This section describes fluorescent indicators for intracellular and extracellular chloride together with an assortment of analytical reagents and methods for direct or indirect quantitation of other inorganic anions, including bromide, iodide, hypochlorite, cyanide,nitrite, nitrate, phosphate, pyrophosphate and selenide.ref

Fluorescent Chloride Indicators

Most of the fluorescent chloride indicators are 6-methoxyquinolinium derivatives, the prototype of which is 6-methoxy-N-(3-sulfopropyl)quinolinium ref (SPQ). Cl detection sensitivity has been improved by modifications of the quinolinium N substituent.ref Our current range of Cl indicators consists of:


  • 6-Methoxy-N-(3-sulfopropyl)quinolinium (SPQ, M440)
  • N-(Ethoxycarbonylmethyl)-6-methoxyquinolinium bromide (MQAE, E3101)
  • 6-Methoxy-N-ethylquinolinium iodide (MEQ, M6886)
  • Lucigenin (L6868)


All of these indicators detect Cl via diffusion-limited collisional quenching.ref This detection mechanism is different from that of fluorescent indicators for Ca2+, Mg2+, Zn2+, Na+ and K+. It involves a transient interaction between the excited state of the fluorophore and a halide ion—no ground-state complex is formed. Quenching is not accompanied by spectral shifts (Figure 21.2.1) and, consequently, ratio measurements are not directly feasible. Quenching by other halides, such as Br and I, and other anions, such as thiocyanate, is more efficient than Cl quenching.ref Fortunately, physiological concentrations of non-choloride ions do not significantly affect the fluorescence of SPQ and other methoxyquinolinium-based Cl indicators. With some exceptions,ref fluorescence of these indicators is not pH sensitive in the physiological range.ref Because Cl-dependent fluorescence quenching is a diffusional process, it is quite sensitive to solution viscosity and volume. Exploiting this property, SPQ has been used to measure intracellular volume changes.ref

The efficiency of collisional quenching is characterized by the Stern–Volmer constant (KSV), defined as the reciprocal of the ion concentration that produces 50% of maximum quenching. For SPQ, KSV is reported to be 118 M-1 in aqueous solution and 12 M-1 inside cells.ref For MQAE, in situ KSV values of 25–28 M-1 have been determined in various cell types,ref compared with the solution value of 200 M-1. Intracellular Cl indicators are generally calibrated using high-K+ buffers and the K+/H+ ionophore nigericin (N1495) in conjunction with tributyltin chloride, an organometallic compound that acts as a Cl/OH antiporter.ref With the exception of diH-MEQ (see below), Cl indicators must be loaded into cells by long-term incubation (up to eight hours) in the presence of a large excess of dye or by brief hypotonic permeabilization. Because membranes are slightly permeable to the indicator, rapid leakage may occur. Experimentally determined estimates of leakage vary quite widely.ref

Measurement of intracellular Cl concentrations and the study of Cl channels have been stimulated by the discovery that cystic fibrosis is caused by mutations in a gene encoding a Cl transport channel, which is known as the cystic fibrosis transmembrane conductance regulator ref (CFTR). Cl permeability assays are used to detect activity of the CFTR and other anion transporters.ref In these assays, SPQ- or MQAE-loaded cells are successively perfused with chloride-containing extracellular medium followed by medium in which the Cl content is replaced by nitrate (NO3). NO3 is used in this assay protocol because it produces no fluorescence quenching of the indicator, yet its channel permeability is essentially the same as that of Cl ref (Figure 21.2.2).


Figure 21.2.1 Fluorescence emission spectra of MQAE (E3101) in increasing concentrations of Cl.


Figure 21.2.2 Detection of cystic fibrosis transmembrane conductance regulator (CFTR) activity using 6-methoxy-N-(3-sulfopropyl)quinolinium, inner salt (SPQ, M440). Fluorescence of intracellular SPQ is quenched by collision with chloride ions, indicated by F0/F > 1 (F0 = fluorescence intensity in absence of chloride, F = fluorescence intensity at time points indicated on the x-axis). Upon addition of cyclic AMP to initiate channel opening, and exchange of extracellular Cl (135 mM) for nitrate (NO3), SPQ quenching decreases in CFTR-expressing cells (filled circles) as CFTR-mediated anion transport results in replacement of intracellular Cl with nonquenching NO3. Control cells with no CFTR expression (open circles) show no response.


