Accelerated Activity-Based Sensing by Fluorogenic Reporter Engineering Enables to Rapidly Determine Unstable Analyte.

Accurate detection of labile analytes through activity based fluorogenic sensing is meaningful but remains a challenge because of nonrapid reaction kinetic. Herein, we present a signaling reporter engineering strategy to accelerate azoreduction reaction by positively charged fluorophore promoted unstable anion recognition for rapidly sensing sodium dithionite (Na2S2O4), a kind of widespread used but harmful inorganic reducing agent. Its quick decomposition often impedes application reliability of traditional fluorogenic probes in real samples because of their slow responses. In this work, four azo-based probes with different charged fluorophores (positive, zwitterionic, neutral, and negative) were synthesized and compared. Among of them, with sequestration effect of positively charged anthocyanin fluorophore for dithionite anion via electrostatic attraction, the cationic probe Azo-Pos displayed ultrafast fluorogenic response (∼2 s) with the fastest response kinetic (kpos' = 0.373 s-1) that is better than other charged ones (kzwi' = 0.031 s-1, kneu' = 0.013 s-1, kneg' = 0.003 s-1). Azo-Pos was demonstrated to be capable to directly detect labile Na2S2O4 in food samples and visualize the presence of Na2S2O4 in living systems in a timely fashion. This new probe has potential as a robust tool to fluorescently monitor excessive food additives and biological invasion of harmful Na2S2O4. Moreover, our proposed accelerating strategy would be versatile to develop more activity-based sensing probes for quickly detecting other unstable analytes of interest.

A Limitation of Using Dithionite Quenching to Determine the Topology of Membrane-inserted Proteins.

Determining the topology of membrane-inserted proteins and peptides often relies upon indirect fluorescent measurements. One such technique uses NBD, an environmentally sensitive fluorophore that can be covalently linked to proteins. Relative to a hydrophilic environment, NBD in a hydrophobic environment shows an increase in emission intensity and a shift to shorter wavelengths. To gain further insight, NBD fluorescence can be chemically quenched using dithionite. As dithionite is an anion, it is only expected to penetrate the outer leaflet interfacial region and should be excluded from the hydrocarbon core, the inner leaflet, and the lumen of LUV. This assumption holds at neutral pH, where a large number of NBD/dithionite experiments are carried out. Here, we report control experiments in which LUV were directly labeled with NBD-PE to assess dithionite quenching in acidic conditions. Results showed that at acidic pH, dithionite moved more freely across the bilayer to quench the inner leaflet. For the buffer conditions used, dithionite exhibited a sharp change in behavior between pH 5.5 and 6.0. Therefore, in acidic conditions, dithionite could not differentiate in which leaflet the NBD resided.

The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism.

[FeFe] hydrogenases are highly active enzymes for interconverting protons and electrons with hydrogen (H2). Their active site H-cluster is formed of a canonical [4Fe-4S] cluster ([4Fe-4S]H) covalently attached to a unique [2Fe] subcluster ([2Fe]H), where both sites are redox active. Heterolytic splitting and formation of H2 takes place at [2Fe]H, while [4Fe-4S]H stores electrons. The detailed catalytic mechanism of these enzymes is under intense investigation, with two dominant models existing in the literature. In one model, an alternative form of the active oxidized state Hox, named HoxH, which forms at low pH in the presence of the nonphysiological reductant sodium dithionite (NaDT), is believed to play a crucial role. HoxH was previously suggested to have a protonated [4Fe-4S]H. Here, we show that HoxH forms by simple addition of sodium sulfite (Na2SO3, the dominant oxidation product of NaDT) at low pH. The low pH requirement indicates that sulfur dioxide (SO2) is the species involved. Spectroscopy supports binding at or near [4Fe-4S]H, causing its redox potential to increase by ∼60 mV. This potential shift detunes the redox potentials of the subclusters of the H-cluster, lowering activity, as shown in protein film electrochemistry (PFE). Together, these results indicate that HoxH and its one-electron reduced counterpart Hred'H are artifacts of using a nonphysiological reductant, and not crucial catalytic intermediates. We propose renaming these states as the "dithionite (DT) inhibited" states Hox-DTi and Hred-DTi. The broader potential implications of using a nonphysiological reductant in spectroscopic and mechanistic studies of enzymes are highlighted.

