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Fluorescent Ion Indicators

We offer a selection of membrane-permeant and impermeant fluorescent indicator dyes for calcium and other ions, as well as calibration buffers, ionophores, and accessory reagents.

Calcium Indicators

Fluorophores coupled to a BAPTA calcium chelator structure to quantitatively monitor calcium concentration

Calcium Chelators

BAPTA chelators to generate calcium buffers with well-defined concentrations or control cytosolic calcium concentration

Calcium Accessory Reagents

A wide variety of calcium calibration buffers, ionophores, caged calcium chelators, and reagents for indicator dyes

Chloride & Zinc Indicators

Fluorescent indicators to monitor chloride or zinc concentrations, with membrane-impermeant and membrane-permeant options

pH-Responsive Dyes

Membrane-permeant and membrane-impermeant fluorescent pH indicator dyes, including BCECF, FAM, and Flubida-2

Calcium Indicators

To study the roles of calcium in cells, often it is essential to quantitatively monitor its concentration. The most widely used method of Ca2+ detection is by the use of fluorescent indicators, a technique pioneered by Roger Tsien and colleagues. Ca2+ indicators are fluorophores coupled to a BAPTA calcium chelator structure. Binding of Ca2+ to the chelator causes a spectral shift in the dye fluorescence and/or increased dye fluorescence. A variety of indicators are available that vary in their Ca2+ dissociation constants (Kd) or Ca2+ response range, excitation/emission wavelengths, spectral shift, and relative fluorescent quantum yields.

You should select a Ca2+ indicator that best suits your needs in consideration of the biological system, instrument settings, and other fluorescent probes used in the experiment. The indicator Kd values give an estimate of the Ca2+ concentration response, usually 0.1 Kd to 10 Kd, with the caveat that Kd values measured in vitro may differ from those in cells due to differences in ionic strength, pH, viscosity, and Ca2+ buffering by lipids and proteins.

Ratiometric vs. Non-Ratiometric Indicators

Upon binding to calcium, ratiometric indicators undergo a shift either excitation wavelength, emission wavelength, or both. Ca2+ concentration is determined by measuring indicator fluorescence at two different excitation and emission settings (corresponding to the maxima with no Ca2+ and high Ca2+) and determining their ratio. These indicators have the advantage of being internally controlled, and therefore, avoid artifacts from uneven dye loading or photobleaching between samples. Ratiometric measurements may require specialized imaging setups or filter cubes. Non-ratiometric indicators show increased fluorescence intensity upon binding to calcium, with no shift in excitation/emission wavelengths.

Cell Membrane-Permeant AM Esters

In their salt forms, indicators are water-soluble and membrane impermeant, so loading them into cells requires microinjection. AM esters are membrane-permeant forms of indicators that themselves do not bind ions. However, once they have entered cells, they are hydrolyzed by esterases to release the parent ion indicator. Thus, cells or tissues can be loaded with indicator by simply incubating them with a buffer containing the AM ester form. Biotium also supplies Pluronic® F-127, a mild non-ionic detergent that can facilitate cell loading of AM ester compounds, and high grade anhydrous DMSO for preparing AM Ester stock solutions.