SPQ (M440) is currently in widespread use for detecting CFTR activity using the Cl/NO3 exchange technique described above.ref SPQ has also has been employed to investigate Cl fluxes through several other transporters such as the GABAA receptor,ref erythrocyte Cl/HCO3 exchangers ref and the mitochondrial uncoupling protein.ref Although SPQ requires UV excitation (as do MQAE and MEQ), techniques for flow cytometric detection and calibration of the indicator using argon-ion laser excitation at 351 nm and 364 nm have been successfully demonstrated.ref


MQAE (E3101) has greater sensitivity to Clref and a higher fluorescence quantum yield than SPQ; consequently, it is currently the more widely used of the two indicators. However, the ester group of MQAE may slowly hydrolyze inside cells, resulting in a change in its fluorescence response.ref MQAE has been used in a fluorescence-based microplate assay that has potential for screening compounds that modify Cl ion-channel activity.ref Other applications have included Cl measurements in cytomegalovirus-infected fibroblasts,ref smooth muscle cells ref and salivary glands,ref as well as in reconstituted membranes containing the GABAA receptor ref or the mitochondrial-uncoupling protein ref (UCP-1).

MEQ and Cell-Permeant Dihydro-MEQ

The Cl indicator 6-methoxy-N-ethylquinolinium iodide (MEQ) can be rendered cell-permeant by masking its positively charged nitrogen to create a lipophilic, Cl-insensitive compound, 6-methoxy-N-ethyl-1,2-dihydroquinoline ref (dihydro-MEQ). This reduced quinoline derivative can then be loaded noninvasively into cells, where it is rapidly reoxidized in most cells to the cell-impermeant, Cl-sensitive MEQ (Figure 21.2.3). Using this technique, researchers have loaded live brain slices and hippocampal neurons with MEQ for confocal imaging of Cl responses to GABAA receptor activation and glutamatergic excitotoxicity.ref Quenching of intracellular MEQ fluorescence by Cl has a KSV of 19 M-1, a value that is slightly higher than that reported for SPQ in fibroblasts. MEQ is available in solid form (M6886) and is supplied with a simple protocol (6-Methoxy-N-ethylquinolinium Iodide) for reducing it to dihydro-MEQ with sodium borohydride (not supplied) just prior to cell loading.


Figure 21.2.3 Intracellular delivery of the fluorescent chloride indicator 6-methoxy-N-ethylquinolinium iodide (MEQ, M6886), via oxidation of the membrane-permeant precursor dihydro-MEQ.


The fluorescence of lucigenin (L6868) is quantitatively quenched by high levels of Cl with a reported KSV = 390 M-1.ref Lucigenin absorbs maximally at both 368 nm (ε = 36,000 cm-1M-1) and 455 nm (ε = 7400 cm-1M-1), with an emission maximum at 505 nm. Its fluorescence emission has a quantum yield of ~0.6 and is insensitive to nitrate, phosphate and sulfate. Lucigenin is a useful Cl indicator in liposomes and reconstituted membrane vesicles; however, because its fluorescence is reported to be unstable in the cytoplasm, it may not always be suitable for determining intracellular Cl.ref Lucigenin has been used to detect chloride uptake in tonoplast vesicles ref and to measure Cl influx across the pleural surface in perfused mouse lungs.ref

Alternative Detection Techniques for Halides

As mentioned above, the fluorescence of SPQ and related Cl indicators is quenched by collision with a variety of anions, including (in order of increasing quenching efficiency) Cl, Br, I and thiocyanate ref (SCN). For example, fluorescence of SPQ is partially quenched by the anionic pH buffer TES (N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid) but not by the protonated TES zwitterion, a property that has been exploited to measure proton efflux from proteoliposomes.ref Anion detectability using diffusional fluorescence quenching of these fluorophores is typically limited to the millimolar range. I quenches many other fluorophores and is commonly used to determine the accessibility of fluorophores to quenching in proteins and membranes.ref

In addition, halides can be oxidized to hypohalites (OCl, OBr, OI), which react with rhodamine 6G (R634, Probes for Mitochondria—Section 12.2) to yield chemiluminescent products.ref A cell produces OCl by oxidizing Cl within the phagovacuole.ref OCl also reacts with fluorescein (F1300, Fluorescein, Oregon Green and Rhodamine Green Dyes—Section 1.5) to yield fluorescent products,ref permitting analysis of OCl levels in water.

