A paper-based resonance energy transfer nucleic acid hybridization assay using upconversion nanoparticles as donors and quantum dots as acceptors

Monodisperse aqueous upconverting nanoparticles (UCNPs) were covalently immobilized on aldehyde modified cellulose paper via reduction amination to develop a luminescence resonance energy transfer (LRET)-based nucleic acid hybridization assay. This first account of covalent immobilization of UCNPs on paper for a bioassay reports an optically responsive method that is sensitive, reproducible and robust. The immobilized UCNPs were decorated with oligonucleotide probes to capture HPRT1 housekeeping gene fragments, which in turn brought reporter conjugated quantum dots (QDs) in close proximity to the UCNPs for LRET. This sandwich assay could detect unlabeled oligonucleotide target, and had a limit of detection of 13 fmol and a dynamic range spanning nearly 3 orders of magnitude. The use of QDs, which are excellent LRET acceptors, demonstrated improved sensitivity, limit of detection, dynamic range and selectivity compared to similar assays that have used molecular fluorophores as acceptors. The selectivity of the assay was attributed to the decoration of the QDs with polyethylene glycol to eliminate non-specific adsorption. The kinetics of hybridization were determined to be diffusion limited and full signal development occurred within 3 min.     

Recombinant cell bioassay systems for the detection and relative quantitation of halogenated dioxins and related chemicals

Proper epidemiological, risk assessment and exposure analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin) and related halogenated aromatic hydrocarbons (HAHs) requires accurate measurements of these chemicals both in the species of interest and in various exposure matrices (i.e. biological, environmental, food and feed). High-resolution instrumental analysis techniques are established for these chemicals, however, these procedures are very costly and time-consuming and as such, they are impractical for large scale sampling studies (i.e. for epidemiological studies and assessment of areas with widespread contamination). Accordingly, numerous bioanalytical methods have been developed for the detection of these chemicals in extracts from a variety of matrices, the majority of which take advantage of the ability of these chemicals to activate the aromatic hydrocarbon receptor (AhR) and the AhR signal transduction pathway. Here we review the currently available in vitro AhR-based cell bioassay systems with a focus on recent recombinant reporter gene cell lines that have been developed for detection and relative quantitation of TCDD and related HAHs. Comparison of the relative sensitivities of the various cell bioassays and examples of their use in screening and analysis of environmental, biological, and food and feed samples are presented. Currently available experimental results and validation studies demonstrate the utility of these cell bioassay systems to provide a relatively rapid, accurate, and cost effective screening approach for the detection of TCDD and related HAHs in a variety of environmental, biological, food and feed samples. The availability of these cell bioassay systems will not only facilitate the large scale sampling studies needed for accurate assessment of contamination and exposure to these environmental chemicals, but they provide avenues for the identification of novel classes of TCDD-like chemicals.     

Toxic Congener-Specific Analysis of PCBs: Assessment of Toxicity in Equivalents of TCDD

Abstract

High resolution capillary gas chromatographic analysis of the polychlorobiphenyls (PCBs) present in snapping turtle eggs, provided quantitative data on selected toxic congeners. The concentrations of these congeners have been converted into equivalent toxic concentrations of 2,3,7,8-tetrachloro-p-dibenzodioxin (TCDD). The toxic equivalent factors (TEFs), necessary to effect this transformation were derived from EC₅₀ values (half the concentration of the toxic congener required to produce the maximum effect) for aryl hydrocarbon hydroxylase (AHH) induction associated with the corresponding toxic PCB congener or isomer. Summation of the resulting toxic equivalents provided a composite assessment of the toxlcity of the PCB mixture in terms of an equivalent concentration of TCDD.     