Properties of Calcium Indicators

IndicatorMW1Ratiometric?Excitation2Emission2Kd3Membrane-Impermeant SaltsMembrane-Permeant AM Esters
Fluo-3770No506 nm525 nm390 nMFluo-3, Pentaammonium
Fluo-3, Pentapotassium
Fluo-3, Pentasodium
Fluo-3, AM Ester
Fluo-3 AM Ester, 1 mM in DMSO
Fluo-4737No494 nm506 nm335 nMFluo-4, PentapotassiumFluo-4, AM Ester
Mag-Fluo-4682No493 nm517 nm22 uMMag-Fluo-4, TetrapotassiumMag-Fluo-4, AM Ester
Fura-2642Yes363/335 nm512/505 nm145 nMFura-2, Pentaammonium
Fura-2, Pentapotassium
Fura-2, Pentasodium
Fura-2, AM Ester
Fura-2, AM Ester, 1 mM in DMSO
Indo-1650Yes349/331 nm482/398 nm230 nMIndo-1, Pentaammonium
Indo-1, Pentapotassium
Indo-1, Pentasodium
Indo-1, AM Ester
Furaptra (Mag-Fura-2)435Yes369/330 nm511 nm1.9 mM (Mg2+)
25 uM (Ca2+)
Furaptra , Pentapotassium
Furaptra, Pentasodium
Furaptra, AM Ester
Rhod-2755No556 nm576 nm1 uMRhod-2, Triammonium
Rhod-2, Tripotassium
Rhod-2, Trisodium
Rhod-2, AM Ester
Rhod-590912No595 nm616 nm610 nMRhod-590, TripotassiumRhod-590, AM Ester
1. Free acid form
2. For non-ratiometric indicators, Ex/Em with calcium is shown; for ratiometric indicators, wavelengths with no calcium/high calcium are shown
3. Ca2+ dissociation constant measured at 22°C, pH 7.2 buffer

Calcium & Other Ion Chelators

Calcium Chelators

BAPTA and its derivatives are calcium chelators that are commonly used to generate calcium buffers with well-defined calcium concentrations. By introducing the chelators into cells, one can control the cytosolic calcium concentration, an important means to study the roles of calcium.

Key advantages of these calcium chelators include relative insensitivity toward intracellular pH change and fast release of calcium. Biotium offers several BAPTA chelators with calcium dissociation constants covering the biologically significant range from 10-7 to 10-2 M.

We offer membrane-impermeant salts of BAPTA chelators for microinjection, or cell-permeant AM ester forms of the chelators that can be loaded into cells by incubation.

Heavy Metal Chelators

TPEN (Cat. No. 59003) is an excellent heavy metal chelator that does not affect calcium, magnesium, sodium, or potassium concentrations. Therefore it is useful tool for distinguishing the effects of heavy metals like zinc, iron, copper, and manganese on fluorescent indicators for calcium, magnesium, sodium and potassium.

Properties of BAPTA Chelators

ChelatorMW1Kd2Membrane-Impermeant SaltsMembrane-Permeant AM Esters
BAPTA477No Mg2+: 0.59 mM

1 mM Mg2+: 0.70 mM
BAPTA, Tetracesium

BAPTA, Tetrapotassium

BAPTA, Tetrasodium
BAPTA, AM Ester
5,5'-Dibromo BAPTA635No Mg2+: 3.6 mM5,5'-Dibromo BAPTA, Tetrapotassium--
5,5'-Difluoro BAPTA513No Mg2+: 0.61 mM

1 mM Mg2+: 0.72 mM
5,5'-Difluoro BAPTA, Tetrapotassium5,5'-Difluoro BAPTA, AM Ester
5,5'-Dimethyl BAPTA505No Mg2+: 0.16 mM

1 mM Mg2+: 0.44 mM
5,5'-Dimethyl BAPTA, Tetrapotassium5,5'-Dimethyl BAPTA, AM Ester
5-Mononitro BAPTA522No Mg2+: 0.94 mM----
4-Trifluoromethyl BAPTA545No Mg2+: 0.57 mM----
1 For free acid forms.
2 Cell Calcium 10, 491 (1989).

Calcium Calibration Buffers, Ionophores, & Reagents

Calcium Calibration Buffers

The Calcium Calibration Buffer Kit is used to prepare buffers with a range of accurate calcium concentrations, and is useful for the calibration of fluorescent calcium indicators. The kit contains 50 mL each of zero calcium buffer and 40 uM free Ca2+ buffer, with a detailed protocol for combining the two buffers to obtain calibration curve from 0.017-39.8 uM free calcium.

Accessory Reagents for Indicator Dyes

Pluronic® F-127 is a mild detergent useful for solubilizing AM esters for cell loading. We also offer anhydrous DMSO in convenient 10 mL size, recommended for preparing stock solutions of AM esters, which are susceptible to hydrolysis. EDC (or EDAC) has been found to be useful for fixing chelators in situ, for subsequent fixation and staining.

