A method to determine reactive oxygen species production in intestinal and liver cell cultures using the 2',7'-dichlorodihydrofluorescein diacetate assay

Exposure to xenobiotics can increase the production of reactive oxygen species (ROS). When detoxification organs such as the intestines and liver cannot neutralise these xenobiotics, it can induce oxidative stress and cause damage to tissues. Therefore, cell-based bioassays that indicate intracellular ROS production are a useful screening tool to evaluate the effect of these chemicals. Although flow cytometry is commonly used to measure ROS in cells, many research laboratories in the Global South do not always have access to such specialised instrumentation. Therefore, we describe a sensitive but low-cost method that can easily be used to determine ROS production in vitro. This method employs the fluorogenic dye, 2',7'-dichlorodihydrofluorescein diacetate (H2DCF-DA), which emits fluorescence after being oxidised to a fluorescent derivative. Since the H2DCF-DA bioassay indicates non-specific ROS production it can be used as a marker of overall oxidative stress. This method was validated by exposing human duodenum epithelial adenocarcinoma (HuTu-80) and rat liver epithelial hepatoma (H4IIE-luc) cells to agricultural soil samples.•Production of ROS can be determined in vitro in intestinal and liver cells.•This method is inexpensive and can be easily performed in standard laboratories.•The method provides a tool for the high-throughput screening of environmental samples.

A fluorogenic nitric oxide donor induced by yellow LED light for cells proliferation inhibition and imaging

Nitric oxide (NO), as a vital cellular signalling molecule in physiological processes, has been found to play an important role in various biological functions. In this study, we rationally designed three NO donors by tethering nitrobenzene derivatives to three fluorescent chromophores. NX-NO was found to release NO and exhibit a high fluorescence turn-on signal ratio upon exposure to LED yellow light. Additionally, it had excellent photo-stability and good inhibitory activity against cancer cell proliferation, and was successfully applied to cell imaging. Moreover, we detected the release of NO and fluorescence response in the blood of a mouse, suggesting its potential therapeutic application in living organisms.

Monitoring H2S fluctuation during autophagic fusion of lysosomes and mitochondria using a lysosome-targeting fluorogenic probe

Hydrogen sulfide (H₂S) plays a cytoprotective role during mitophagy by detoxifying superfluous reactive oxygen species (ROS), and its concentration fluctuates in this process. However, no work has been reported to reveal the variation in H₂S levels during autophagic fusion of lysosomes and mitochondria. Herein, we present a lysosome-targeted fluorogenic probe, named NA-HS, for real-time monitoring of H₂S fluctuation for the first time. The newly synthesized probe exhibits good selectivity and high sensitivity (detection limit of 23.6 nM). Fluorescence imaging results demonstrated that NA-HS could image exogenous and endogenous H₂S in living cells. Interestingly, the colocalization results revealed that the level of H₂S was upregulated after autophagy began because of the cytoprotective effect, and was finally gradually reduced during subsequent autophagic fusion. This work not only affords a powerful fluorescence tool to monitor the variations in H₂S levels during mitophagy, but also offers new insights into targeting small molecules for elaborating the complex cellular signal pathways.

Rapid genotyping of 32 insertion/deletion panel for human identification using fluorogenic probes-based multiplex real-time PCR

BACKGROUND

Insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because of their low mutation rate and small amplicons. At present, InDel polymorphisms detection based on the technique of capillary electrophoresis is the main technique used in forensic DNA laboratory. However, this method is complicated and time-consuming, and is not suitable for rapid on-site paternity and personal identification. Next-generation sequencing analysis of InDels polymorphisms requires expensive instruments, large upfront reagent and supply costs, computational requirements and complex bioinformatics, increased the time to obtain results. Thus, there is an urgent need to establish a method to provide reliable, rapid, sensitive and economical genotyping for InDels.

METHOD

A rapid InDels (32 InDels) panel was established using fluorogenic probes-based multiplex real-time PCR with microfluidic test cartridge and portable real-time PCR instrument. Then, we performed several validation studies including concordance, accuracy, sensitivity, stability, species specificity.