A competitive displacement assay with quantum dots as fluorescence resonance energy transfer donors

The unique optoelectronic properties of semiconductor quantum dots (QDs) make them well-suited as fluorescent bioprobes for use in various biological applications. Modification of CdSe/ZnS QDs with biologically relevant molecules provides for multipotent probes that can be used for cellular labeling, bioassays, and localized optical interrogation by means of fluorescence resonance energy transfer (FRET). Herein, we demonstrate the use of red-emitting streptavidin-coated QDs (QD₆₀₅) as donors in FRET to introduce a competitive displacement-based assay for the detection of oligonucleotides. Various QD–DNA bioconjugates featuring 25-mer probe sequences diagnostic of Hsp23 were prepared. The single-stranded oligonucleotide probes were hybridized to dye-labeled (Alexa Fluor 647) reporter sequences, which were provided for a FRET-sensitized emission signal due to proximity of the QD and dye. The dye-labeled sequence was designed to be partially complementary and include base-pair mismatches to facilitate displacement by a more energetically favorable, fully complementary recognition motif embedded within a 98-mer displacer sequence. Overall, this study demonstrates proof-of-concept at the nM level for competitive displacement hybridization assays in vitro by reduction of fluorescence intensity that directly correlates to the presence of oligonucleotides of interest. This work demonstrates an analytical method that could potentially be implemented for monitoring of intracellular gene expression in the future.     

The novel 4-hydroxyphenylpyruvate dioxygenase inhibitors in vivo and in silico approach: 3D-QSAR analysis,molecular docking,bioassay and molecular dynamics

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only an important target enzyme for the treatment of type I tyrosinemia, but also a new target for design bleaching herbicides, and it plays key role in the biosynthesis of tocopherol and plastoquinone. Thirty-six known active pyridine derivatives were collected, and comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models based on common skeleton were constructed to obtain novel HPPD herbicides with higher activity. Two new HPPD inhibitors were rationally designed and synthesized according to the CoMFA and CoMSIA models and verified by enzyme activity, biological assays, and molecular docking. The promising compound W1 ((E)-5-(3-(4-bromophenyl)acryloyl)-6-hydroxy-2,3-dihydropyridin-4(1H)-one) showed better AtHPPD inhibitory activity, and the bioassay results revealed that some weeds showed bleaching symptoms. The good binding stability of W1 and protein was confirmed by molecular dynamics simulation in 100 ns. These results would be highly useful in the progress of new HPPD inhibitors discovery.     

Temperature sensitivity and fluorescence detection

Fluorescence detectors are about three orders of magnitude more sensitive and specific making them ideal for trace analysis and complex sample matrices. However, temperature dependence of the signal is a disadvantage to fluorescence detectors. We have previously reported degradation of malondialdehyde (MDA)-thiobarbituric acid (TBA) adduct at room temperature. The present experiments tested the notion that the detector response may be blunted due to increase in temperature over time. Repeated injections of the same standard curve over 4 h found a significant effect of time on the slopes of peak area-concentration curves. When the samples were iced and injected alternating with ambient temperature standard curve samples, no differences in slopes were seen between iced and ambient temperature samples. Cooling the housing of the fluorescence lamp significantly increased the fluorescence in the samples. Fluorescence increased 2.5% (95% confidence interval, 1.5-3.6%) for each 1 degrees C fall in temperature. MDA-TBA adduct remained stable at room temperature. Since the fluorescence signal is temperature sensitive, letting the detector warm up for 2 h to obtain a steady temperature is more likely to give reproducible results compared to a detector that has not warmed up. These results have implications for other applications utilizing fluorescence detectors.     

Syntheses and Preliminary Biological Evaluations of the Dibromopyrrole-Containing Marine Natural Products Agesasine A,Agesasine B,Longamide E and Various Congeners

Total syntheses of the title marine natural products have been achieved and so confirming the structures originally assigned to them. Upon subjecting agesasine A and its corresponding ethyl ester to Mitsunobu conditions, a 1,5-cyclodehydration reaction takes place to give 2-oxazolines. In contrast, on subjecting agesasine B to the same Mitsunobu conditions, a simple dehydration reaction occurs to give the corresponding acrylate. A total synthesis of longamide E was achieved by engaging a 1,2-disubstituted pyrrole in a lactam-forming reaction and this was followed by a two-fold and fully regio-controlled bromination reaction. A distinctly different and possibly biomimetic route was used to synthesize, via the open-chain natural product nakamurine B, longamide B and its methyl ester. Preliminary biological evaluations of the title alkaloids and various analogues against a small human cancer cell line panel reveals cytotoxic properties that vary significantly with structure.     