Alternatively, 3'-(p-aminophenyl) fluorescein (APF) and 3'-(p-hydroxyphenyl) fluorescein (HPF) (A36003, H36004; Generating and Detecting Reactive Oxygen Species—Section 18.2) can be used for the selective detection of OCl. Both of these fluorescein derivatives are essentially nonfluorescent until they react with the hydroxyl radical (HO·) or peroxynitrite anion (ONOO) (Figure 21.2.4). APF will also react with the hypochlorite anion (OCl), making it possible to use APF and HPF together to selectively detect hypochlorite anion. In the presence of these specific ROS, both APF and HPF yield a bright green-fluorescent product (excitation/emission maxima ~490/515 nm) and are compatible with all fluorescence instrumentation capable of visualizing fluorescein. Using APF, researchers have been able to detect the OCl generated by activated neutrophils, a feat that has not been possible with traditional ROS indicators.ref

Figure 21.2.4 Detection of reactive oxygen species (ROS) with 3'-(p-hydroxyphenyl) fluorescein (HPF, H36004) and 3'-(p-aminophenyl) fluorescein (APF, A36003).

Premo Halide Sensor

The fluorescent protein–based Premo Halide Sensor (P10229) is a pharmacologically relevant sensor for functional studies of ligand- and voltage-gated chloride channels and their modulators in cells. Chloride channels are involved in cellular processes as critical and diverse as transepithelial ion transport, electrical excitability, cell volume regulation and ion homeostasis. Given their physiological significance, it follows that defects in their activity can have severe implications, including such conditions as cystic fibrosis and neuronal degeneration. Thus, chloride channels represent important targets for drug discovery.ref

Premo Halide Sensor combines a yellow-fluorescent protein (YFP) variant sensitive to halide ions with the efficient and noncytopathic BacMam delivery and expression technology (BacMam Gene Delivery and Expression Technology—Note 11.1), yielding a highly sensitive, robust and easy-to-use tool for efficiently screening halide ion channels and transporter modulators in their cellular models of choice. Premo Halide Sensor is based on the Venus variant of Aequorea Victoria green-fluorescent protein (GFP), which displays enhanced fluorescence, increased folding, and reduced maturation time when compared with YFP.ref Additional mutations H148Q and I152L were made within the Venus sequence to increase the sensitivity of the Venus fluorescent protein to changes in local halide concentration, in particular iodide ions.ref Because chloride channels are also permeable to the iodide ion (I), iodide can be used as a surrogate of chloride. Upon stimulation, a chloride channel or transporter opens and iodide flows down the concentration gradient into the cells, where it quenches the fluorescence of the expressed Premo Halide Sensor protein (Figure 21.2.5, Figure 21.2.6). The decrease in Premo Halide Sensor fluorescence is directly proportional to the ion flux, and therefore the chloride channel or transporter activity. Premo Halide Sensor shows a similar excitation and emission profile to YFP (Figure 21.2.7) and can be detected using standard GFP/FITC or YFP filter sets. Halide-sensitive YFP-based constructs in conjunction with iodide quenching have been used in high-throughput screening (HTS) to identify modulators of calcium-activated chloride channels.ref

Premo Halide Sensor (P10229) is pre-packaged and ready for immediate use. It contains all components required for cellular delivery and expression—including baculovirus carrying the genetically encoded biosensor, BacMam enhancer and stimulus buffer—in ten 96- or 384-well plates. Premo Halide Sensor has been demonstrated to transduce multiple cell lines including BHK, U2OS, HeLa, CHO, and primary human bronchial epithelial cells (HBEC), providing the flexibility to assay chloride permeable channels in a wide range of cellular models.

Schematic of Premo Halide Sensor Expression
Figure 21.2.5
Schematic representation of Premo Halide Sensor expression and halide sensitivity. Baculoviral particles encoding Premo Halide Sensor Sensor (P10229) enter the cells via an endocytic pathway. Following cellular entry, the baculovirus moves to the nucleus where Premo Halide Sensor gene is expressed. Premo Halide Sensor protein is localized throughout the cytoplasm and is free to react with iodide ions upon chloride channel activation, resulting in a loss of fluorescence emission intensity.

Figure 21.2.6 Principle of Premo Halide Sensor Sensor (P10229): Iodide redistribution upon chloride channel activation. Basal fluorescence from Premo Halide Sensor is high when chloride channels are closed or blocked. Upon activation (opening) of chloride channels, the iodide ions enter the cell, down its concentration gradient, and quench the fluorescence from Premo Halide Sensor.


Figure 21.2.7
Quenching of Premo Halide Sensor fluorescence by increasing concentrations of iodide and chloride. U2OS cells were transduced with Premo Halide Sensor. After 24 hours, cells were trypsinized and lysed by resuspension in sterile distilled water. Fluorescence quenching of the lysate was examined using increasing concentrations of NaCl (A) and NaI (B). Iodide induces substantially greater quenching of Premo Halide Sensor fluorescence than chloride.

