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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Free Radic Biol Med. Author manuscript; available in PMC 2014 February 3.
Published in final edited form as:
PMCID: PMC3911769

Measuring reactive oxygen and nitrogen species with fluorescent probes: challenges and limitations


The purpose of this position paper is to present a critical analysis of the challenges and limitations of the most widely used fluorescent probes for detecting and measuring reactive oxygen and nitrogen species. Where feasible, we have made recommendations for the use of alternate probes and appropriate analytical techniques that measure the specific products formed from the reactions between fluorescent probes and reactive oxygen and nitrogen species. We have proposed guidelines that will help present and future researchers with regard to the optimal use of selected fluorescent probes and interpretation of results.


The generation of reactive oxygen and nitrogen species has been implicated in the onset and progression of several diseases (e.g., atherosclerosis, cancer, diabetes, neurodegeneration) [1]. At a molecular level, reactive oxygen and nitrogen species exhibit signaling and cell-function-modifying roles [2]. As pointed out in a recent review [3], reactive oxygen and nitrogen species are not single entities but represent a broad range of chemically distinct reactive species with diverse biological reactivities [3,4]. To clearly attribute a particular cell signaling event to a specific reactive oxygen or nitrogen species, it is essential to detect and characterize these species accurately. Several analytical approaches (EPR, chemiluminescence, fluorescence) have been used to detect reactive oxygen and nitrogen species. Many reviews on this subject have been published in this journal. In this position paper, we discuss the relative merits and weaknesses of the fluorescent probes (e.g., dichlorodihydrofluorescein, hydroethidine, and dihydrorhodamine) that are being used frequently for measuring hydrogen peroxide, superoxide, and peroxynitrite in biological systems.

Is dichlorodihydrofluorescein diacetate (DCFH-DA) a suitable probe for measuring intracellular H2O2 and other oxidants?

DCFH-DA is the most widely used probe for detecting intracellular H2O2 and oxidative stress. This probe is cell-permeable and is hydrolyzed intracellularly to the DCFH carboxylate anion, which is retained in the cell. Two-electron oxidation of DCFH results in the formation of a fluorescent product, dichlorofluorescein (DCF), which can be monitored by several fluorescence-based techniques (e.g., confocal microscopy, flow cytometry). This is a relatively easy and user-friendly assay that has become immensely popular. Investigators have routinely used DCFH-DA to measure intracellular generation of H2O2 and other oxidants or monitor redox signaling changes in cells in response to intra- or extracellular activation with oxidative stimulus [510].

However, as shown in Fig. 1 and outlined below, the intracellular redox chemistry of DCFH is complex and there are several limitations and artifacts associated with the DCF assay for intracellular H2O2 measurement [1113]. It is essential to keep these limitations in mind for proper interpretation of data obtained with the DCFH-DA probe. Specifically:

  1. DCFH does not directly react with H2O2 to form the fluorescent product, DCF. Therefore, DCF fluorescence cannot be used as a direct measure of H2O2.
  2. Several one-electron-oxidizing species will oxidize DCFH to DCF (Fig. 1). These include hydroxyl radicals (OH), compounds I and II formed from peroxidase or heme interaction with H2O2, NO2 formed from the myeloperoxidase/H2O2/ NO2 system, hypochlorous acid (HOCl), and reactive species formed from peroxynitrite (ONOO/ONOOH) decomposition. Peroxynitrite decomposition also forms OH or carbonate anion radicals ( CO3) in the presence of bicarbonate.
  3. The intermediate radical, DCF•−, formed from the one-electron oxidation of DCFH, rapidly reacts with O2 (k=108 M−1 s−1) to form superoxide ( O2) (Fig. 1). The dismutation of O2 yields additional H2O2[14], which can establish a redox-cycling mechanism leading to artifactual amplification of the fluorescence signal intensity.
  4. Cytochrome c, a heme protein that is released from mitochondria to the cytosol during apoptosis, is capable of oxidizing DCFH directly or indirectly via a peroxidase-type mechanism, forming DCF [8, 11]. The increase in DCF fluorescence that occurs during apoptosis of cells loaded with DCFH-DA has frequently been associated with enhanced oxidant production.
  5. Redox-active metals (e.g., Fe2+) promote DCFH oxidation in the presence of oxygen or H2O2 [15].
  6. In addition, one cannot always assume that control and experimental samples exhibit the same efficiency in DCF radical generation and the same linear dependence of self-propagating redox-cycling reactions induced by the DCF radical (Fig. 1).
Fig. 1
Oxidative reactions mediated by the dichlorodihydrofluorescein radical (DCF•−) in the presence of oxygen, heme proteins, and glutathione (reproduced from Ref. [35]).