Drug profiling using planar microelectrode arrays

Microelectrode arrays (MEAs) with evenly distributed multiple sensor spots have been designed for specific applications. Using the MEAs, we determined the relative profiles of potassium channel openers (KCOs) on cultured embryonic Sprague-Dawley rat cardiac myocytes. KCO, pinacidil (PIN), cromakalim (CROM), SDZ PCO400 (SDZ), or its vehicle, was added to the myocytes cumulatively. The action potential signal shapes in the presence of PIN and SDZ show that the changes in voltage over time and the magnitudes of the associated voltage change were reduced concentration-dependently. CROM affected sodium influx more than PIN and SDZ. The comparisons of changes in the rate of beating and propagation speed in the presence of KCOs were made using their corresponding pD(2) values (the negative log of EC(50)). All KCOs caused concentration-dependent reductions in the rate of beating and propagation speed, with SDZ being the most potent. In addition to the signal shapes, rate of beating, and propagation speed, the origin of excitation and the excitation pattern inside the culture can be also extracted. The results show that the present system can differentiate the effects of different KCOs on myocytes. It might be possible to utilise the MEA as a means to classify drug action based upon a combined interpretation of the three different datasets gained from the extracellular recordings. The combination of these observations might be used as 'drug signatures' when profiling drugs in the future.     

Analysing traces of autoinducer-2 requires standardization of the <Emphasis Type="Italic">Vibrio harveyi</Emphasis> bioassay

Autoinducer-2 (furanosyl borate diester) is a biologically active compound whose role as a universal bacterial signalling molecule is currently under intense investigation. Because of its instability and the low concentrations of it found in biological samples, its detection relies at present on a bioassay that measures the difference in the timing of the luminescence of the Vibrio harveyi BB170 sensor strain with and without externally added AI-2. Here we systematically investigated which parameters affected the fold induction values of luminescence obtained in the bioassay and developed a modified protocol. Our experiments showed that growth and luminescence of V. harveyi BB170 are strongly influenced by trace elements. In particular, addition of Fe³⁺ within a certain concentration range to the growth medium of the preinoculum culture improved the reproducibility and reduced the variance of the bioassay. In contrast, trace elements and vitamins introduced directly into the bioassay caused inhibitory effects. The initial density and luminescence of the sensor strain are very important and the values required for these parameters were defined. Borate interferes with the detection of AI-2 by giving false positive results. The response of V. harveyi BB170 to chemically synthesized AI-2 in the bioassay is nonlinear except over a very small concentration range; it is maximum over three orders of magnitude and shows inhibition above 35 μM. Based on the modified protocol, we were able to detect AI-2 in the absence of inhibitors with maximum fold induction values for the positive control (chemically synthesized AI-2) of >120 with a standard deviation of ~30% in a reliable and reproducible way.     

Synthesis of aqueous CdTe quantum dots embedded silica nanoparticles and their applications as fluorescence probes

This paper presents the synthesis of aqueous CdTe QDs embedded silica nanoparticles by reverse microemulsion method and their applications as fluorescence probes in bioassay and cell imaging. With the aim of embedding more CdTe QDs in silica spheres, we use poly(dimethyldiallyl ammonium chloride) to balance the electrostatic repulsion between CdTe QDs and silica intermediates. By modifying the surface of CdTe/SiO₂ composite nanoparticles with amino and methylphosphonate groups, biologically functionalized and monodisperse CdTe/SiO₂ composite nanoparticles can be obtained. In this work, CdTe/SiO₂ composite nanoparticles are conjugated with biotin-labeled mouse IgG via covalent binding. The biotin-labeled mouse IgG on the CdTe/SiO₂ composite nanoparticles surface can recognize FITC-labeled avidin and avidin on the surface of polystyrene microspheres by protein-protein binding. Finally, the CdTe/SiO₂ composite nanoparticles with secondary antibody are used to label the MG63 osteosarcoma cell with primary antibody successfully, which demonstrates that the application of CdTe/SiO₂ composite nanoparticles as fluorescent probes in bioassay and fluorescence imaging is feasible.