Optochemical Sensor for Ammonia Based on a Lipophilized pH Indicator in a Hydrophobic Matrix

Abstract

An optical sensor for the determination of ammonia in water based on ion pairing has been investigated. A pH-sensitive dye is immobilized as an ion pair in a silicone matrix. The colour of the dye changes from yellow to blue depending on the concentration of ammonia in the sample solution. This change is reversible. The concentration of ammonia can be determined by measuring the transmittance at a given wavelength.

All measurements were performed with a dual-beam optical meter. The measurement range was from 5.9 × 10^?7 to 1 × 10^?3 M (0.01 to 17 mg/l) in 0.1 M phosphate buffer of pH 8. The detection limit was 10 μg/l. The response times at a flow rate of 2.5 ml/min were 4 min for t₉₀ and 10 min for t₁₀₀ at a change from 41.9 to 82.5 μM ammonia and 12 min for t₉₀ and 48 min for t₁₀₀ at a change from 160 to 0 μM ammonia. The operational lifetime of the ammonia sensor was limited to a period of a few days only. A continuous decrease in baseline signal and relative signal change was observed over the whole measurement. The storage stability was more than 10 months (dry). With respect to possible application of the ammonia sensor to environmental analysis, the influence of pH, typical interferences, such as amines and various detergents on the sensor response was investigated. No interference due to pH was observed in the range from pH 5 to pH 9. With methyl- and ethylamine the response was not completely reversible. The sensor was affected by cationic detergents, but not by anionic or neutral detergents.     

Optochemical sensing of hydrogen chloride gas using meso-tetramesitylporphyrin deposited glass plate

Meso-tetramesitylporphyrin (MTMP) deposited glass plate (solid state sensor) was used to sense hydrogen chloride (HCl) gas based on optochemical method. Exposure of the solid state sensor to HCl vapor results in the formation of protonated meso-tetramesitylporphyrin (PMTMP). UV-vis and fluorescence spectral techniques were used to study the protonation of MTMP in dichloromethane-methanol mixture. The optical spectra of MTMP show an intense Soret band at 418 nm with a 14 nm red shift upon protonation by HCl. Ab-initio calculations were carried out to visualize the effect of protonation on planarity and stability of the porphyrin ring. The solid state sensor was characterized by UV-vis spectral technique. The sensor exhibits characteristic Soret and Q bands for the deposited MTMP with slight red shift when compared to MTMP in dichloromethane. The concentration of gaseous HCl was monitored from the changes in the absorbance of Soret band of PMTMP at 452 nm. The detection limit of the solid state sensor towards gaseous HCl was found to be 0.03 ppm. The present solid state sensor was highly stable for several months.     

Optochemical sensing by immobilizing fluorophore-encapsulating liposomes in sol–gel thin films

The chemical stability of optochemical sensors depends largely on the physiochemical properties of the supportive matrix of the sensor and on the method used to immobilize sensing reagents to the supportive matrix of the sensor. Leaking of physically immobilized sensing reagents from the matrix support decreases the stability of the sensor and its overall usefulness. Covalent immobilization eliminates leakage of the sensing reagent from the support but may lead to alteration of spectral properties and loss of analyte response. This paper presents a new method for physical immobilization of polar fluorescence dyes in a sensing support. The method is based on the immobilization of fluorescent dye encapsulating liposomes in a sol–gel film of micrometer thickness. The encapsulation of the dye molecules in the liposomes effectively increases the molecular dimensions of the sensing reagent, thus preventing its leakage from the matrix support. This paper describes the analytical properties of a pH sensor fabricated by immobilizing carboxyfluorescein-encapsulating liposomes in a sol–gel thin film. The sensor shows excellent stability with respect to dye leaking which in turn leads to high reproducibility and sensitivity of about 0.01 pH units. The linear dynamic range of the sensor is between pH 6 and 7.5 and its response time is at the sub-seconds time scale.     

Optochemical sensor for determining ozone based on novel soluble indigo dyes immobilised in a highly permeable polymeric film

An optochemical ozone sensor is described that has been manufactured by immobilisation of novel soluble indigo derivatives in permeable transparent polymeric films of polydimethylsiloxane–polycarbonate copolymer. From a number of investigated indigo derivatives, 4,4,7,7-tetraalkoxyindigo 9 has been selected for optimal sensitivity and specificity of ozone detection. A linear calibration for ozone can be obtained in the range between 0.01 and 0.5 ppm. The limit of quantitation is 0.03 ppm, and the accuracy exceeds 8%. It takes about 134 s to measure the relatively low occupational exposure concentration of 0.1 ppm. A reduction of the sensor response time could be achieved through application of double-sided coated sensors instead of single-sided variants. The stability of the sensors and the effect of external parameters like relative humidity (RH), temperature and gas flow on the sensor response have been investigated. The sensor response is affected by varying the gas flow or temperature; however, humidity in the range between 0 and 90% RH does not affect sensor response. The indigo derivative 9 remained stable inside the polymeric film and no chemical reaction, crystallisation or leaching occurred during 10 months of observation. Proper choice of indicator dye and polymeric material and successful application of kinetic evaluation method for the exposure experiments determine the desired features of the sensor.     