Synthesis of Na2S2O4 mediated cleavable affinity tag for labeling of O-GlcNAc modified proteins via azide-alkyne cycloaddition.

A facile and convergent procedure for the synthesis of azobenzene-based probe was reported, which could selectively release interested proteins conducted with sodium dithionite. Besides, the cleavage efficiency is closely associated with the structural features, in which an ortho-hydroxyl substituent is necessary for reactivity. In addition, the azobenzene tag applied in the Ac4GlcNAz-labled proteins demonstrated high efficiency and selectivity in comparison with Biotin-PEG4-Alkyne, which provides a useful platform for enrichment of any desired bioorthogonal proteomics.

Oxygenation state of hemoglobin defines dynamics of water molecules in its vicinity.

This study focuses on assessing the possible impact of changes in hemoglobin (Hb) oxygenation on the state of water in its hydration shell as it contributes to red blood cell deformability. Microwave Dielectric Spectroscopy (MDS) was used to monitor the changes in interactions between water molecules and Hb, the number of water molecules in the protein hydration shell, and the dynamics of pre-protein water in response to the transition of Hb from the tense (T) to the relaxed (R) state, and vice versa. Measurements were performed for Hb solutions of different concentrations (5 g/dl-30 g/dl) in phosphate-buffered saline buffer. Cole-Cole parameters of the main water relaxation peak in terms of interactions of water molecules (dipole-dipole/ionic dipole) during the oxygenation-deoxygenation cycle were used to analyze the obtained data. The water mobility-represented by α as a function of ln τ-differed dramatically between the R (oxygenated) state and the T (deoxygenated) state of Hb at physiologically relevant concentrations (30 g/dl-35 g/dl or 4.5 mM-5.5 mM). At these concentrations, oxygenated hemoglobin was characterized by substantially lower mobility of water in the hydration shell, measured as an increase in relaxation time, compared to deoxyhemoglobin. This change indicated an increase in red blood cell cytosolic viscosity when cells were oxygenated and a decrease in viscosity upon deoxygenation. Information provided by MDS on the intraerythrocytic water state of intact red blood cells reflects its interaction with all of the cytosolic components, making these measurements powerful predictors of the changes in the rheological properties of red blood cells, regardless of the cause.

The conversion of azo-quenchers to fluorophores.

In this short note we describe the conversion of the widely used fluorescence quenching azo-dyes DABCYL and HABA to fluorophores. The dyes were conjugated to the proteins RNase and human serum albumin (HSA) and subsequently reduced using sodium dithionite (Na2S2O4), thus forming amine-containing fluorophores. Since this chemical reaction can be applied to any azo-containing quencher compound, a great variety of substances can be readily obtained synthetically. This approach provides a promising tool in the use of fluorescence-based investigations of biomolecular interactions.

Spectroscopic Characterisation of the Naphthalene Dioxygenase from Rhodococcus sp. Strain NCIMB12038.

Polycyclic aromatic hydrocarbons (PAHs), such as naphthalene, are potential health risks due to their carcinogenic and mutagenic effects. Bacteria from the genus Rhodococcus are able to metabolise a wide variety of pollutants such as alkanes, aromatic compounds and halogenated hydrocarbons. A naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038 has been characterised for the first time, using electron paramagnetic resonance (EPR) spectroscopy and UV-Vis spectrophotometry. In the native state, the EPR spectrum of naphthalene 1,2-dioxygenase (NDO) is formed of the mononuclear high spin Fe(III) state contribution and the oxidised Rieske cluster is not visible as EPR-silent. In the presence of the reducing agent dithionite a signal derived from the reduction of the [2Fe-2S] unit is visible. The oxidation of the reduced NDO in the presence of O2-saturated naphthalene increased the intensity of the mononuclear contribution. A study of the "peroxide shunt", an alternative mechanism for the oxidation of substrate in the presence of H2O2, showed catalysis via the oxidation of mononuclear centre while the Rieske-type cluster is not involved in the process. Therefore, the ability of these enzymes to degrade recalcitrant aromatic compounds makes them suitable for bioremediative applications and synthetic purposes.

