Optimization of Experimental Parameters to Explore Small‐Ligand/Aptamer Interactions through Use of 1H NMR Spectroscopy and Molecular Modeling

Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand‐binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design‐of‐experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L ‐tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg²⁺‐ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand‐observed NMR spectroscopic techniques and molecular mechanics.     

Saccharin as an Organocatalyst for Quinoxalines and Pyrido[2,3-b]pyrazines Syntheses

A room-temperature procedure using saccharin as catalyst has been described for the cyclocondensation of different 1,2-arylenediamines with various 1,2-dicarbonyl compounds, yielding either quinoxalines or pyrido[2,3-b]pyrazines. The reactions proceed in very short reaction times in methanol, and the target heterocycles are isolated in quantitative yields after addition of water, filtration, and drying. Substituted pyrido[2,3-b]pyrazines can also be reached regioselectively by reacting α-ketoaldehydes with 2,3-diaminopyridine.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Performance evaluation on a wide set of matrix-assisted laser desorption ionization matrices for the detection of oligosaccharides in a high-throughput mass spectrometric screening of carbohydrate depolymerizing enzymes

Compared to other analytical methods, matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) presents several unique advantages for the structural characterization of degradation products of carbohydrates. Our final goal is to implement this technique as a high-throughput platform, with the aim of exploring natural bio-diversity to discover new carbohydrate depolymerizing enzymes. In this approach, a variety of carbohydrates will be used as enzymes substrates and MALDI-MS will be employed to monitor the oligosaccharides produced. One drawback of MALDI, however, is that the choice of the matrix is largely dependent on the chemical properties of the analyte. In this context, our objective in the present work was to find the smallest set of MALDI matrices able to detect chemically heterogeneous oligosaccharides. This was done through the performance evaluation of more than 40 MALDI matrices preparations. Homogeneity of analyte-matrix deposits was considered as a critical feature, especially since the final objective is to fully automate the analyses. Evaluation of the matrices was done by means of a rigorous statistical approach. Amongst all tested compounds, our work proposes the use of the DHB/DMA ionic matrix as the most generic matrix, for rapid detection of a variety of polysaccharides including neutral, anionic, methylated, sulfated, and acetylated compounds. The selected matrices were then used to screen crude bacterial incubation media for the detection of enzymatic degradation products.     

Deprotonative metalation of chloro- and bromopyridines using amido-based bimetallic species and regioselectivity-computed CH acidity relationships

A series of chloro- and bromopyridines have been deprotometalated by using a range of 2,2,6,6-tetramethylpiperidino-based mixed lithium-metal combinations. Whereas lithium-zinc and lithium-cadmium bases afforded different mono- and diiodides after subsequent interception with iodine, complete regioselectivities were observed with the corresponding lithium-copper combination, as demonstrated by subsequent trapping with benzoyl chlorides. The obtained selectivities have been discussed in light of the CH acidities of the substrates, determined both in the gas phase and as a solution in THF by using the DFT B3LYP method.     

On-chip multi-electrochemical sensor array platform for simultaneous screening of nitric oxide and peroxynitrite

In this work we report on the design, microfabrication and analytical performances of a new electrochemical sensor array (ESA) which allows for the first time the simultaneous amperometric detection of nitric oxide (NO) and peroxynitrite (ONOO(-)), two biologically relevant molecules. The on-chip device includes individually addressable sets of gold ultramicroelectrodes (UMEs) of 50 μm diameter, Ag/AgCl reference electrode and gold counter electrode. The electrodes are separated into two groups; each has one reference electrode, one counter electrode and 110 UMEs specifically tailored to detect a specific analyte. The ESA is incorporated on a custom interface with a cell culture well and spring contact pins that can be easily interconnected to an external multichannel potentiostat. Each UME of the network dedicated to the detection of NO is electrochemically modified by electrodepositing thin layers of poly(eugenol) and poly(phenol). The detection of NO is performed amperometrically at 0.8 V vs. Ag/AgCl in phosphate buffer solution (PBS, pH = 7.4) and other buffers adapted to biological cell culture, using a NO-donor. The network of UMEs dedicated to the detection of ONOO(-) is used without further chemical modification of the surface and the uncoated gold electrodes operate at -0.1 V vs. Ag/AgCl to detect the reduction of ONOOH in PBS. The selectivity issue of both sensors against major biologically relevant interfering analytes is examined. Simultaneous detection of NO and ONOO(-) in PBS is also achieved.     