Optochemical Control of Biological Processes in Cells and Animals

Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.     

In Situ Self-Assembly of Fluorogenic RNA Nanozipper Enables Real-Time Imaging of Single Viral mRNA Translation

Real-time visualization of individual viral mRNA translation activities in live cells is essential to obtain critical details of viral mRNA dynamics and to detect its transient responses to environmental stress. Fluorogenic RNA aptamers are powerful tools for real-time imaging of mRNA in live cells, but monitoring the translation activity of individual mRNAs remains a challenge due to their intrinsic photophysical properties. Here, we develop a genetically encoded turn-on 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI)-binding RNA nanozipper with superior brightness and high photostability by in situ self-assembly of multiple nanozippers along single mRNAs. The nanozipper enables real-time imaging of the mobility and dynamic translation of individual viral mRNAs in live cells, providing information on the spatial dynamics and translational elongation rate of viral mRNAs.     

An Optochemical Oxygen Scavenger Enabling Spatiotemporal Control of Hypoxia

We present an optochemical O₂ scavenging system that enables precise spatiotemporal control of the level of hypoxia in living cells simply by adjusting the light intensity in the illuminated region. The system employs rhodamine containing a selenium or tellurium atom as an optochemical oxygen scavenger that rapidly consumes O₂ by photochemical reaction with glutathione as a coreductant upon visible light irradiation (560–590 nm) and has a rapid response time, within a few minutes. The glutathione-consuming quantum yields of the system were calculated as about 5 %. The spatiotemporal O₂ consuming in cultured cells was visualized with a hypoxia-responsive fluorescence probe, MAR. Phosphorescence lifetime imaging was applied to confirmed that different light intensities could generate different levels of hypoxia. To illustrate the potential utility of this system for hypoxia research, we show that it can spatiotemporally control calcium ion (Ca²⁺) influx into HEK293T cells expressing the hypoxia-responsive Ca²⁺ channel TRPA1.     

Translation of genetic information on the ribosome

The information for protein structure that is contained in the base sequence of the nucleic acids is translated on the ribosome into the amino acid sequence. This translation can be divided into chain initiation, chain growth, and chain termination. Several specific protein factors and nucleic acids are involved in each section.—For chain initiation, start complexes are formed from the initiating amino acyl-tRNA, mRNA carrying the start signal, and the small and large subunits of a ribosome. GTP and the initiating factors are also involved in this process.—In chain elongation, one amino acid at a time is transferred, in a reaction cycle, from the linkage with tRNA into a linkage with the polypeptide chain. The amino acid to be incorporated is initially bound to the ribosome as amino acyl-tRNA, a process for which GTP and protein factors are necessary. The subsequent formation of a peptide linkage is catalyzed by the peptidyl transferase of the large ribosomal subunit. The peptidyl-tRNA with its newly added amino acid residue is then transferred from the amino acyl-tRNA acceptor site A to the peptidyl donor site P of the ribosome. This requires another protein factor and cleavage of GTP into GDP and phosphate.–Ghain termination begins as soon as one of the three terminator triplets UAA, UAG, or UGA in the mRNA reaches the ribosome. The mRNA is moving in relation to the ribosome from the 5′ end to the 3′ end. Release of the completed polypeptide chain from the ribosome is dependent on release factors. Before initiation of a new polypeptide chain, the ribosomes dissociate into their subunits.     

Photocatalysis in Chemical Biology: Extending the Scope of Optochemical Control and Towards New Frontiers in Semisynthetic Bioconjugates and Biocatalysis

Biomedical research has been empowered by tools that enable spatial and temporal control of biological systems. These have predominantly come from photocaged bioactive molecules (optochemical control; N. Ankenbruck, T. Courtney, Y. Naro, A. Deiters, Angew. Chem. Int. Ed. 2018 , 57, 2768–2798) and light-dependent proteins (optogenetic control; L. Fenno, O. Yizhar, K. Deisseroth, Annu. Rev. Neurosci. 2011 , 34, 389–412). Recent advances in photocatalysis offer the opportunity to amplify these strategies by providing new dimension of biorthogonality. Photocatalysis also empowers bioconjugation with unprecedented reactivities enabling new crosslinking chemistry or biomolecule functionalization, while merging photocatalysis with biocatalysis extends the scope of both of these powerful classes of transformation.     