Calcium Ionophores and Caged Calcium

Calcium ionophores facilitate the equilibration of calcium across cellular membranes and are used to calibrate calcium indicators or alter intracellular calcium concentration.

A-23187 (calcimycin, calcium ionophore III) equilibrates intracellular and extracellular calcium, is used for in situ calibration of fluorescent calcium indicators, and also Mn2+ to enter the cells and quench intracellular fluorescence of calcium indicators.

Ionomycin is used to modify intracellular calcium concentrations, calibrate fluorescent calcium indicators, and stimulate cytokine production and cell proliferation in lymphocytes. In other cell types it can induce apoptosis and inhibit proliferation.

DMNP-EDTA (DM-Nitrophen™) is a caged Ca2+ chelator. UV light cleaves the chelator to release calcium. Upon photolysis, the Kd for Ca2+ increases from 5 nM to 3 mM, resulting in a pulse of free Ca2+.

Other Ion Indicators

Chloride Indicators

The fluorescence of SPQ 6(-methoxy-N-(3-sulfopropyl)quinolinium) is specifically quenched by chloride via collision. Therefore, chloride concentration is measured by monitoring the degree of fluorescence decrease. The dye can be loaded into cells by hypotonic shock. The dye has excitation/emission at 344/443 nm.

MQAE (N-(ethoxycarbonylmethyl)-6-methoxyquinolinium bromide) is an improved chloride indicator that has greater sensitivity to chloride (Ksv= 200 M-1) than SPQ (Ksv= 118 M-1) and higher fluorescence quantum yield. The ester group of MQAE may slowly hydrolyze inside cells, resulting in a change in its fluorescence response. The dye has excitation/emission at 350/460 nm.

Zinc Indicators

Zinc is believed to be involved in the suppression of apoptosis and play important roles in many neural activities. Zinquin is an UV-excitable, blue fluorescent zinc indicator with excitation/emission maxima at 350/460 nm. Biotium offers two variations of Zinquin that differ in cell permeability. Zinquin free acid is a membrane-impermeant form, while Zinquin ethyl ester is membrane-permeant and is hydrolyzed into Zinquin free acid after entering cells.

Also see Accessory Reagents for Indicator Dyes.

Chloride & Zinc Indicators

ProductIndicatorMembrane permeabilityEx/EmCatalog numberUnit size
SPQ ChlorideImpermeant344/443 nm5201050 mg
MQAEPermeant350/460 nm52011100 mg
Zinquin free acidZincImpermeant350/460 nm520225 mg
Zinquin ethyl esterPermeant350/460 nm520205 mg

pH Indicators

BCECF pH Indicators

BCECF is the most widely used fluorescent pH sensor. With a pKa of 6.97, close to physiological pH, it can detect changes in cytosolic pH with high sensitivity. At low pH, the dye is weakly fluorescent but becomes more fluorescent with increasing pH. The excitation spectrum of the dye undergoes a slight shift with pH change, while the wavelength of the emission maximum remains unchanged. The pH is determined ratiometrically by the relative fluorescent intensities at 535 nm when the dye is excited at 439 nm and 505 nm. Available in membrane-impermeant free acid and cell-permeant AM ester forms.

Flubida and Flubi-2 pH Indicators

Flubida-2 has been used to detect pH at a specific site in a cell, such as cell organelles, by directing the probe to where avidin-chimera proteins are located. The probe is a conjugate of biotin and fluorescein diacetate, which is nonfluorescent until the probe has entered the cells and is hydrolyzed by cellular esterases. Flubida-2 is membrane-permeant and can be delivered into cells via simple incubation. Flubi-2 is the membrane-impermeant hydrolyzed product of Flubida-2. Its spectral properties and pH response are similar to those of BCECF.

Carboxyfluorescein pH Indicators

Carboxyfluorescein (FAM) has a pKa of 6.5 and can be used as a pH indicator or cellular tracer. Its excitation spectrum and fluorescence response to pH are similar to those of BCECF. Carboxyfluorescein is also available in membrane-permeant diacetate form (CFDA). CFDA-SE is a membrane-permeant amine-reactive form that covalently reacts with cytoplasmic proteins for stable labeling.