Cyanide Detection

The homologous aromatic dialdehydes, o-phthaldialdehyde ref (OPA, P2331MP) and naphthalene-2,3-dicarboxaldehyde ref (NDA, N1138), are essentially nonfluorescent until reacted with a primary amine in the presence of excess cyanide or a thiol, such as 2-mercaptoethanol, 3-mercaptopropionic acid or the less obnoxious sulfite,ref to yield a fluorescent isoindole (Figure 21.2.8, Figure 21.2.9). Modified protocols that use an excess of an amine and limiting amounts of other nucleophiles permit the determination of cyanide in blood, urine and other samples.ref

We also offer the ATTO-TAG CBQCA (A6222) and ATTO-TAG FQ (A10192) reagents, which are similar to OPA and NDA in that they react with primary amines in the presence of cyanide or thiols to form highly fluorescent isoindoles ref (Figure 21.2.10). The ATTO-TAG CBQCA and ATTO-TAG FQ reagents should also be useful for detecting cyanide in a variety of biological samples.

We have found that our Thiol and Sulfide Quantitation Kit (T6060, Introduction to Thiol Modification and Detection—Section 2.1) also provides an ultrasensitive enzymatic assay for cyanide, with a detection limit of ~5 nanomoles. In this case, interference would be expected from thiols, sulfides, sulfites and other reducing agents.


Figure 21.2.8 Fluorogenic amine-derivatization reaction of o-phthaldialdehyde (OPA) (P2331MP).

Figure 21.2.9 Fluorogenic amine-derivatization reaction of naphthalene-2,3-dicarboxaldehyde (NDA) (N1138).

Figure 21.2.10 Fluorogenic amine-derivatization reaction of CBQCA (A6222, A2333).

Phosphate and Pyrophosphate Detection

PiPer Phosphate Assay Kit

The PiPer Phosphate Assay Kit (P22061) provides an ultrasensitive assay that detects free phosphate in solution through formation of the fluorescent product resorufin. Because resorufin also has strong absorption, the assay can be performed either fluorometrically or spectrophotometrically. This kit can be used to detect inorganic phosphate (Pi) in a variety of samples or to monitor the kinetics of phosphate release by a variety of enzymes, including ATPases, GTPases, 5'-nucleotidase, protein phosphatases, acid and alkaline phosphatases and phosphorylase kinase. Furthermore, the assay can be modified to detect virtually any naturally occurring organic phosphate molecule by including an enzyme that can specifically digest the organic phosphate to liberate inorganic phosphate.

In the PiPer phosphate assay (Figure 21.2.11), maltose phosphorylase converts maltose (in the presence of Pi) to glucose 1-phosphate and glucose. Then glucose oxidase converts the glucose to gluconolactone and H2O2. Finally, with horseradish peroxidase as a catalyst, the H2O2 reacts with the Amplex Red reagent (10-acetyl-3,7-dihydroxyphenoxazine) to generate resorufin, which has absorption/emission maxima of ~571/585 nm.ref The resulting increase in fluorescence or absorption is proportional to the amount of Pi in the sample. This kit can be used to detect as little as 0.2 µM Pi by fluorescence (Figure 21.2.12) or 0.4 µM Pi by absorption.

The PiPer Phosphate Assay Kit contains:

  • Amplex Red reagent
  • Dimethylsulfoxide (DMSO)
  • Concentrated reaction buffer
  • Recombinant maltose phosphorylase from Escherichia coli
  • Maltose
  • Glucose oxidase from Aspergillus niger
  • Horseradish peroxidase
  • Phosphate standard
  • Hydrogen peroxide
  • Detailed protocols for detecting phosphatase activity (PiPer Phosphate Assay Kit

Each kit provides sufficient reagents for approximately 1000 assays using a reaction volume of 100 µL per assay and either a fluorescence or absorbance microplate reader.


Figure 21.2.11
Principle of the PiPer Phosphate Assay Kit (P22061). In the presence of inorganic phosphate, maltose phosphorylase converts maltose to glucose 1-phosphate and glucose. Then, glucose oxidase converts the glucose to gluconolactone and H2O2. Finally, with horseradish peroxidase (HRP) as a catalyst, the H2O2 reacts with the Amplex Red reagent to generate the highly fluorescent resorufin. The resulting increase in fluorescence or absorption is proportional to the amount of Pi in the sample.