Ribosome Subunit Stapling for Orthogonal Translation in E. coli

The creation of orthogonal large and small ribosomal subunits, which interact with each other but not with endogenous ribosomal subunits, would extend our capacity to create new functions in the ribosome by making the large subunit evolvable. To this end, we rationally designed a ribosomal RNA that covalently links the ribosome subunits via an RNA staple. The stapled ribosome is directed to an orthogonal mRNA, allowing the introduction of mutations into the large subunit that reduce orthogonal translation, but have minimal effects on cell growth. Our approach provides a promising route towards orthogonal subunit association, which may enable the evolution of key functional centers in the large subunit, including the peptidyl‐transferase center, for unnatural polymer synthesis in cells.     

Bidirectional Regulation of mRNA Translation in Mammalian Cells by Using PUF Domains

The regulation of gene expression is crucial in diverse areas of biological science, engineering, and medicine. A genetically encoded system based on the RNA binding domain of the Pumilio and FBF (PUF) proteins was developed for the bidirectional regulation (i.e., either upregulation or downregulation) of the translation of a target mRNA. PUF domains serve as designable scaffolds for the recognition of specific RNA elements and the specificity can be easily altered to target any 8‐nucleotide RNA sequence. The expression of a reporter could be varied by over 17‐fold when using PUF‐based activators and repressors. The specificity of the method was established by using wild‐type and mutant PUF domains. Furthermore, this method could be used to activate the translation of target mRNA downstream of PUF binding sites in a light‐dependent manner. Such specific bidirectional control of mRNA translation could be particularly useful in the fields of synthetic biology, developmental biology, and metabolic engineering.     

Synthetic Biology Tools for Bioprospecting of Natural Products in Eukaryotes

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Rational hydrothermal synthesis of graphene quantum dots with optimized luminescent properties for sensing applications

Hydrothermal synthesis using graphene oxide (GO) as a precursor has been used to produce luminescent graphene quantum dots (GQDs). However, such a method usually requires many reagents and multistep pretreatments, while can give rise to GQDs with low quantum yield (QY). Here, we investigated the concentration, the temperature of synthesis, and the pH of the GO solution used in the hydrothermal method through factorial design experiments aiming to optimize the QY of GQDs to reach a better control of their luminescent properties. The best synthesis condition (2 mg/mL, 175 °C, and pH = 8.0) yielded GQDs with a relatively high QY (8.9%) without the need of using laborious steps or dopants. GQDs synthesized under different conditions were characterized to understand the role of each synthesis parameter in the materials' structure and luminescence properties. It was found that the control of the synthesis parameters enables the tailoring of the amount of specific oxygen functionalities onto the surface of the GQDs. By changing the synthesis' conditions, it was possible to prioritize the production of GQDs with more hydroxyl or carboxyl groups, which influence their luminescent properties. The as-developed GQDs with tailored composition were used as luminescent probes to detect Fe³⁺. The lowest limit of detection (0.136 μM) was achieved using GQDs with higher amounts of carboxylic groups, while wider linear range was obtained by GQDs with superior QY. Thus, our findings contribute to rationally produce GQDs with tailored properties for varied applications by simply adjusting the synthesis conditions and suggest a pathway to understand the mechanism of detection of GQDs-based optical sensors.     

A hydrogel based fluorescent micro array used for the characterization of liquid analytes

A fluorimetric micro spot array using non-specific recognition function is described for the analysis of liquid samples. The array was composed of binary mixtures of various fluorescence dyes which were embedded in a hydrogel matrix. The interactions between the fluorescent dyes and their molecular surrounding inside the hydrogel, influence their fluorescence wave length and intensities. The array was used for the characterization of solvent mixtures. Developed fluorescence patterns of the complete array as well as the fluorescence intensity changes of single spots were analysed. It was proven, that specific analytical information can be gained using this non-specific recognition approach. The identification of some alcoholic beverages is described as an example of the application of this method when used for quality control purposes. Analogous to the appellation “electronic nose” and “electronic tongue” the described micro spot array acts as an “optochemical tongue”.     

离子液体表面活性剂在水溶液中的自组装及其调控研究进展

离子液体表面活性剂在化学合成、材料制备和环境污染控制等方面的应用与它们在水溶液中的自组装及其微观结构密切相关。因此,研究离子液体表面活性剂在水溶液中的自组装行为具有重要的意义。本文重点综述了阳离子的结构、阴离子的类型、外加电解质、有机添加剂、环境因素(温度、溶液pH值和光)等对离子液体表面活性剂在水中的自组装行为以及对组装体结构影响的研究进展,总结了这些因素对离子液体表面活性剂在水中自组装的调控规律,展望了该领域的发展方向及面临的挑战。