Functional Magnetic Mesoporous Silica Microparticles Capped with an Azo-Derivative: A Promising Colon Drug Delivery Device.

Magnetic micro-sized mesoporous silica particles were used for the preparation of a gated material able to release an entrapped cargo in the presence of an azo-reducing agent and, to some extent, at acidic pH. The magnetic mesoporous microparticles were loaded with safranin O and the external surface was functionalized with an azo derivative 1 (bearing a carbamate linkage) yielding solid S1. Aqueous suspensions of S1 at pH 7.4 showed negligible safranin O release due to the presence of the bulky azo derivative attached onto the external surface of the inorganic scaffold. However, in the presence of sodium dithionite (azoreductive agent), a remarkable safranin O delivery was observed. At acidic pH, a certain safranin O release from S1 was also found. The pH-triggered safranin O delivery was ascribed to the acid-induced hydrolysis of the carbamate moiety that linked the bulky azo derivatives onto the mesoporous inorganic magnetic support. The controlled release behavior of S1 was also tested using a model that simulated the gastro intestinal tract.

Removal of arsenite by reductive precipitation in dithionite solution activated by UV light.

This study investigates the removal of arsenite (As(III)) from water using dithionite activated by UV light. This work evaluated the removal kinetics of As(III) under UV light irradiation as affected by dithionite dose and light intensity, and characterized the nature of the precipitated solids using XPS and SEM-EDS. Photolysis of dithionite was observed by measuring dithionite concentration using UV absorbance at 315nm. This study also investigated the effect of UV light path length on soluble As concentrations to understand resolubilization mechanisms. Total soluble As concentrations were observed to decrease with reaction time due to reduction of arsenite to form solids having a yellow-orange color. The removal mechanism was found to be reductive precipitation that formed solids of elemental arsenic or arsenic sulfide. However, these solids were observed to resolubilize at later times after dithionite had been consumed. Resolubilization of As was prevented and additional As removal was obtained by frequent dosing of dithionite throughout the experiment. As(III) removal is attributed to photolysis of dithionite by UV light and production of reactive radicals that reduce As(III) and convert it to solid forms.

The interaction of sorafenib and regorafenib with membranes is modulated by their lipid composition.

Sorafenib and regorafenib are small-molecule kinase inhibitors approved for the treatment of locally recurrent or metastatic, progressive, differentiated thyroid carcinoma, renal cell carcinoma, and hepatocellular carcinoma (sorafenib) and of colorectal cancer (regorafenib). As of now, the mechanisms, which are responsible for their antitumor activities, are not completely understood. Given the lipophilic nature of the molecules, it can be hypothesized that the pharmacological impact is mediated by the interaction with cellular membranes as it is true for many pharmacologically active molecules. However, an interaction of sorafenib or regorafenib with lipid membranes has not yet been investigated in detail. Here, we characterized the interaction of both drugs with lipid membranes by applying a variety of biophysical approaches including nuclear magnetic resonance, electron spin resonance, and fluorescence spectroscopy. We found that sorafenib and regorafenib bind to lipid membranes by inserting into the lipid-water interface of the bilayer. This membrane embedding causes a disturbance of bilayer structure leading to an increased permeability of the membrane for polar molecules. One approach shows that the extent of the effects depends on the membrane lipid composition underlining a particular role of phosphatidylcholine and cholesterol. Our data for the first time characterize the impact of sorafenib and regorafenib on the lipid membrane structure and dynamics, which may contribute to a better understanding of their effectiveness in the treatment of malignancies as well as of their side effects.

DNA-Compatible Nitro Reduction and Synthesis of Benzimidazoles.

DNA-encoded chemical libraries have emerged as a cost-effective alternative to high-throughput screening (HTS) for hit identification in drug discovery. A key factor for productive DNA-encoded libraries is the chemical diversity of the small molecule moiety attached to an encoding DNA oligomer. The library structure diversity is often limited to DNA-compatible chemical reactions in aqueous media. Herein, we describe a facile process for reducing aryl nitro groups to aryl amines. The new protocol offers simple operation and circumvents the pyrophoric potential of the conventional method (Raney nickel). The reaction is performed in aqueous solution and does not compromise DNA structural integrity. The utility of this method is demonstrated by the versatile synthesis of benzimidazoles on DNA.