Figure 21.2.12 Detection of inorganic phosphate using the PiPer Phosphate Assay Kit (P22061). Each reaction contained 50 µM Amplex Red reagent, 2 U/mL maltose phosphorylase, 1 mM maltose, 1 U/mL glucose oxidase and 0.2 U/mL HRP in 1X reaction buffer. Reactions were incubated at 37°C. After 60 minutes, fluorescence was measured in a fluorescence microplate reader using excitation at 530 ± 12.5 nm and fluorescence detection at 590 ± 17.5 nm. Data points represent the average of duplicate reactions, and a background value of 43 (arbitrary units) was subtracted from each reading.


The PiPer Pyrophosphate Assay Ki

tThe PiPer Pyrophosphate Assay Kit (P22062) provides a sensitive fluorometric or colorimetric method for measuring the inorganic pyrophosphate (PPi) in experimental samples or for monitoring the kinetics of PPi release by a variety of enzymes, including DNA and RNA polymerases, adenylate cyclase and S-acetyl coenzyme A synthetase. In the PiPer pyrophosphate assay, inorganic pyrophosphatase hydrolyzes PPi to two molecules of inorganic phosphate (Pi). The Pi then enters into the same cascade of reactions as it does in the PiPer Phosphate Assay Kit (Figure 21.2.11). In this case, the resulting increase in fluorescence or absorption is proportional to the amount of PPi in the sample. This kit can be used to detect as little as 0.1 µM PPi by fluorescence or 0.2 µM PPi by absorption (Figure 21.2.13).PiPer Pyrophosphate Assay Kit

The PiPer Pyrophosphate Assay Kit contains:


  • Amplex Red reagent
  • Dimethylsulfoxide (DMSO)
  • Concentrated reaction buffer
  • Recombinant maltose phosphorylase from Escherichia coli
  • Maltose
  • Glucose oxidase from Aspergillus niger
  • Horseradish peroxidase
  • Inorganic pyrophosphatase from baker's yeast
  • Pyrophosphate standard
  • Detailed protocols for detecting pyrophosphatase activity (PiPer Pyrophosphate Assay Kit)


Each kit provides sufficient reagents for approximately 1000 assays using a reaction volume of 100 µL per assay and either a fluorescence or absorbance microplate reader.


Figure 21.2.13
Detection of pyrophosphate using the PiPer Pyrophosphate Assay Kit (P22062). Each reaction contained 50 µM Amplex Red reagent, 0.01 U/mL inorganic pyrophosphatase, 2 U/mL maltose phosphorylase, 0.2 mM maltose, 1 U/mL glucose oxidase and 0.2 U/mL HRP in 1X reaction buffer. Reactions were incubated at 37°C. After 60 minutes, A) fluorescence was measured in a fluorescence-based microplate reader using excitation at 530 ± 12.5 nm and fluorescence detection at 590 ± 17.5 nm or B) absorbance was measured in an absorption-based microplate reader at 576 ± 5 nm. Data points represent the average of duplicate reactions. In panel A, a background value of 78 (arbitrary units) was subtracted from each reading; in panel B, a background absorbance of 0.011 was subtracted from each reading.

EnzChek Phosphate Assay Kit

The EnzChek Phosphate Assay Kit (E6646), which is based on a method originally described by Webb,ref provides an easy enzymatic assay for detecting Pi from multiple sources through formation of a chromophoric product (Figure 21.2.14). Although this kit is usually used to determine the Pi produced by a wide variety of enzymes such as ATPases, kinases and phosphatases (Detecting Enzymes That Metabolize Phosphates and Polyphosphates—Section 10.3), it can also be used to specifically quantitate Pi with a sensitivity of ~2 µM Pi (~0.2 µg/mL) (Figure 21.2.15). Moreover, this colorimetric assay has proven useful for determining the level of Pi contamination in the presence of high concentrations of acid-labile phosphates using a microplate reader.ref Because the sulfate anion competes with Pi for binding to purine nucleoside phosphorylase (PNP), this kit can be adapted for measurement of sulfate concentrations between 0.1 and 10 mM in the presence of a low (<100 µM) fixed Pi concentration.ref

The EnzChek Phosphate Assay Kit contains:

  • 2-Amino-6-mercapto-7-methylpurine riboside (MESG)
  • Purine nucleoside phosphorylase (PNP)
  • Concentrated reaction buffer
  • KH2PO4 standard
  • Detailed protocols for detecting and quantitating Pi (EnzChek Phosphate Assay Kit)

Each kit provides sufficient reagents for about 100 phosphate assays using 1 mL assay volumes and standard cuvettes.


