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Quantitate Calcium, Other Ions, or pH

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. Jump to a section below, or see product listings for Calcium Indicators & Chelators or Indicators for chloride, zinc, or pH.

Fluorescent Calcium Indicators & Related Reagents

Calcium Indicators

To study the roles of the important intracellular messenger 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 Ca2+ indicators, a technique pioneered by Roger Tsien and colleagues. Ca2+ indicators are fluorophores coupled to a BAPTA calcium chelator structure. Binding of calcium to the chelator portion of the molecule 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 considerably 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

Indicator MW1 Ratiometric? Excitation2 Emission2 Kd3 Membrane-Impermeant Salts Membrane-Permeant AM Esters
Fluo-3 770 No 506 nm 525 nm 390 nM Fluo-3, Pentaammonium
Fluo-3, Pentapotassium
Fluo-3, Pentasodium
Fluo-3, AM Ester
Fluo-3 AM Ester, 1 mM in DMSO
Fluo-4 737 No 494 nm 506 nm 335 nM Fluo-4, Pentapotassium Fluo-4, AM Ester
Mag-Fluo-4 682 No 493 nm 517 nm 22 uM Mag-Fluo-4, Tetrapotassium Mag-Fluo-4, AM Ester
Fura-2 642 Yes 363/335 nm 512/505 nm 145 nM Fura-2, Pentaammonium
Fura-2, Pentapotassium
Fura-2, Pentasodium
Fura-2, AM Ester
Fura-2, AM Ester, 1 mM in DMSO
Indo-1 650 Yes 349/331 nm 482/398 nm 230 nM Indo-1, Pentaammonium
Indo-1, Pentapotassium
Indo-1, Pentasodium
Indo-1, AM Ester
Furaptra (Mag-Fura-2) 435 Yes 369/330 nm 511 nm 1.9 mM (Mg2+)
25 uM (Ca2+)
Furaptra , Pentapotassium
Furaptra, Pentasodium
Furaptra, AM Ester
Rhod-2 755 No 556 nm 576 nm 1 uM Rhod-2, Triammonium
Rhod-2, Tripotassium
Rhod-2, Trisodium
Rhod-2, AM Ester
Rhod-590 912 No 595 nm 616 nm 610 nM Rhod-590, Tripotassium Rhod-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

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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 (catalog 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

Chelator MW1 Kd2 Membrane-Impermeant Salts Membrane-Permeant AM Esters
BAPTA 477 No Mg2+: 0.59 mM

1 mM Mg2+: 0.70 mM
BAPTA, Tetracesium

BAPTA, Tetrapotassium

BAPTA, Tetrasodium
5,5′-Dibromo BAPTA 635 No Mg2+: 3.6 mM 5,5′-Dibromo BAPTA, Tetrapotassium
5,5′-Difluoro BAPTA 513 No Mg2+: 0.61 mM

1 mM Mg2+: 0.72 mM
5,5′-Difluoro BAPTA, Tetrapotassium 5,5′-Difluoro BAPTA, AM Ester
5,5′-Dimethyl BAPTA 505 No Mg2+: 0.16 mM

1 mM Mg2+: 0.44 mM
5,5′-Dimethyl BAPTA, Tetrapotassium 5,5′-Dimethyl BAPTA, AM Ester
5-Mononitro BAPTA 522 No Mg2+: 0.94 mM
4-Trifluoromethyl BAPTA 545 No Mg2+: 0.57 mM
1 For free acid forms.
2 Cell Calcium 10, 491 (1989).

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Calcium Calibration Buffers, Ionophores, & Accessory 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.

Calcium Ionophores and Caged Calcium

Calcium ionophores are ion carriers that facilitate the equilibration of calcium across cellular membranes. They are useful tools for calibrating calcium indicators and manipulating intracellular calcium concentration.

A-23187 (calcimycin, calcium ionophore III) rapidly equilibrates intracellular and extracellular calcium concentrations. It is commonly  used for in situ calibration of fluorescent calcium indicators. The ionophore also allows Mn2+ to enter the cells and quench intracellular fluorescence of calcium indicators. A-23187 has blue fluorescence, which can contribute to fluorescence background when used with UV-excited calcium indicators. 4-Bromo A-23187 is non-fluorescent ionophore, preferred for calibrating UV-excited Ca2+ indicators such as Indo-1 and Fura-2.