RESULTS

It showed that the complete genotypes could be obtained from ≥100 pg of input DNA and from a series of challenging samples with high accuracy and specificity within 90 min.

CONCLUSION

This method provides a rapid and cost-effective solution for InDels genotyping and personal identification in portable format.

Design of Fluorogenic Probe Based on Intramolecular Condensation for Specific Detection of HDAC3

It is crucial to develop fluorogenic probes for selective targeting of HDACs to explore the roles of HDACs in the tumor onset and progression as well as HDAC-related drug development. However, considerable non-specific signals were produced by spontaneous hydrolysis and undesirable intermolecular attack of the unstable caging moiety in the detection of HDACs with previous probes. To improve the detection specificity, we proposed an intramolecular condensation strategy by the replacement of the traditional acetamide moiety with a trans-enamide unit. Upon deacetylation by HDACs, rapid intramolecular condensation reaction between newly formed terminal aldehyde and hydrazine moiety would occur to afford highly fluorescent hydrazone product. Systematic studies demonstrated that the probe exhibited an extraordinary selectivity for HDAC3 over other HDAC isoforms and interfering substances. The stability and specificity of the indicator make it a powerful tool for HDAC3 activity detection and HDAC3-related drug development.

A two-photon fluorogenic probe based on a coumarin schiff base for formaldehyde detection in living cells

A novel two-photon fluorogenic probe has been developed to detect formaldehyde with fast response, low cytotoxicity, and excellent selectivity. This probe exhibits a strong turn-on fluorescence response to formaldehyde under excitation at 370 nm and has been successfully applied to detect formaldehyde in living cells. Theoretical calculations at the B3LYP/6-31 + G(d,p), APFD/6-311++G, and APFD/6-311 + G(2d,p) levels of theory for the absorption and emission wavelengths of the probes were in agreement with those obtained experimentally.

Extending optical chemical tools and technologies to mice by shifting to the shortwave infrared region

Fluorescence imaging is an indispensable method for studying biological processes non-invasively in cells and transparent organisms. Extension into the shortwave infrared (SWIR, 1000-2000 nm) region of the electromagnetic spectrum has allowed for imaging in mammals with unprecedented depth and resolution for optical imaging. In this review, we summarize recent advances in imaging technologies, dye scaffold modifications, and incorporation of these dyes into probes for SWIR imaging in mice. Finally, we offer an outlook on the future of SWIR detection in the field of chemical biology.

Extraction of RNA and Analysis of Estrogen-Responsive Genes by RT-qPCR

Reverse transcription-quantitative RT-PCR (RT-qPCR) is a powerful tool for assessing gene transcription levels. The technique is especially useful for measuring estrogen receptor transcript levels as well as gene expression changes in response to estrogen stimulation as it is quick, accurate, and robust and allows the measurement of gene expression in a variety of tissues and cells. This chapter describes the protocols used for RNA extraction and analysis as well as for RT-qPCR assay using hydrolysis (TaqMan-type) probes.

Design, synthesis and mechanistic studies of a TICT based fluorogenic probe for lighting up protein HSA

Human serum albumin (HSA) in blood serves as an important biomarker for clinical diagnosis, and fluorescence sensing method has attracted extensive attention. In this work, a small organic molecule probe, YS8, involving twisted intramolecular charge transfer (TICT) characteristic, was designed and investigated to detect HSA. YS8 kept silent state in fluorescence under physiological conditions, but the encapsulation of YS8 in the hydrophobic subdomain IB region of HSA inhibited the TICT state and produced a clear light-up fluorescent signal. Especially, YS8 was demonstrated to be an efficient fluorogenic probe to discriminate HSA from other proteins including the bovine serum albumin (BSA). Moreover, YS8/HSA complex could be applied in fluorescence imaging in living cells and is also useful in the study of artificial fluorescent protein (AFP).