Figure 21.2.14
Enzymatic conversion of 2-amino-6-mercapto-7-methylpurine riboside (MESG) to ribose 1-phosphate and 2-amino-6-mercapto-7-methylpurine by purine nucleoside phosphorylase (PNP), reagents supplied in the EnzChek Phosphate Assay Kit (E6646). The accompanying change in the absorption maximum (Abs) allows quantitation of inorganic phosphate (Pi) consumed in the reaction.

Figure 21.2.15 Quantitative analysis of inorganic phosphate using the EnzChek Phosphate Assay Kit (E6646). KH2PO4 was used as the source for the inorganic phosphate, and the absorbance at 360 nm was corrected for background absorbance. The inset shows an enlargement of the standard curve, demonstrating the lower range of the assay; the units are the same.

EnzChek Pyrophosphate Assay Kit

In the EnzChek Pyrophosphate Assay Kit (E6645), we have adapted the method provided in the EnzChek Phosphate Assay Kit to permit the sensitive spectrophotometric detection of PPi, which is converted by the enzyme pyrophosphatase to Pi.ref Because two moles of Pi are released per mole of PPi consumed, the sensitivity limit of the EnzChek Pyrophosphate Assay Kit is 1 µM PPi (~0.2 µg/mL). This assay has been modified to continuously detect several enzymes that liberate PPi ref such as aminoacyl-tRNA synthetase,ref luciferase, cytidylyl transferase ref and S-acetyl coenzyme A synthetase ref and potentially DNA and RNA polymerases, adenylate cyclase and guanylyl cyclase.ref

The EnzChek Pyrophosphate Assay Kit contains:

  • Inorganic pyrophosphatase
  • 2-Amino-6-mercapto-7-methylpurine riboside (MESG)
  • Purine nucleoside phosphorylase (PNP)
  • Concentrated reaction buffer
  • Na2P2O7 standard
  • Detailed protocols for detecting and quantitating PPi (EnzChek Pyrophosphate Assay Kit)

Each kit provides sufficient reagents for about 100 PPi assays using standard 1 mL assay volumes and standard cuvettes.


Nitrite, Nitrate and Nitric Oxide Detection

With the discovery of the role of nitric oxide in signal transduction (Probes for Nitric Oxide Research—Section 18.3), assays for nitrite (NO2) have assumed new importance. Because inorganic nitrite is spontaneously produced by air oxidation of nitric oxide, the same reagents that have been utilized to detect nitric oxide production in cells should be useful for detecting nitrite in aqueous samples. Furthermore, inorganic nitrate (NO3) can be reduced to NO2 by both chemical and enzymatic means, permitting the quantitative analysis of NO3 in samples.

Measure-iT High-Sensitivity Nitrite Assay Kit

The Measure-iT High-Sensitivity Nitrite Assay Kit (M36051) provides an easy and accurate method for quantitating nitrite. This kit has an optimal range of 20–500 picomoles nitrite (Figure 21.2.16) , making it up to 50 times more sensitive than colorimetric methods utilizing the Griess reagent. Nitrates may be analyzed after quantitative conversion to nitrites through enzymatic reduction.ref

Each Measure-iT High-Sensitivity Nitrite Assay Kit contains:

  • Measure-iT nitrite quantitation reagent (100X concentrate in 0.62 M HCl)
  • Measure-iT nitrite quantitation developer (2.8 M NaOH)
  • Measure-iT nitrite quantitation standard (11 mM sodium nitrite)
  • Detailed protocols (Measure-iT High-Sensitivity Nitrite Assay Kit)

Simply dilute the reagent 1:100, load 100 µL into the wells of a microplate, add 1–10 µL sample volumes and mix. After a 10-minute incubation at room temperature, add 5 µL of developer and read the fluorescence. The assay signal is stable for at least 3 hours, and common contaminants are well tolerated in the assay. The Measure-iT High-Sensitivity Nitrite Assay Kit provides sufficient material for 2000 assays, based on a 100 µL assay volume in a 96-well microplate format; this nitrite assay can also be adapted for use in cuvettes or 384-well microplates.


Figure 21.2.16 Linearity and sensitivity of the Measure-iT high-sensitivity nitrite assay. Triplicate 10 µL samples of nitrite were assayed using the Measure-iT High-Sensitivity Nitrite Assay Kit (M36051). Fluorescence was measured using excitation/emission of 365/450 nm and plotted versus picomoles of nitrite. Background fluorescence was not subtracted. The variation (CV) of replicate samples was <2%.