Therefore, even if differences in DCF fluorescence are documented under control and experimental conditions, one has to consider the various caveats listed above for proper interpretation of the data. Failure to recognize these limitations often leads to erroneous interpretations and diverts the researchers' attention away from the more significant findings (e.g., increased peroxidase activity induced by the experimental conditions, or a new redox signaling/redox modification mechanism). Our recommendation to researchers in this field is that the DCFH-DA probe cannot be reliably used to measure intracellular H2O2 and other reactive oxygen species.

Now the important question: What type of useful information can one obtain using the fluorescent probe DCFH-DA? On a positive note, it is conceivable that useful redox-signaling mechanisms can be explored using this probe [68]. There are numerous examples in the literature that support the role of oxidant-induced iron signaling in DCFH oxidation, of which a few are discussed here. Previous studies implicated a role for redox-active iron in intracellular oxidation of DCFH to DCF [16], although the origin of the cellular iron was not known. In earlier studies, it was shown that H2O2- and lipid hydroperoxide-induced intracellular DCFH oxidation to DCF was mediated by transferrin receptor (TfR)-dependent uptake of iron [57]. Intracellular DCF fluorescence was inhibited by the monoclonal IgA-class anti-TfR antibody that blocked TfR endocytosis and the iron uptake. These studies also showed that peroxide-dependent DCF fluorescence was critically dependent on intracellular glutathione levels [5]. DCFH-DA was also used to monitor doxorubicin-induced iron signaling and the associated mitochondrial damage in endothelial cells [7]. DCFH-DA was used as an indicator for mitochondrial generation of oxidants and peroxynitrite in endothelial cells treated with oxidized low-density lipoprotein (oxLDL) [9]. A role for iron, endothelial nitric oxide synthase activity, and complex II activity in oxLDL-dependent DCF fluorescence was proposed [9,10,17]. DCFH-DA may be used as a redox indicator probe that responds to changes in intracellular iron signaling or peroxynitrite formation.

Are there other probes for measuring intracellular H2O2?

Very few small organic molecules stoichiometrically react with H2O2 to form a detectable intracellular fluorescent product. However, aromatic boronates (boronic acids and esters) react with H2O2 to form a single major product, the corresponding phenol (reaction yield is nearly 100% [18]). Recently, the boronate moiety was attached to a fluorophore (e.g., fluorescein) that, upon reaction with H2O2, forms a highly fluorescent molecule [19]. The boronate esters attached to a fluorophore are cell-permeable and interact directly with intracellular H2O2 to form fluorescent products in cells. However, the rate constant for the reaction between boronates and H2O2 is relatively low (0.1–1.0 M−1 s−1). It is unlikely to compete with H2O2-detoxifying enzymes such as the peroxiredoxins, which react 7 orders of magnitude faster with H2O2[3,4]. Nevertheless, even a small fraction of the reaction between the fluorescein boronate molecule and H2O2 would result in detectable intracellular fluorescence. This assay has been used to detect intracellular H2O2 formation [19,20]. Mitochondrial-targeted boronate (aromatic boronate conjugated to an alkyl triphenylphosphonium group) was recently used in vivo to quantitate H2O2 in fly mitochondria [21]. Mass spectrometry was used to quantitate the product [21]. However, aromatic boronates also react nearly stoichiometrically with ONOO a million times faster than they do with H2O2[18,22], which should be taken into consideration (see Is dihydrorhodamine a specific probe for measuring intracellular peroxynitrite?). The use of inhibitors (L-NAME, catalase, PEG–catalase, SOD, or PEG–SOD) should help distinguish ONOO from H2O2 in boronate-based fluorescence assays.