Multifunctional fluorescent probes for high-throughput characterization of hexosaminidase enzyme activity

Microbial polysaccharides composed of N-acetylglucosamine (GlcNAc), such as chitin, peptidoglycan and poly-β-(1 → 6)-GlcNAc (dPNAG), play a critical role in maintaining cell integrity or in facilitating biofilm formation in numerous fungal and bacterial pathogens. Glycosyl hydrolase enzymes that catalyze the degradation of these β-GlcNAc containing polysaccharides play important roles in normal microbial cell physiology and can also be exploited as biocatalysts with applications as anti-fungal, anti-bacterial, or biofilm dispersal agents. Assays to rapidly detect and characterize the activity of such glycosyl hydrolase enzymes can facilitate their development as biocatalyst, however, currently available probes such as 4-methylumbelliferyl-β-GlcNAc (4MU-GlcNAc) are not universally accepted as substrates, and their fluorescent signal is sensitive to changes in pH. Here, we present the development of a new multifunctional fluorescent substrate analog for the detection and characterization of hexosaminidase enzyme activity containing a 7-amino-4-methyl coumarin (AMC) carbamate aglycone. This probe is widely tolerated as a substrate for exo-acting β-hexosaminidase, family 19 endo-chitinase, and the dPNAG hydrolase enzyme Dispersin B (DspB) and enables detection of hexosaminidase enzyme activity via either single wavelength fluorescent measurements or ratiometric fluorescent detection. We demonstrate the utility of this probe to screen for recombinant DspB activity in Escherichia coli cell lysates, and for the development of a high-throughput assay to screen for DspB inhibitors.

A GLUT1 inhibitor-based fluorogenic probe for Warburg effect-targeted drug screening and diagnostic imaging of hyperglycolytic cancers

Increased expression of glucose transporters, especially GLUT1 has been proven to be involved in the Warburg effect. Therefore, GLUT1-targeted oncological approaches are being successfully employed for clinical tumor diagnostic imaging (e.g. the ¹⁸F-FDG/PET), drug delivery and novel anticancer drug development. Despite the long history of the Warburg effect-targeted cancer diagnosis, other than antibody labeling, there have been no imaging tools developed for direct detection of the GLUT1 expression. Herein, we report the new strategy of using a non-antibody GLUT1 binding probe for Warburg effect-based tumor detection and diagnostic imaging. By specifically inhibits the transport function of GLUT1, the newly designed fluorescent probe, CUM-5, was found to be a useful tool not only for sensitive GLUT1-mediated cancer cell detection, but also for cell-based high-throughput GLUT inhibitor screening. In in vivo studies, CUM-5 shows clear advantages including desirable tumor-to-normal tissue contrast and excellent tumor selectivity (Tm/Bkg and Tm/Torg), as well as high fluorescence stability (long response time) and ideal physiological biocompatibility. In particular, the GLUT1 inhibitor probe offers the potential use for glycolysis-based diagnostic imaging in triple-negative breast cancer which is claimed to have unsatisfactory results with FDG/PET diagnosis, thus remaining a highly metastatic and lethal disease with a need for sensitive and precise identification.

Design, synthesis and evaluation of enzyme-responsive fluorogenic probes based on pyridine-flanked diketopyrrolopyrrole dyes

The ever-growing demand for fluorogenic dyes usable in the rapid construction of analyte-responsive fluorescent probes, has recently contributed to a revival of interest in the chemistry of diketopyrrolopyrrole (DPP) pigments. In this context, we have explored the potential of symmetrical and unsymmetrical DPP derivatives bearing two or one 4-pyridyl substituents acting as optically tunable group(s). The unique fluorogenic behavior of these molecules, closely linked to N-substitution/charge state of their pyridine unit (i.e., neutral pyridine or cationic pyridinium), has been used to design DPP-based fluorescent probes for detection of hypoxia-related redox enzymes and penicillin G acylase (PGA). In this paper, we describe synthesis, spectral characterization and bioanalytical validations of these probes. Dramatic differences in terms of aqueous stability and enzymatic fluorescence activation were observed. This systematic study enables to delineate the scope of application of pyridine-flanked DPP fluorophores in the field of enzyme biosensing.