Griess Reagent Kit

Under physiological conditions, NO is readily oxidized to NO2 and NO3 or it is trapped by thiols as an S-nitroso adduct. The Griess reagent provides a simple and well-characterized colorimetric assay for nitrites—and nitrates that have been reduced to nitrites—with a detection limit of about 100 nM.ref The Griess assay is suitable for measuring the activity of nitrate reductase in a microplate.ref Nitrite reacts with the Griess reagent to form a purple azo derivative that can be monitored by absorbance at 548 nm (Figure 21.2.17).

The Griess Reagent Kit (G7921) contains all of the reagents required for NO2 quantitation, including:


  • N-(1-Naphthyl)ethylenediamine dihydrochloride
  • Sulfanilic acid in 5% H3PO4
  • A concentrated nitrite quantitation standard for generating calibration curves
  • Detailed protocols for spectrophotometer- and microplate reader–based assays (Griess Reagent Kit for Nitrite Determination


Both the N-(1-naphthyl)ethylenediamine dihydrochloride and the sulfanilic acid in 5% H3PO4 are provided in convenient dropper bottles for easy preparation of the Griess reagent. Sample pretreatment with nitrate reductase and glucose 6-phosphate dehydrogenase is reported to reduce NO3 without producing excess NADPH, which can interfere with the Griess reaction.ref NO that has been trapped as an S-nitroso derivative can also be analyzed with the Griess Reagent Kit after first releasing the NO from its complex using mercuric chloride or copper (II) acetate.ref

Figure 21.2.17 Principle of nitrite quantitation using the Griess Reagent Kit (G7921). Formation of the azo dye is detected via its absorbance at 548 nm.


DAF-FM ref (4-amino-5-methylamino-2',7'-difluorofluorescein, D23841) and its diacetate derivative (DAF-FM diacetate, D23842D23844Probes for Nitric Oxide Research—Section 18.3) have significant utility for measuring nitric oxide and nitrite production in live cells and solutions. The fluorescence quantum yield of DAF-FM is reported to be 0.005 but increases about 160 fold to 0.81 after reacting with nitrite ref (Figure 21.2.18). DAF-FM has some important advantages over the similar nitric oxide sensor, DAF-2, and other aromatic diamines:


  • Spectra of the NO (NO2) adduct of DAF-FM are independent of pH above pH 5.5.ref
  • NO2 adduct of DAF-FM is significantly more photostable than that of DAF-2.ref
  • DAF-FM is a more sensitive reagent for NO2 than is DAF-2; the NO and NO2 detection limit for DAF-FM is ~3 nM ref versus ~5 nM for DAF-2.ref)
  • The higher absorptivity and greater water solubility of the NO2 adduct of DAF-FM should make this assay much more sensitive than detection with 2,3-diaminonaphthalene (see below) or other aromatic diamines.


Because the reaction of DAF-FM with NO requires a preliminary nonspecific oxidation step, it is important to also perform control experiments with nitric oxide synthase inhibitors to confirm the source of the fluorescent species.ref


Figure 21.2.18 Fluorescence emission spectra of DAF-FM (D23841, D23842, D23844) in solutions containing zero to 1.2 µM nitric oxide (NO).


We also offer 2,3-diaminonaphthalene (D7918), which reacts with NO2 to form the fluorescent product 1H-naphthotriazole. A rapid, quantitative fluorometric assay that employs 2,3-diaminonaphthalene can reportedly detect from 10 nM to 10 µM NO2, and is compatible with a 96-well microplate format.ref Nitrate (NO3) does not interfere with this assay; however, NO3 can be reduced to NO2 by bacterial nitrate reductase and then detected using the same reagent.ref A detailed protocol for measuring the stable products of the nitric oxide pathway (NO2 and NO3) using 2,3-diaminonaphthalene has been published and is shown to be approximately 50 times more sensitive than the Griess assay.ref

NBD Methylhydrazine

NBD methylhydrazine (N-methyl-4-hydrazino-7-nitrobenzofurazan, M20490) has been used to measure NO2 in water.ref Reaction of NBD methylhydrazine with NO2 in the presence of mineral acids leads to formation of fluorescent products with excitation/emission maxima of ~468/537 nm. This reaction serves as the principle behind a selective fluorogenic method for the determination of NO2 (Figure 21.2.19). The assay is suitable for measurements by absorption or fluorescence spectroscopy or by fluorescence-detected HPLC.ref


Figure 21.2.19
Reaction scheme illustrating the principle of nitrite detection by NBD methylhydrazine (M20490).

