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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 number Size Product
00060 1 mg Tetrodotoxin, Citrate-Free
00061 1 mg Tetrodotoxin, 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

Product Ex/Em Catalog number Size
α-Bungarotoxin N/A 00010-1 1 mg
CF®405S α-Bungarotoxin 404/431 nm 00002 100 ug or 0.5 mg
CF®488A α-Bungarotoxin 490/515 nm 00005
CF®543 α-Bungarotoxin 541/560 nm 00026
CF®555 α-Bungarotoxin 555/565 nm 00018
CF®568 α-Bungarotoxin 562/583 nm 00006
CF®594 α-Bungarotoxin 596/614 nm 00007
CF®633 α-Bungarotoxin 630/650 nm 00009
CF®640R α-Bungarotoxin 642/662 nm 00004
CF®680R α-Bungarotoxin 680/701 nm 00003
Biotin-XX-α-Bungarotoxin N/A 00017 0.5 mg
FITC α-Bungarotoxin 494/518 nm 00011
10×50 ug or
0.5 mg
Tetramethylrhodamine α-Bungarotoxin 553/577 nm 00012
Sulforhodamine-101 (Texas Red®) α-Bungarotoxin 593/613 nm 00015
Texas Red is a registered trademark of Thermo Fisher Scientific.

CF® Dye Cholera Toxin Conjugates

Conjugation Ex/Em Size Catalog No. Dye Features
CF®405M 408/452 nm 100 ug 00068 CF®405M Features
CF®488A 490/515 nm 100 ug 00070 CF®488A Features
CF®532 527/558 nm 100 ug 00074 CF®532 Features
CF®543 541/560 nm 100 ug 00075 CF®543 Features
CF®568 562/583 nm 100 ug 00071 CF®568 Features
CF®594 593/614 nm 100 ug 00072 CF®594 Features
CF®633 630/650 nm 100 ug 00077 CF®633 Features
CF®640R 642/662 nm 100 ug 00073 CF®640R Features
CF®647 650/665 nm 100 ug 00069 CF®647 Features
CF®660R 663/682 nm 100 ug 00078 CF®660R Features
CF®680R 680/701 nm 100 ug 00079 CF®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 Dye m* n* Fixable? Size Catalog number Features
SynaptGreen™ Dyes (Ex/Em ~480/660 nm in membranes)
SynaptoGreen™ C1 0 1 No 5 mg, 5 x 1 mg 70042, 70043 • Green nerve terminal probe
• Shortest tail for slowest on-rate & fastest off-rate
SynaptoGreen™ C2 (equivalent to FM®2-10) 1 1 No 70044, 70045 • Equivalent to FM®2-10
SynaptoGreen™ C3 2 1 No 70023, 70026 • Green nerve terminal probe
SynaptoGreen™ C4 (equivalent to FM®1-43) 3 1 No 70020, 70022 • Equivalent to FM®1-43
SynaptoGreen™ C5 (equivalent to FM®1-84) 4 1 No 70046, 70047 • Equivalent to FM®1-84
SynaptoGreen™ C18 (equivalent to FM®3-25) 17 1 No 70048, 70049 • Equivalent to FM®3-25
AM1-43 3 1 Yes 1 mg 70024 • Fixable version of SynaptoGreen C4
• Equivalent to FM®1-43FX
AM1-44 4 1 Yes 70038 • Improved fixability over AM1-43
AM2-10 1 1 Yes 70036 • Fixable analog of SynaptoGreen™ C2
AM3-25 17 1 Yes 70051 • Fixable far-red nerve terminal probe
HM1-43 3 1 Yes 70053 • Fixable red nerve terminal probe
SynaptoRed Dyes™ (Ex/Em ~510/750 nm in membranes)
SynaptoRed™ C1 0 3 No 5 mg, 5 x 1 mg 70040, 70041 • One carbon shorter than SynaptoRed™ C2
SynaptoRed™ C2 (equivalent to FM®4-64) 1 3 No 70021, 70027 • Equivalent to FM®4-64
SynaptoRed™ C2M** (equivalent to FM®5-95) 1 3 No 70019, 70028 • More water soluble than SynaptoRed™ C2
• Equivalent to FM®5-95
AM4-64 1 3 Yes 1 mg 70025 • Fixable version of SynaptoRed™ C2
AM4-65 3 3 Yes 70039 • Fixable version of SynaptoRed™ C2
AM4-66 4 3 Yes 70050 • 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 Kit Nerve Terminal Dye Background Reducer Catalog number
Nerve Terminal Staining Kit I SynaptoGreen™ 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 III SynaptoGreen™ C4 (5 x 1 mg) Sulforhodamine 101 (100 mg) 70032
Nerve Terminal Staining Kit V SynaptoRed™ 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

Product Ex/Em Catalog number
Hydroxystilbamidine (Fluoro-Gold™) 361/536 nm 80014
Hydroxystilbamidine (Fluoro-Gold™), 4% in H2O 361/536 nm 80023
Biotin ethylenediamine, hydrobromide (Neurobiotin™) N/A 90057
Biotin ethylenediamine, hydrochloride N/A 90075
Cholera Toxin Conjugates Choice of 10 colors
Wheat Germ Agglutinin Conjugates Choice of 13 colors, plus HRP
Dextran Conjugates Choice 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

Product Features
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

Product Ex/Em Catalog number
DiBAC4(3) 493/516 nm 61011
DiOC2(3) 482/497 nm 70008
DiOC5(3) 482/497 nm 70007
DiOC6(3) 484/501 nm 70009
TMRE, 2 mM in DMSO 549/574 nm 70005
TMRE 549/574 nm 70016
TMRM 548/573 nm 70017

Fast-Responding Membrane Potential Dyes

Product Ex/Em Catalog number
Di-4-ANEPPS 496/705 nm1 61010
Di-8-ANEPPS 498/713 nm1 61012
Di-2-ANEPEQ (JPW 1114) See Note 2 61013
Di-8-ANEPPQ 61014
Di-12-ANEPPQ 61015
RH237 528/782 nm 61018
RH414 532/706 nm 61016
RH421 515/704 nm 61017
RH795 530/712 nm 61019
DiO/DPA Membrane Potential Kit 484/501 nm 30037
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

Product Ex/Em Catalog number
Congo Red, High Purity 497/614 nm 80028
DCDAPH 597/665 nm 80030
Thioflavin T, High Purity 450/482 nm 80033
PathoGreen™ Histofluorescent Stain, 1000X in Water 497/520 nm 80027

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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