Performance of a novel fluorogenic probe assay for the detection of extended-spectrum-β-lactamase or plasmid AmpC β-lactamase-producing Enterobacterales directly from simulated blood culture bottles

Resistance to third generation cephalosporins is widely disseminated in Enterobacteriaceae mainly because of extended-spectrum-β-lactamases (ESBL), plasmid AmpC β-lactamases (PABL), and hyper-production of chromosomal AmpC β-lactamases. Here, we evaluated the performance of rapid test using novel fluorogenic probe assay in simulated blood cultures and compared the results with the phenol red assay using a total of 172 characterized isolates (39 ESBL producers, 13 PABL producers, and 120 susceptible isolates). We prepared a pellet by centrifugation and washing, which can also be used for identification with MALDI-TOF directly from positive blood cultures. After that, we mixed the pellet with fluorogenic probe and measured the fluorescent signal using fluorometer. The fluorogenic probe assay showed higher sensitivity than the phenol red assay (96.2% vs. 71.2%, p < .0001) in 172 simulated blood culture bottles especially in detecting PABL (84.6% vs. 0%, p = .0026) and the turnaround time was 1.5 h. This fluorogenic probe assay, combined with the direct identification of pathogens, could be very useful for rapid identification of isolates and detecting cephalosporin resistance caused by ESBL and PABL directly from positive blood cultures.

Design and synthesis of fluorogenic substrate-based probes for detecting Cathepsin B activity

Cathepsin B plays key roles in tumor progression with its overexpression being associated with invasive and metastatic phenotypes and is a primary target of protease activated antibody-directed prodrug therapy. It therefore represents a potential therapeutic and diagnostic target and effort has been made to develop fluorescent probes to report on Cathepsin B activity in cells and animal models of cancer. We have designed, synthesized, and thoroughly evaluated four novel "turn on" probes that employ a lysosomotropic dansylcadaverine dye to report on Cathepsin B activity. Enzyme activity assays using a recombinant human enzyme and cancer cell lysates coupled with confocal microscopy experiments demonstrated that one of the probes, derivatized with the self-immolative prodrug linker p-aminobenzyl alcohol, can selectively report on Cathepsin B in biological samples including live cells.

Validation of quantitative real-time RT-PCR assays for the detection of six honeybee viruses

Acute bee paralysis virus (ABPV), Black queen cell virus (BQCV), Chronic bee paralysis virus (CBPV), Deformed wing virus (DWV), Sacbrood virus (SBV) and Varroa destructor virus 1 (VDV1) are the six main honeybee viruses reported in Europe. We assessed the accuracy (trueness and precision) of reverse transcriptase quantitative TaqMan® PCR methods (RT-qPCR) for quantifying ABPV, BQCV, DWV, VDV1 and SBV loads. Once the systematic bias in quantitative results had been corrected (overestimation in ABPV and BQCV quantification and underestimation in that of SBV and VDV1), measurements were taken to determine the viral load ranges for which quantification uncertainty was below ± 1 log₁₀ equivalent of genome copies per bee (hereafter reported as genome copies/bee). The accuracy range of RT-qPCR was found to be between 6.4 and 10.4 log₁₀ genome copies/bee for ABPV, between 3.0 and 10.0 log₁₀ genome copies/bee for BQCV, between 2.4 and 10.4 log₁₀ genome copies/bee for DWV and between 3.4 and 10.4 log₁₀ genome copies/bee for SBV. Outside these ranges, the results' uncertainty is higher. VDV1 RT-qPCR accuracy was outside accuracy limits for all viral loads. Using these RT-qPCR methods, we quantified viral loads in naturally-infected honeybees. The viral load distribution and clinical signs reported with the honeybee samples allowed us to define a threshold that could be used to differentiate between covert and overt infections. These methods will be useful in diagnosing the main viral infections impairing honeybee health.