Other Nitrate Detection Reagents

Rhodamine 110 (R6479) has proven useful in a fluorescence quenching method for determining trace nitrite.ref This sensitive assay takes advantage of the reaction of the green-fluorescent rhodamine 110 with nitrite at acidic pH to form a nitroso product that exhibits much weaker fluorescence. With a linear range of 1 × 10-8 to 3 × 10-7moles/L and a detection limit of 7 × 10-10 moles/L, this assay has been used to measure nitrite in tap water and lake water without any prior extraction procedures.

Efficient quenching of SPQ or MQAE fluorescence (M440E3101; see above) by nitrite (but not nitrate) has been used for direct measurement of NO2 transport across erythrocyte membranes ref and for functional assays of bacterial nitrite extrusion transporters.ref


Data Table

Cat. No.
A6222305.29F,D,LMeOH465ND560MeOH 1, 2, 3
A10192251.24F,LEtOH486ND591MeOH 2, 4
D7918158.20LDMSO, MeOH3405100377MeOH 5
D23841412.35F,D,LDMSO48784,000see NotespH 8 6
E3101326.19F,D,LH2O3502800460H2O200 M-17, 8, 9, 10
E6645313.33FF,DH2O33216,000nonepH 7 11, 12
E6646313.33F,DH2O33216,000nonepH 7 11, 12
L6868510.50LH2O4557400505H2O390 M-17, 8, 10, 13, 14
M440281.33LH2O3443700443H2O118 M-17, 8, 9, 10
M6886315.15LH2O3443900442H2O145 M-17, 8, 9, 10, 15
M20490209.16F,LMeCN48724,000noneMeOH 16
N1138184.19LDMF, MeCN4199400493see Notes 17
N1495724.97F,DMeOH<300 none   
P2331MP134.13LEtOH3345700455pH 9 18
  1. Spectral data are for the reaction product with glycine in the presence of cyanide. Unreacted reagent in MeOH: Abs = 254 nm (EC = 46,000 cm-1M-1), nonfluorescent.
  2. ND = not determined.
  3. Solubility in methanol is improved by addition of base (e.g., 1–5% (v/v) 0.2 M KOH).
  4. Spectral data are for the reaction product with glycine in the presence of cyanide. Unreacted reagent in MeOH: Abs = 282 nm (EC = 21,000 cm-1M-1), nonfluorescent.
  5. Fluorescence of D7918 is weak. Reaction with nitrite yields highly fluorescent 1H-naphthotriazole (Abs = 365 nm, Em = 415 nm in H2O (pH 12)).ref
  6. DAF-FM fluorescence is very weak. Reaction with nitrite or nitric oxide generates a highly fluorescent benzotriazole derivative with Abs = 495 nm (EC = 73,000 cm-1M-1), Em = 515 nm in pH 7.4 buffer.ref
  7. Values of KSV are taken from published references.ref
  8. KSV is the Stern-Volmer quenching constant for Cl ions (units are M-1), representing the reciprocal of the ion concentration that produces 50% fluorescence quenching. The quenching constant is very dependent on viscosity and is usually significantly lower in cells. These indicators are quenched more effectively by bromide, iodide and certain other anions.
  9. This quinolinium dye also has a slightly stronger (~50%) absorption peak 25–30 nm shorter than the listed Abs wavelength.
  10. This product undergoes Cl-dependent fluorescence quenching with essentially no change in absorption or emission wavelengths.
  11. Data represent the substrate component of this kit.
  12. Enzymatic phosphorylation of this substrate yields 2-amino-6-mercapto-7-methylpurine (Abs = 355 nm).ref
  13. L6868 has much stronger absorption at shorter wavelengths (Abs = 368 nm (EC = 36,000 cm-1M-1)).
  14. This compound emits chemiluminescence upon oxidation in basic aqueous solutions. Emission peaks are at 425 nm (L8455) and 470 nm (L6868).
  15. M6886 may be chemically reduced to cell-permeant diH-MEQ.ref
  16. NBD methylhydrazine reacts with nitrite in the presence of strong acid to form fluorescent N-methyl-4-amino-7-nitrobenzofurazan (Abs = 459 nm, Em = 537 nm in MeCN).ref
  17. Spectral data are for the reaction product with glycine in the presence of cyanide, measured in pH 7.0 buffer/MeCN (40:60).ref Unreacted reagent in MeOH: Abs = 279 nm (EC = 5500 cm-1M-1), Em = 330 nm.
  18. Spectral data are for the reaction product of P2331MP with alanine and 2-mercaptoethanol. The spectra and stability of the adduct depend on the amine and thiol reactants.ref Unreacted reagent in H2O: Abs = 257 nm (EC = 1000 cm-1M-1).