely used green fluorescent tracers for neuronal morphology and gap junction studies
• Fixable Lucifer Yellow CH and Lucifer Yellow Cadaverine
• Lucifer Yellow Cadaverin Biotin-X for secondary detection with streptavidin
Hydroxystilbamidine (equivalent to Fluoro-Gold™)• Widely used UV-excitable green fluorescent retrograde neuronal tracer
• Available in solid and 4% solution in water
Biotin Derivatives• Biotin-based tracers for secondary detection with streptavidin
CF® Dye Biotin• Biotin conjugates of our bright & photostable CF® dyes
CF® Dye Biocytin• Aldehyde-fixable biocytin conjugated with bright & photostable CF® dyes.

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Membrane Potential Dyes

Slow-Response Membrane Potential Dyes

Translational (or slow-response) voltage-sensing membrane potential dyes undergo a change in their membrane distribution as a result of changes in membrane potential.

The fluorescence of DiBAC4(3) is enhanced with membrane depolarization. The rate of fluorescence response of the dye is slower than styryl dyes like the ANEPPS dyes (see below), but the fluorescence change is significantly larger.

DiOC2(3) has been used for measuring membrane potential in bacteria. The green fluorescent dye forms red fluorescent aggregates with increasing membrane potential, allowing ratiometric potential measurements.

DiOC5(3) and DiOC6(3) are two of the most widely used carbocyanine dyes for membrane potential measurements.

Tetramethylrhodamine ethyl ester (TMRE) and Tetramethylrhodamine methyl ester (TMRM) can be used for quantitative measurements of membrane potential and mitochondrial membrane potential.

DiO/DPA Membrane Potential Kit

The membrane localization of the fluorescence quencher dipicrylamine (DPA) is a function of the polarity and magnitude of membrane potential. The DiO/DPA system detects cytoplasmic membrane potential changes using the principle of fluorescence resonance energy transfer (FRET). The green fluorescent membrane dye DiO is a “stationary” FRET donor while DPA acts as a mobile FRET acceptor, resulting in a membrane potential-dependent quenching of fluorescence by FRET. The DiO/DPA system has been reported to produce a fluorescence signal change of >56% in HEK-293 cells and >25% in neuronal cultures and brain slices per 100 mV membrane potential change.

Fast-Response Membrane Potential Dyes

Fast-response membrane voltage-sensitive dyes are styryl dyes that undergo changes in fluorescence intensity in response to changes in membrane potential, on the order of 2-10% change in fluorescence per 100 mV. The dyes also undergo spectral shift with changes in membrane potential, allowing ratiometric measurements. Fast response dyes have been used to measure electrical activity in neural and cardiac cells.

Di-4-ANNEPS has been used for studies of human stem cell-derived cardiomyocytes. Di-8-ANNEPPS is more hydrophobic and better retained in the outer leaflet of the plasma membrane than Di-4-ANNEPS, and therefore is more suitable for long-term membrane potential studies. It is also more photostable and less phototoxic than Di-4-ANNEPS.

Di-2-ANEPEQ (also known as JPW 1114) is a highly water soluble fast-responding dye that is usually introduced into cells by microinjection. Di-8-ANEPPQ and Di-12-ANEPPQ are successively more hydrophobic, and have been used for potential-sensitive retrograde labeling of neurons.

RH237, RH414, RH421, and RH795 are fast-responding potentiometric probes generally used for functional imaging of neurons. RH421 exhibits >20% fluorescence change per 100 mV on neuroblastoma cells. These dyes can differ in their physiological effects, for example RH414 causes arterial constriction during cortex staining, while the spectrally similar dye RH795 does not.

Slow-Responding Membrane Potential Dyes

ProductEx/EmCatalog number
DiBAC4(3)493/516 nm61011
DiOC2(3)482/497 nm70008
DiOC5(3)482/497 nm70007
DiOC6(3)484/501 nm70009
TMRE, 2 mM in DMSO549/574 nm70005
TMRE549/574 nm70016
TMRM548/573 nm70017

Fast-Responding Membrane Potential Dyes

ProductEx/EmCatalog number
Di-4-ANEPPS496/705 nm161010
Di-8-ANEPPS498/713 nm161012
Di-2-ANEPEQ (JPW 1114)See Note 261013
RH237528/782 nm61018
RH414532/706 nm61016
RH421515/704 nm61017
RH795530/712 nm61019
DiO/DPA Membrane Potential Kit484/501 nm30037
1Ex/Em is shown for dyes in methanol. In cell membranes, spectra of styryl dyes are typically blue-shifted by as much as 20 nm for absorption/excitation and 80 nm for emission.
2Spectrally similar to the ANEPPS dyes.

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Amyloid Stains & Neurodegeneration Dyes

Amyloid Stains

Congo Red is commonly used to detect amyloid protein aggregates associated with Alzheimer’s disease, Bovine Spongiform Encephalopathy, and related diseases. The staining can be detected by either colorimetric or fluorescence imaging (Ex/Em 497/614 nm).

DCDAPH is a far-red fluorescent probe (Ex/Em 597/665 nm) with high affinity (Kd=27 nM) to Aβ1-42 aggregates. It has been used for fluorescent staining of brain sections, as well as in vivo small animal near-IR imaging.

Thioflavin T is a cell-permeable benzothiazole dye that exhibits enhanced fluorescence (Ex/Em 450/482 nm) upon binding to amyloid fibrils. Thioflavin T has also been used in histology and for protein characterization.

Amyloid & Neurodegeneration Stains

ProductEx/EmCatalog number
Congo Red, High Purity 497/614 nm80028
DCDAPH597/665 nm80030
Thioflavin T, High Purity450/482 nm80033
PathoGreen™ Histofluorescent Stain, 1000X in Water497/520 nm80027

PathoGreen™ Histofluorescent Stain for Neurodegeneration

PathoGreen™ is an anionic green fluorescent dye functionally similar to Fluoro-Jade® dyes. These dyes stain degenerating neurons and their processes in brain sections and cell culture. The mechanism of staining by this class of dyes has not been determined, but the negatively charged dyes may bind to positively charged polyamines generated in dying neurons.

We also offer a wide selection of cell viability and apoptosis assays.

Figure 5. Section of mouse hippocampus stained with PathoGreen™. Degenerating neurons are stained green.

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More Probes for Neuronal Research

Ion indicators

  • Fluorescent indictators calcium & other ions
  • Chelators, calibrations buffers, & ionophores

 Cellular stains

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