Fluorogenic approach to evaluating prodrug hydrolysis and stability in live cells

Fluorescein diester which is conjugated with cell membrane permeable Arg9 peptide was proposed as probe for ester prodrug stability and drug release study in living cells. α-Amino protected d-Val and l-Ala which bear differently hindered side chains were used to afford model diesters of 5-maleimide-fluorescein. Such fluorescein diesters were further conjugated with a Cys containing cell membrane permeable Arg9 peptide via thiol-ene crosslink reaction. The resulted conjugates of fluorescein diester and Arg9 peptide were purified with HPLC and characterized with MALDI-TOF MS. Upon incubation with cultured cells, the fluorescein diesters were delivered into the cells, the following hydrolysis of fluorescein diesters and release of fluorescein inside living cells were observed by monitoring the fluorescence accumulation. Fluorescence microscopic imaging studies of HeLa cells treated with fluorescein l-Ala diester show strong fluorescence accumulation in 30 min indicating fast hydrolysis of fluorescein diester and fluorescein release; in contrast d-Val diester remains stable inside cells evidenced by margin fluorescence formation. Further flowcytometry studies on the fluorescein diester-Arg9 conjugate treated cells show that the hydrolysis t_1/2 for l-Ala diester is 15 min. The results also show that Arg9 peptide not only transports the ester probes into cell efficiently but also can retain and concentrate hydrolytic product fluorescein inside cells so that the accumulated fluorescence can be accurately quantified. This fluorogenic probe approach provides feasible applications in dynamic studies on ester prodrug hydrolysis and release, facilitating screening and optimization of prodrug structures in living cell settings.

Effect of antioxidant supplements on lipid peroxidation levels in primary cortical neuron cultures

Oxidative stress, specifically lipid peroxidation, is a major driving force in neurodegenerative processes. However, the exact role of lipid peroxidation remains elusive as reliable real-time detection and quantification of lipid peroxyl radicals proves to be challenging in vitro and in vivo. Motivated by this methodological limitation, we have optimized conditions for real-time imaging and quantification of lipid peroxyl radical generation in primary neuron cultures using the lipophilic fluorogenic antioxidant H₄BPMHC (8-((6-hydroxy-2,5,7,8-tetramethylchroman-2-yl)-methyl)-1,5-di(3-chloropropyl)-pyrromethene fluoroborate), an α-tocopherol analog probe. By subjecting neurons to different antioxidant conditions in the presence and absence of lipid peroxidation inducing stressors (Haber-Weiss reagents), we maximized H₄BPMHC sensitivity and confirmed its potential to temporally resolve subtle and marked differences in lipid peroxidation levels in real-time. Herein we report imaging and quantification of homeostatic and induced lipid peroxidation in primary neuron cultures, supporting the use of this probe for investigating healthy and diseased states. Overall these results provide the necessary foundation and impetus towards using H₄BPMHC for elucidating and mapping lipid peroxyl radical contributions to ROS-associated pathological processes in neurons.

Highly selective and sensitive fluorogenic ferric probes based on aggregation-enhanced emission with -SiMe3 substituted polybenzene

In this study, thiophene was linked to polybenzene to generate novel fluorescent probes, namely 3,4-diphenyl-2,5-di(2-thienyl)phenyl-trimethylsilane (DPTB-TMS) with a -SiMe₃ substituent and 3,4-diphenyl-2,5-di(2-thienyl)phenyl (DPTB) without the -SiMe₃ substituent, respectively. Both of the two compounds exhibit aggregation-enhanced emission (AEE) properties in tetrahydrofuran/water mixtures due to restricted intramolecular rotation of the peripheral groups, which make the two compounds good candidates for the detection of Fe³⁺ ions in aqueous-based solutions. The fluorescence intensity of the two compounds decreases immediately and obviously upon addition of a trace amount of Fe³⁺, and decreases continuously as the amount of Fe³⁺ increases. The fluorescence was quenched to 92% of its initial intensity when the amount of Fe³⁺ ions reached 6μmol for DPTB-TMS and to 80% for DPTB in the systems, indicating that the compound with the -SiMe₃ group is a more effective probe. The detection limit was found to be 1.17μM (65ppb). The detection mechanism is proposed to be static quenching. DPTB-TMS is highly efficient for the detection of ferric ions even in the presence of other metal ions. In addition, the method is also successfully applied to the detection of ferric ions in water, blood serum, or solid films. This indicates that these polybenzene compounds can be applied as low-cost, high selectivity, and high efficiency Fe³⁺ probes in water or in clinical applications.