Another probe that is frequently used to measure H2O2 is Amplex red [23]. Amplex red is oxidized by horseradish peroxidase (HRP) and H2O2 to a fluorescent product, resorufin [23]. Although other one-electron oxidants are capable of oxidizing Amplex red to resorufin, the oxidation catalyzed by HRP in the presence of H2O2 is highly efficient and vastly increases the yield of resorufin. Therefore this assay is a viable method to continuously measure the extracellular formation of H2O2. A major complicating factor is light-mediated photochemical oxidation of resorufin in the presence of biological reductants (glutathione, NADH) that induce resorufin radical-mediated formation of O2 and H2O2[24]. Because of the confounding radical reactions induced by resorufin, the use of Amplex red or cell-permeable Amplex red analog to measure intracellular H2O2 could pose problems. Under conditions where H2O2 is released from the cell or in isolated mitochondrial preparations, the Amplex red probe can be used to measure H2O2 in the presence of HRP.

Other approaches for monitoring intracellular H2O2 levels include the use of a redox-active biosensor, HyPer, whose design is based on OxyR, a natural bacterial H2O2 sensor [25]. Recent developments include HyPer targeted to various cellular compartments. This ratio-metric assay for H2O2 is potentially promising, although its range of applications in biology has not yet been critically examined.

Measurement of intracellular and mitochondrial superoxide using hydroethidine (HE) and Mito-SOX

HE, or dihydroethidium, is another widely used probe for detecting intracellular O2[26]. The red fluorescence formed from the two-electron oxidation product, ethidium (E+), is usually equated to intracellular superoxide formation. Previous research suggests that E+ is not formed from the direct oxidation of HE by O2[27,28]. Instead, another product, 2-hydroxyethidium (2-OH-E+), with similar fluorescence characteristics, is formed from the HE/ O2 reaction [29]. To the best of our knowledge, 2-OH-E+ is not formed during the reaction between HE and other oxidants (ONOO, OH, H2O2, compounds I and II), although they oxidize HE to E+ and other dimeric products. However, one cannot rule out the direct hydroxylation of HE to form 2-OH-E+ by cytochrome P-450 or by a similar enzymatic metabolism. Hydroethidine-derived radicals do not react with oxygen to form superoxide. Because of other oxidative reactions of HE, we suggest that 2-OH-E+ formation is only a qualitative and not a quantitative indicator of intracellular and/or extracellular O2[30] (Scheme 1). However, it will not be possible to use fluorescence-based intracellular techniques alone to assess O2 formation because intracellular red fluorescence detection, using HE, does not automatically translate to O2 measurement. One has to confirm the formation of 2-OH-E+ using other analytical techniques (HPLC-fluorescence or electrochemical detection or LC–MS). Another advantage of measuring E+ and other dimers of HE (HE–HE, HE–E+, E+–E+) is that they can be used as an indicator for one-electron oxidant formation in cells.

Scheme 1
Oxidative reactions of HE and Mito-HE.