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

DMNP-EDTA (also known as DM-Nitrophen™)  is a caged Ca2+ chelator. UV light cleaves the chelator, allowing controlled release of calcium. Upon photolysis, the Kd for Ca2+ increases from 5 nM to 3 mM, resulting in a pulse of free Ca2+. Biotium also offers a membrane-permeant DMNP-EDTA, AM Ester that may be used for live cell studies.

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 & Accessory Reagents

Product Catalog number Size
Calcium Calibration Buffer Kit 59100 50 mL each buffer
A-23187 Free Acid 59001 1 mg
4-Bromo A-23187, Free Acid 59006 1 mg
Ionomycin, Calcium Salt 59007 1 mg
DMNP-EDTA, Tetrapotassium Salt 50050 5 mg
DMNP-EDTA (Caged Calcium), AM Ester 50051 1 mg, 5 mg
EDC (EDAC) 59002 100 mg
Pluronic® F-127 59000 1 g
Pluronic® F-127, 20% in DMSO 59004 1 mL
Pluronic® F-127, 10% in H2O 59005 30 mL
Probenecid, Sodium Salt, Water Soluble 50027 10 x 77 mg
DMSO, Anhydrous 90082 10 mL
Pluronic is a registered trademark of BASF.

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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 at 350/460 nm. Zinquin free acid is membrane-impermeant, while Zinquin ethyl ester is membrane-permeable and is hydrolyzed into Zinquin free acid after entering cells.

Also see Accessory Reagents for Indicator Dyes

Chloride & Zinc Indicators

Product Indicator Membrane permeability Ex/Em Catalog number Unit size
SPQ Chloride Impermeant 344/443 nm 52010 50 mg
MQAE Permeant 350/460 nm 52011 100 mg
Zinquin free acid Zinc Impermeant 350/460 nm 52022 5 mg
Zinquin ethyl ester Permeant 350/460 nm 52020 5 mg

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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-permeable AM ester forms.

Flubida & 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-permeable and can be delivered into cells via simple incubation. Flubi-2 is the membrane-impermeable 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 permeable diacetate form (CFDA). CFDA-SE is a membrane-permeable 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 therefore is useful for detecting pH in more acidic environment. It is also available in membrane-permeable diacetate, and membrane-permeable, amine-reactive diacetate succinimidyl ester forms.

The pKa of 5-carboxy-2’,7’-dichlorosulfonefluorescein is near 4.0 and thus the dye is potentially an excellent 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.

Membrane-Permeant pH Indicators

Product pKa Catalog number Unit size
BCECF AM Ester, 1 mg/mL in DMSO pKa 6.97 51009 1 mL
BCECF AM Ester 51011

10 x 100 ug
20 x 50 ug
1 mg
5-Carboxyfluorescein diacetate, single isomer (5-CFDA) pKa 6.5 51018 100 mg
6-Carboxyfluorescein diacetate, single isomer (6-CFDA) 51021 100 mg
5-(and 6)-Carboxyfluorescein diacetate, mixed isomers (5(6)-CFDA) 51014 100 mg
5-(and-6)-Carboxyfluorescein diacetate, succinimidyl ester (CFDA, SE) 90041 25 mg
Flubida-2 51022 2 mg
5-(and-6)-Carboxy-2′,7′-dichlorofluorescein diacetate pKa 4.8 51016 100 mg
5-(and-6)-Carboxy-2′,7′-dichlorofluorescein diacetate, succinimidyl ester (SE) 90040 25 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.

Membrane-Impermeant pH Indicators

Product pKa Catalog number Unit size
BCECF, free acid pKa 6.97 51010 1 mg
5-Carboxyfluorescein (5-FAM, single isomer) pKa 6.5 51019 100 mg
6-Carboxyfluorescein (6-FAM, single isomer) 51020 100 mg
(5(6)-FAM, mixed isomers)
51013 100 mg
Flubi-2 51024 5 mg
5-Carboxy-2′,7′-dichlorofluorescein pKa 4.8 51017 100 mg
5-(and-6)-Carboxy-2′,7′-dichlorofluorescein 51015 200 mg
5-Carboxy-2′,7′-dichlorosulfonefluorescein pKa 4 51023 10 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.

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