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81.
Optimization of Experimental Parameters to Explore Small‐Ligand/Aptamer Interactions through Use of 1H NMR Spectroscopy and Molecular Modeling
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Dr. Florence Souard Dr. Sandrine Perrier Dr. Vincent Noël Dr. Claire Fave Emmanuelle Fiore Prof. Eric Peyrin Prof. Julian Garcia Dr. Cécile Vanhaverbeke 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(44):15740-15748
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. 相似文献
82.
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.] 相似文献
83.
Ropartz D Bodet PE Przybylski C Gonnet F Daniel R Fer M Helbert W Bertrand D Rogniaux H 《Rapid communications in mass spectrometry : RCM》2011,25(14):2059-2070
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. 相似文献
84.
Snégaroff K Nguyen TT Marquise N Halauko YS Harford PJ Roisnel T Matulis VE Ivashkevich OA Chevallier F Wheatley AE Gros PC Mongin F 《Chemistry (Weinheim an der Bergstrasse, Germany)》2011,17(47):13284-13297
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. 相似文献
85.
Quinton D Girard A Thi Kim LT Raimbault V Griscom L Razan F Griveau S Bedioui F 《Lab on a chip》2011,11(7):1342-1350
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. 相似文献
86.
Smaoui S Mellouli L Lebrihi A Coppel Y Fguira LF Mathieu F 《Natural product research》2011,25(8):806-814
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. 相似文献
87.
Naima Bouyahia Mohamed Larbi Hamlaoui Mouna Hnaien Florence Lagarde Nicole Jaffrezic-Renault 《Bioelectrochemistry (Amsterdam, Netherlands)》2011,80(2):155-161
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 KMapp = 84 ± 3 mM and maximal initial velocity VMapp = 13.4 μS min? 1. Inhibition by cyanide was found to be non-competitive and inhibition binding constant Ki 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 RP. 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). 相似文献
88.
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. 相似文献
89.
Hnaien M Lagarde F Bausells J Errachid A Jaffrezic-Renault N 《Analytical and bioanalytical chemistry》2011,400(4):1083-1092
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. 相似文献
90.
Folliet N Roiland C Bégu S Aubert A Mineva T Goursot A Selvaraj K Duma L Tielens F Mauri F Laurent G Bonhomme C Gervais C Babonneau F Azaïs T 《Journal of the American Chemical Society》2011,133(42):16815-16827
In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces. 相似文献