Mitochondrial-targeted HE or Mito-SOX, a triphenylphosphonium cation conjugated to HE via a linker carbon–carbon alkyl chain, has been used to measure mitochondrial O2[31]. The chemistry of Mito-SOX with O2 is similar to that of HE and O2[32] and the same caveats apply as above. Being a positively charged molecule, Mito-SOX reacts slightly faster with O2 compared to HE [31]. Mito-SOX reacts with O2 and forms a red-fluorescent product, 2-hydroxymitoethidium (2-OH-Mito-E+), and not Mito-E+ (Scheme 1). 2-OH-Mito-E+ (specific reaction product of O2 with Mito-SOX) and Mito-E+ (nonspecific oxidation product of Mito-SOX) have overlapping fluorescence spectra. Thus, the red fluorescence formed from Mito-SOX localized in mitochondria is not a reliable indicator of mitochondrial O2 formation. Mito-SOX red fluorescence could arise from the O2 product, from a composite of O2 product and an oxidation product, or solely from an oxidation product of Mito-SOX induced by one-electron oxidants (cytochrome c, peroxidase, and H2O2). As shown for the HE probe, it is necessary to separate and identify 2-OH-Mito-E+ by HPLC. For details, see previous publications [2931].

Is dihydrorhodamine a specific probe for measuring intracellular peroxynitrite?

Dihydrorhodamine (DHR) is the most frequently used probe for measuring ONOO[33,34]. This assay is based on the oxidative conversion of DHR to its corresponding two-electron-oxidized fluorescent product, rhodamine. In many respects, the oxidative mechanisms of DHR and DCFH are very similar [15]. DHR oxidation to rhodamine is triggered by several oxidants (OH, compounds I and II, and NO2), similar to DCFH oxidation by oxidants as shown in Fig. 1. Thus, DHR oxidation to rhodamine is also nonspecific. The oxidative conversion of DHR to rhodamine is mediated by an intermediate DHR radical. The overall reaction profile of DHR to rhodamine in the presence of cogenerated NO and O2 is influenced by the free radical chemistry of DHR radical, showing a bell-shaped response [34]. The oxidation of DHR by cogenerated NO and O2 is mediated by oxidants (NO2 and OH) formed from the rapid and spontaneous decomposition of ONOO, and DHR oxidation is not induced directly by ONOO. The intermediate radical, DHR, formed from the one-electron oxidation of DHR, also rapidly reacts with oxygen (k=7×108 M−1 s−1) [15,33], setting up a redox cycling mechanism leading to artifactual amplification of the fluorescence signal intensity (see Fig. 1). The limitations and caveats associated with DCF assay apply to DHR assay as well. The roles of NO and O2 or iron in intracellular DHR oxidation should be independently confirmed with appropriate inhibitors (e.g., L-NAME, PEG–SOD, desferrioxamine). Thus, DHR can be used only as a nonspecific indicator of intracellular ONOO and HOCl formation [33].

Emerging probes for measurement of peroxynitrite

Recent research shows that aromatic boronates can be rapidly oxidized by ONOO yielding the corresponding phenols as a major product (85% yield) [18,22]. Boronate-containing fluorophores (e.g., coumarin boronate) react in a similar fashion with ONOO giving rise to the corresponding fluorescent products. Some of these boronate-based fluorophores are cell-permeable and can be effectively used to measure intracellular ONOO. With increased availability of these probes, significant advances and new understanding in reactive oxygen and nitrogen research are likely. Synthesis of newer cell-permeable probes, coupled with enhanced understanding of their radical/nonradical chemistry, will provide additional research tools with which the complex roles of reactive oxygen and nitrogen species in cell signaling, cell growth, and cell differentiation can be unraveled.

We hope that this position paper clarifies some aspects of the appropriate use of fluorescent probes in the detection and characterization of reactive oxygen and nitrogen species in biology, and that it also highlights the many challenges and limitations of detection, characterization, and measurement of intracellular reactive oxygen and nitrogen species. The advantages, disadvantages, and recommendations of selected fluorescent probes listed in Table 1 should help alleviate some confusion with regard to the choice of suitable probes for detecting reactive oxygen and nitrogen species.

Table 1
Guidelines for proper use of fluorescent probes.


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