5-(and-6)-Carboxy-2′,7′-dichlorofluorescein is similar to carboxyfluorescein, but has a pKa of 4.8, and is useful for detecting pH in more acidic environments. It is also available in membrane-permeant diacetate, and membrane-permeant, amine-reactive diacetate succinimidyl ester forms.

The pKa of 5-carboxy-2’,7’-dichlorosulfonefluorescein is near 4.0 and the dye may be a pH indicator for acidic organelles.

Fluorescein derivatives are available as single isomer or mixed isomers; the isomers have the same spectral properties. For certain coupling reactions, single isomer may be preferable, but mixed isomers are suitable for most applications.

ProductpKaCatalog numberUnit size
BCECF, free acidpKa 6.97510101 mg
5-Carboxyfluorescein (5-FAM, single isomer)pKa 6.551019100 mg
6-Carboxyfluorescein (6-FAM, single isomer)51020100 mg
5-(and-6)-Carboxyfluorescein
(5(6)-FAM, mixed isomers)
51013100 mg
Flubi-2510245 mg
5-Carboxy-2′,7′-dichlorofluoresceinpKa 4.851017100 mg
5-(and-6)-Carboxy-2′,7′-dichlorofluorescein51015200 mg
5-Carboxy-2′,7′-dichlorosulfonefluoresceinpKa 45102310 mg
Ex/Em for all indicators shown is 505/525 (high pH). pH is determined ratiometrically by the relative fluorescent intensities at 535 nm when the dye is excited at 439 nm and 505 nm.

FAQs

BAPTA-based calcium indicators and chelators have been shown to be fixable in situ by EDC (EDAC)1, #59002 which would be compatible with subsequent immunofluorescence and IHC.

1Cell Calcium. 1997. 21(3), 175; DOI:10.1016/S0143-4160(97)90042-7.

Most of our products are stable at room temperature for many days, so in all likelihood the product will still work just fine. To be on the safe side, we recommend performing a small scale positive control experiment to confirm that the product still works for your application before processing a large number of samples or precious samples.

One exception that we are aware of is GelGreen™, which is more sensitive to light exposure than most of our other fluorescent dyes. If GelGreen™ is exposed to ambient light for a prolonged period of time (days to weeks), its color will change from dark orange to brick red. If this occurs, the GelGreen will no longer work for gel staining.

Bioscience kits

The guaranteed shelf life from date of receipt for bioscience kits is listed on the product information sheet. Some kits have an expiration date printed on the kit box label, this is the guaranteed shelf life date calculated from the day that the product shipped from our facility. Kits often are functional for significantly longer than the guaranteed shelf life. If you have an older kit in storage that you wish to use, we recommend performing a small scale positive control experiment to confirm that the kit still works for your application before processing a large number of samples or precious samples.

Antibodies and other conjugates

The guaranteed shelf life from date of receipt for antibodies and conjugates is listed on the product information sheet. Antibodies and other conjugates often are functional for significantly longer than the guaranteed shelf life. If you have an older conjugate in storage that you wish to use, we recommend performing a small scale positive control experiment to confirm that the product still works for your application before processing a large number of samples or precious samples.

For lyophilized antibodies, we recommend reconstituting the antibody with glycerol and antimicrobial preservative like sodium azide for the longest shelf life (note that sodium azide is not compatible with HRP-conjugates).

Chemicals, dyes, and gel stains

Biotium guarantees the stability of chemicals, dyes, and gel stains for at least a year from the date you receive the product. However, the majority of these products are highly stable for many years, as long as they are stored as recommended. Storage conditions can be found on the product information sheet or product safety and data sheet, material safety data sheet, and on the product label. Fluorescent compounds should be protected from light for long term storage.

If you have a Biotium compound that has been in storage for longer than one year that you wish to use, we recommend performing a small scale positive control experiment to confirm that the compound still works for your application before processing a large number of samples or precious samples.

Expiration date based on date of manufacture (DOM)

If your institution requires you to document expiration date based on date of manufacture for reagents, please contact techsupport@biotium.com for assistance.This is a block of text.