Remediation of hexavalent chromium contamination in chromite ore processing residue by sodium dithionite and sodium phosphate addition and its mechanism.

Large amounts of chromite ore processing residue (COPR) wastes have been deposited in many countries worldwide, generating significant contamination issues from the highly mobile and toxic hexavalent chromium species (Cr(VI)). In this study, sodium dithionite (Na2S2O4) was used to reduce Cr(VI) to Cr(III) in COPR containing high available Fe, and then sodium phosphate (Na3PO4) was utilized to further immobilize Cr(III), via a two-step procedure (TSP). Remediation and immobilization processes and mechanisms were systematically investigated using batch experiments, sequential extraction studies, X-ray diffraction (XRD) and X-ray Photoelectron Spectroscopy (XPS). Results showed that Na2S2O4 effectively reduced Cr(VI) to Cr(III), catalyzed by Fe(III). The subsequent addition of Na3PO4 further immobilized Cr(III) by the formation of crystalline CrPO4·6H2O. However, addition of Na3PO4 simultaneously with Na2S2O4 (via a one-step procedure, OSP) impeded Cr(VI) reduction due to the competitive reaction of Na3PO4 and Na2S2O4 with Fe(III). Thus, the remediation efficiency of the TSP was much higher than the corresponding OSP. Using an optimal dosage in the two-step procedure (Na2S2O4 at a dosage of 12× the stoichiometric requirement for 15 days, and then Na3PO4 in a molar ratio (i.e. Na3PO4: initial Cr(VI)) of 4:1 for another 15 days), the total dissolved Cr in the leachate determined via Toxicity Characteristic Leaching Procedure (TCLP Cr) testing of our samples was reduced to 3.8 mg/L (from an initial TCLP Cr of 112.2 mg/L, i.e. at >96% efficiency).

Non-photochemical Fluorescence Quenching in Photosystem II Antenna Complexes by the Reaction Center Cation Radical.

In direct experiments, rate constants of photochemical (kP) and non-photochemical (kP(+)) fluorescence quenching were determined in membrane fragments of photosystem II (PSII), in oxygen-evolving PSII core particles, as well as in core particles deprived of the oxygen-evolving complex. For this purpose, a new approach to the pulse fluorometry method was implemented. In the "dark" reaction center (RC) state, antenna fluorescence decay kinetics were measured under low-intensity excitation (532 nm, pulse repetition rate 1 Hz), and the emission was registered by a streak camera. To create a "closed" [P680(+)QA(-)] RC state, a high-intensity pre-excitation pulse (pump pulse, 532 nm) of the sample was used. The time advance of the pump pulse against the measuring pulse was 8 ns. In this experimental configuration, under the pump pulse, the [P680(+)QA(-)] state was formed in RC, whereupon antenna fluorescence kinetics was measured using a weak testing picosecond pulsed excitation light applied to the sample 8 ns after the pump pulse. The data were fitted by a two-exponential approximation. Efficiency of antenna fluorescence quenching by the photoactive RC pigment in its oxidized (P680(+)) state was found to be ~1.5 times higher than that of the neutral (P680) RC state. To verify the data obtained with a streak camera, control measurements of PSII complex fluorescence decay kinetics by the single-photon counting technique were carried out. The results support the conclusions drawn from the measurements registered with the streak camera. In this case, the fitting of fluorescence kinetics was performed in three-exponential approximation, using the value of τ1 obtained by analyzing data registered by the streak camera. An additional third component obtained by modeling the data of single photon counting describes the P680(+)Pheo(-) charge recombination. Thus, for the first time the ratio of kP(+)/kP = 1.5 was determined in a direct experiment. The mechanisms of higher efficiency for non-photochemical antenna fluorescence quenching by RC cation radical in comparison to that of photochemical quenching are discussed.

Redox tuning of the catalytic activity of soluble fumarate reductases from Shewanella.