Purification and structure elucidation of three naturally bioactive molecules from the new terrestrial Streptomyces sp. TN17 strain

Thirty litres of fermentation broth was extracted from the newly isolated Streptomyces sp. strain TN17 and various separation and purification steps led to the isolation of three pure bioactive compounds (1-3). Compound 1: cyclo (L-Leu-L-Arg), a diketopiperazine 'DKP' derivative; 2: di-(2-ethylhexyl) phthalate, a phthalate derivative; and 3: cyclo 1-[2-(cyclopentanecarbonyl-3-phenyl-propionyl]-pyrrolidine-2-carboxylic acid (1-carbamoyl-propyl)-amide, a cyclic tetrapeptide derivative. The chemical structure of these three active compounds was established on the basis of spectroscopic studies (MS and NMR) and by comparison with data from the literature. According to our biological studies, the pure compounds (1-3) possess antibacterial and antifungal activities.     

Impedance spectroscopy and conductometric biosensing for probing catalase reaction with cyanide as ligand and inhibitor

In this work, a new biosensor was prepared through immobilization of bovine liver catalase in a photoreticulated poly (vinyl alcohol) membrane at the surface of a conductometric transducer. This biosensor was used to study the kinetics of catalase–H₂0₂ reaction and its inhibition by cyanide. Immobilized catalase exhibited a Michaelis–Menten behaviour at low H₂0₂ concentrations (< 100 mM) with apparent constant K_M^app = 84 ± 3 mM and maximal initial velocity V_M^app = 13.4 μS min^? 1. Inhibition by cyanide was found to be non-competitive and inhibition binding constant K_i was 13.9 ± 0.3 μM. The decrease of the biosensor response by increasing cyanide concentration was linear up to 50 μM, with a cyanide detection limit of 6 μM. In parallel, electrochemical characteristics of the catalase/PVA biomembrane and its interaction with cyanide were studied by cyclic voltammetry and impedance spectroscopy. Addition of the biomembrane onto the gold electrodes induced a significant increase of the interfacial polarization resistance R_P. On the contrary, cyanide binding resulted in a decrease of Rp proportional to KCN concentration in the 4 to 50 μM range. Inhibition coefficient I₅₀ calculated by this powerful label-free and substrate-free technique (24.3 μM) was in good agreement with that determined from the substrate-dependent conductometric biosensor (24.9 μM).     

Cell-based electrochemical biosensors for water quality assessment

During recent decades, extensive industrialisation and farming associated with improper waste management policies have led to the release of a wide range of toxic compounds into aquatic ecosystems, causing a rapid decrease of world freshwater resources and thus requiring urgent implementation of suitable legislation to define water remediation and protection strategies. In Europe, the Water Framework Directive aims to restore good qualitative and quantitative status to all water bodies by 2015. To achieve that, extensive monitoring programmes will be required, calling for rapid, reliable and cost-effective analytical methods for monitoring and toxicological impact assessment of water pollutants. In this context, whole cell biosensors appear as excellent alternatives to or techniques complementary to conventional chemical methods. Cells are easy to cultivate and manipulate, host many enzymes able to catalyse a wide range of biological reactions and can be coupled to various types of transducers. In addition, they are able to provide information about the bioavailability and the toxicity of the pollutants towards eukaryotic or prokaryotic cells. In this article, we present an overview of the use of whole cells, mainly bacteria, yeasts and algae, as sensing elements in electrochemical biosensors with respect to their practical applications in water quality monitoring, with particular emphasis on new trends and future perspectives. In contrast to optical detection, electrochemical transduction is not sensitive to light, can be used for analysis of turbid samples and does not require labelling. In some cases, it is also possible to achieve higher selectivities, even without cell modification, by operating at specific potentials where interferences are limited.     

A new bacterial biosensor for trichloroethylene detection based on a three-dimensional carbon nanotubes bioarchitecture

Trichloroethylene (TCE), a suspected human carcinogen, is one of the most common volatile groundwater contaminants. Many different methodologies have already been developed for the determination of TCE and its degradation products in water, but most of them are costly, time-consuming and require well-trained operators. In this work, a fast, sensitive and miniaturised whole cell conductometric biosensor was developed for the determination of trichloroethylene. The biosensor assembly was prepared by immobilising Pseudomonas putida F1 bacteria (PpF1) at the surface of gold interdigitated microelectrodes through a three-dimensional alkanethiol self-assembly monolayer/carbon nanotube architecture functionalised with Pseudomonas antibodies. The biosensor response was linear from 0.07 to 100 μM of TCE (9–13,100 μg L⁻¹). No significant loss of the enzymatic activity was observed after 5 weeks of storage at 4 °C in the M457 pH 7 defined medium (two or three measurements per week). Ninety-two per cent of the initial signal still remained after 7 weeks. The biosensor response to TCE was not significantly affected by cis-1,2-dichloroethylene and vinyl chloride and, in a limited way, by phenol. Toluene was the major interference found. The bacterial biosensor was successfully applied to the determination of TCE in spiked groundwater samples and in six water samples collected in an urban industrial site contaminated with TCE. Gas chromatography–mass spectrometric analysis of these samples confirmed the biosensor measurements.