Chemical products with special stability considerations:

Esters

Ester compounds include the following:

  • Succinimidyl esters (SE, also known as NHS esters), such as our amine-reactive dyes
  • Acetoxymethyl esters (AM esters) such as our membrane-permeable ion indicator dyes
  • Diacetate-modified dyes, like ViaFluor™ 405, CFDA, and CFDA-SE cell viability/cell proliferation dyes

Ester dyes are stable in solid form as long as they are protected from light and moisture. Esters are not stable in aqueous solution. Concentrated stock solutions should be prepared in anhydrous DMSO (see Biotium catalog no. 90082). Stock solutions in anhydrous DMSO can be stored desiccated at -20°C for one month or longer. Esters should be diluted in aqueous solution immediately before use. Succinimidyl esters (SE) should be dissolved in a solution that is free of amine-containing compounds like Tris, glycine, or protein, which will react with the SE functional group. AM esters and diacetate compounds should be dissolved in a solution that is free of serum, because serum could contain esterases that would hydrolyze the compound.

A note on CF® Dye succinimidyl ester stability

Succinimidyl esters (SE) are generally susceptible to hydrolysis, which can result in lower labeling efficiency. Many commercially available fluorescent dyes used for life science research are heavily sulfonated dyes which makes them particularly hygroscopic, worsening the hydrolysis problem. In addition, for several commercially available SE reactive dyes, the SE group is derived from an aromatic carboxylic acid, while the SE group in all of Biotium’s CF® Dyes is prepared from an aliphatic carboxylic acid. This structural difference reduces the susceptibility of CF® Dye SE reactive groups to hydrolysis, resulting in relatively stable reactive dyes with consistently higher labeling efficiency compared to other SE derivatives of other fluorescent dyes.

Maleimides, MTS and thiosulfate dyes

Like the succinimidyl ester dyes, these dyes are also susceptible to hydrolysis, although generally to a much lower degree. Thus, for long term storage, anhydrous DMSO is recommended for making stock solutions.

Other reactive dyes

Amines, aminooxy (also known as oxylamine), hydrazide, azide, alkyne, BCN, and tyramide reactive dyes, as well as dye free acids, are generally stable in aqueous solution when stored at -20°C for 6-12 months or longer, as long as no compounds are present that may react with the dye’s functional group. See the product information sheets for specific reactive dyes more information.

Coelenterazines and D-luciferin

Coelenterazines are stable in solid form when stored as recommended; they are not stable in aqueous solution. Concentrated coelenterazine stock solutions (typically 1-100 mg/mL) should be prepared in ethanol or methanol; do not use DMSO or DMF to dissolve coelenterazines, because these solvents will oxidize the compounds. Ethanol or methanol stocks of coelenterazine can be stored at -20°C or below for six months or longer; alcohol stocks may evaporate during storage, so use tightly sealing screw cap vials and wrap the vials with Parafilm for long term storage. Propylene glycol also can be used as a solvent to minimize evaporation. If the solvent evaporates, the coelenterazine will still be present in the vial, so note the volume in the vial prior to storage so that you can adjust the solvent volume to correct for evaporation if needed. Prepare working solutions in aqueous buffers immediately before use. Coelenterazines are stable for up to five hours in aqueous solution.

Aquaphile™ coelenterazines are water soluble formulations of coelenterazines. They are stable in solid form when stored as recommended. Aquaphile™ coelenterazines should be dissolved in aqueous solution immediately before use. They are stable for up to five hours in aqueous solution.

Note that coelenterazines are predominantly yellow solids, but may contain dark red or brown flecks. This does not affect product stability or performance. If your coelenterazine is uniformly brown, then it is oxidized and needs to be replaced.

D-luciferin is stable in solid form and as a concentrated stock solution when stored as recommended; it is not stable at dilute working concentrations in aqueous solution. Prepare concentrated D-luciferin stock solutions (typically 1-100 mg/mL) in water, and store in aliquots at -20°C or below for six months or longer. Prepare working solutions immediately before use.

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