Many enzymes involved in bioenergetic processes contain chains of redox centers that link the protein surface, where interaction with electron donors or acceptors occurs, to a secluded catalytic site. In numerous cases these redox centers can transfer only single electrons even when they are associated to catalytic sites that perform two-electron chemistry. These chains provide no obvious contribution to enhance chemiosmotic energy conservation, and often have more redox centers than those necessary to hold sufficient electrons to sustain one catalytic turnover of the enzyme. To investigate the role of such a redox chain we analyzed the transient kinetics of fumarate reduction by two flavocytochromes c3 of Shewanella species while these enzymes were being reduced by sodium dithionite. These soluble monomeric proteins contain a chain of four hemes that interact with a flavin adenine dinucleotide (FAD) catalytic center that performs the obligatory two electron-two proton reduction of fumarate to succinate. Our results enabled us to parse the kinetic contribution of each heme towards electron uptake and conduction to the catalytic center, and to determine that the rate of fumarate reduction is modulated by the redox stage of the enzyme, which is defined by the number of reduced centers. In both enzymes the catalytically most competent redox stages are those least prevalent in a quasi-stationary condition of turnover. Furthermore, the electron distribution among the redox centers during turnover suggested how these enzymes can play a role in the switch between respiration of solid and soluble terminal electron acceptors in the anaerobic bioenergetic metabolism of Shewanella.

Kinetic and equilibrium studies of bile salt-liposome interactions.

Research has suggested that exposure to sub-micellar concentrations of bile salts (BS) increases the permeability of lipid bilayers in a time-dependent manner. In this study, incubation of soy phosphatidylcholine small unilamellar vesicles (liposomes) with sub-micellar concentrations of cholate (C), deoxycholate (DC), 12-monoketocholate (MKC) or taurocholate (TC) in pH 7.2 buffer increased membrane fluidity and negative zeta potential in the order of increasing BS liposome-pH 7.2 buffer distribution coefficients (MKC < C ≈ TC < DC). In liposomes labeled with the dithionite-sensitive fluorescent lipid N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)phosphatidylethanolamine (NBD-PE) in both leaflets and equilibrated with sub-micellar concentrations of BS, fluorescence decline during continuous exposure to dithionite was biphasic involving a rapid initial phase followed by a slower second phase. Membrane permeability to dithionite as measured by the rate of the second phase increased in the order control < MKC < TC ∼ C < DC. In liposomes labeled with NBD-PE in the inner leaflet only and incubated with the same concentrations of C, DC and MKC, membrane permeability to dithionite initially increased very rapidly in the order MKC < C < DC before impermeability to dithionite was restored after which fluorescence decline was consistent with NBD-PE flip-flop. For liposomes incubated with TC, membrane permeability to dithionite was only slightly increased and the decline in fluorescence was mainly the result of NBD-PE flip-flop. These results provide evidence that BS interact with lipid bilayers in a time-dependent manner that is different for conjugated and unconjugated BS. MKC appears to cause least disturbance to liposomal membranes but, when the actual MKC concentration in liposomes is taken into account, MKC is actually the most disruptive.

Recovery of Cu(II) by chemical reduction using sodium dithionite: effect of pH and ligands.

Wastewaters containing Cu(II) and ligands are ubiquitous in various industrial sectors, and efficacy of copper removal processes, especially precipitation, is greatly compromised by ligands. Chemical reduction, being commonly employed for production of metal nanoparticles, is also effective for metal removal. Adjustment of pH and addition of ligands are important to control the particle size in metallic nanoparticle production. Exploiting the fact that ligands and metals coexist in many wastewaters, chemical reduction was employed to treat ligand-containing wastewater in this study. The experimental result shows that depending on pH, type of ligands, and copper:ligand molar ratio, copper could be removed by either the reduction or precipitation mechanism. Almost complete copper removal could be achieved by the reduction mechanism under optimal condition for solutions containing either EDTA (ethylenediaminetetraacetic acid) or citrate ligands. For solutions containing ammonia, depending on pH and Cu:ammonia molar ratio, copper was removed by both precipitation and reduction mechanisms. At pH of 9.0, formation of nano-sized particles, which readily pass through a 0.45 µm filter used for sample pretreatment before residual copper analysis, results in the lowest copper removal efficiency. Both cuprous oxide and metallic copper are identified in the solids produced, and the possible explanations are provided.