Performance of a novel fluorogenic chimeric analog for the detection of third-generation cephalosporin resistant bacteria

Resistance to third generation cephalosporins is widely disseminated in Enterobacteriaceae mainly due to extended-spectrum-β-lactamases, plasmid AmpC β-lactamases, and hyperproduction of chromosomal AmpC β-lactamases. Here we evaluated the performance of a novel fluorogenic probe rapid test and compared the results with the phenol red assay using a total of 77 characterized organisms (44 extended-spectrum-β-lactamases, 33 chromosomal or plasmid AmpC β-lactamases) and 46 susceptible organisms. The fluorescent assay showed higher sensitivity than the phenol red assay in cefotaximase type extended-spectrum-β-lactamases, non- cefotaximase type extended-spectrum-β-lactamases, chromosomal AmpC β-lactamases, and plasmid AmpC β-lactamases (96.7% vs. 90.0%, p=0.157; 71.4% vs. 7.1%, p=0.003; 100.0% vs. 64.7%, p<0.001; 100.0% vs. 6.3%, p<0.001). The fluorescent assay had a positive correlation with the exponents of cefotaxime and ceftazidime minimum inhibitory concentrations (p<0.001 for both). The new fluorescent assay will be very useful for the rapid detection of resistance to third generation cephalosporins that originates from various β-lactamases.

The Use of Real-Time Reverse Transcription-PCR for Assessing Estrogen Receptor and Estrogen-Responsive Gene Expression

Real-time reverse transcription-polymerase chain reaction (RT-PCR), also known as quantitative RT-PCR (qRT-PCR), is a powerful tool for assessing gene transcription levels. The technique is especially useful for measuring estrogen receptor transcript levels as well as gene expression changes in response to estrogen stimulation as it is quick, accurate, robust, and allows the measurement of gene expression in a variety of tissues and cells. This chapter describes the protocols used for the real-time RT-PCR assay using hydrolysis (TaqMan-type) probes.

Development of surface immobilized 3-azidocoumarin-based fluorogenic probe via strain promoted click chemistry

A new class of imaging probe, a fluorogenic version of 1, 3-dipolar cycloaddition of azides and alkynes has been developed. 3-azidocoumarin scaffolds were selectively immobilized on the DBCO modified bead surface via SPAAC and provide direct and strong fluorescence in fluorescence microscopy. This developed click-on beads could be applied to label various biomolecules, such as nucleic acids, proteins and other molecules. To this end, 5'(7-hydroxy 3-azido coumarin) labelled DNA primer also displayed strong fluorescence upon successful immobilization on the bead surface.

N-(3-Imidazolyl)propyl dansylamide as a selective Hg(2+) sensor in aqueous media through electron transfer

N-Imidazolylpropyl dansylamide 1 was synthesized for the sensing of metal ions and found to be selective and sensitive toward Hg(2+) ions in a PBS-EtOH (1:4, pH=7.4) solution. The sensing ability of probe 1 was examined by UV-Vis, fluorescence, and (1)H NMR spectroscopy. The sensing of Hg(2+) exhibited a quenching of emission band at λmax=515 nm of probe 1, which was associated with quenching of green fluorescence emission under 365 nm illumination. Probe 1 showed a good association constant with Hg(2+) (Ka=6.48×10(4) M(-1)) with a stoichiometry of 1:1 in PBS-EtOH (1:4, pH=7.4) having the lowest detection limit of 1 μM for Hg(2+); on the other hand, probe 2, which has no imidazole moiety, was not able to detect any metal ion. In the case of probe 1, electrons on the imidazole nitrogen are available for electron transfer (ET), which was responsible for its green emission band that was quenched on addition of Hg(2+); this clearly indicates that these electrons were used for the formation of a coordinate bond with Hg(2+) and that ET was switched off.

Marine natural products as inhibitors of cystathionine beta-synthase activity

A library consisting of characterized marine natural products as well as synthetic derivatives was screened for compounds capable of inhibiting the production of hydrogen sulfide (H2S) by cystathionine beta-synthase (CBS). Eight hits were validated and shown to inhibit CBS activity with IC50 values ranging from 83 to 187μM. The majority of hits came from a series of synthetic polyandrocarpamine derivatives. In addition, a modified fluorogenic probe for H2S detection with improved solubility in aqueous solutions is reported.