Integration of polyelectrolyte enhanced ultrafiltration and chemical reduction for metal-containing wastewater treatment and metal recovery.

Chemical reduction was firstly employed to treat synthetic wastewaters of various compositions prepared to simulate the retentate stream of polyelectrolyte enhanced ultrafiltration (PEUF). With fixed Cu:polyethylenimine (PEI) monomer:dithionite molar ratio, increasing copper concentration increases copper removal efficiency. Under fixed Cu:dithionite molar ratio and fixed Cu concentration, increasing PEI monomer:copper molar ratio decreases copper removal efficiency. The formation of nano-sized copper particles, which readily pass through 0.45 µm filter used for sample pretreatment before residual copper analysis, might be the reason behind the decreasing copper removal efficiency observed. Particle size analysis shows that the size of copper particles, which are formed through reduction reaction, increases with decreasing pH value and increasing reaction time. As ultrafiltration is capable of removing these nano-sized particles, integration of chemical reduction and PEUF is proposed to simultaneously achieve regeneration of polyelectrolyte and recovery of copper in one process. Results show that the proposed process could achieve almost complete copper removal without being affected by reaction pH.

Characterization of colloidal Fe from soils using field-flow fractionation and Fe K-edge X-ray absorption spectroscopy.

Colloids may facilitate the transport of trace elements and nutrients like phosphate in soil. In this study, we characterized soil colloids (<0.45 µm), extracted from four agricultural soils by Na-bicarbonate and Na-pyrophosphate, by two complementary analytical techniques; asymmetric flow field-flow fractionation (AF4) and X-ray absorption spectroscopy (XAS). The combined results from AF4 and XAS show that colloidal Fe is present as (i) free Fe-(hydr)oxide nanoparticles, (ii) Fe-(hydr)oxides associated with clay minerals, and (iii) Fe in clay minerals. Free Fe-(hydr)oxide nanoparticles, which can be as small as 2-5 nm, are extracted with Na-pyrophosphate but not with Na-bicarbonate, except for one soil. In contrast, Fe-(hydr)oxides associated with clay minerals are dispersed by both extractants. XAS results show that the speciation of Fe in the colloidal fractions closely resembles the speciation of Fe in the bulk soil, indicating that dispersion of colloidal Fe from the studied soils was rather unselective. In one Fe-rich soil, colloidal Fe was dominantly dispersed in the form of free Fe-(hydr)oxide nanoparticles. In the other three soils, dispersed Fe-(hydr)oxides were dominantly associated with clay minerals, suggesting that their dispersion as free nanoparticles was inhibited by strong attachment. However, in these soils, Fe-(hydr)oxides can be dispersed as oxide-clay associations and may as such facilitate the transport of trace elements.

Bioorthogonal cleavage and exchange of major histocompatibility complex ligands by employing azobenzene-containing peptides.

Bioorthogonal cleavable linkers are attractive building blocks for compounds that can be manipulated to study biological and cellular processes. Sodium dithionite sensitive azobenzene-containing (Abc) peptides were applied for the temporary stabilization of recombinant MHC complexes, which can then be employed to generate libraries of MHC tetramers after exchange with a novel epitope. This technology represents an important tool for high-throughput studies of disease-specific T cell responses.

Fast detection of sodium dithionite in sugar using a xanthylium-based fluorescent probe.

Dithionite remained in the foodstuff may pose a great threat to the health of consumers. Three xanthylium-based probes were synthesized and their responses to dithionite were explored. Probe SH-1 could respond to dithionite selectively in PBS buffer (15% DMSO, 10 mM, pH = 7.4). Upon the addition of dithionite, the fluorescent emission of SH-1 at 684 nm dropped quickly (within 10 s) and the fluorescence decline was proportional to the concentration of dithionite (0-7.0 µM). The limit of detection was determined to be 0.139 µM. Then, the sensing mechanism was tentatively presented and the structure of resulted adduct (SH-1-SO3-) which was the reaction product of SH-1 and dithionite via a Micheal addition reaction followed by an oxidation reaction was verified. Moreover, white granulated sugar was subjected to the standard spike experiments and the results demonstrated a great potential of SH-1 for the quantitative monitoring of dithionite in foodstuffs.