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.     

Synthesis and Characterization of a [Mn12O12(O2CR)16(H2O)4] Complex Bearing Paramagnetic Carboxylate Ligands. Use of a Modified Acid Replacement Synthetic Approach

Summary.  A new modified approach for the synthesis of Mn₁₂ clusters, based on the use of complex [Mn₁₂O₁₂(O₂C ^t Bu)₁₆(H₂O)₄] (2) as starting material to promote the acidic ligand replacement, is presented here. This new synthetic approach allowed us to obtain complex [Mn₁₂O₁₂(O₂CC₆H₄N(O^•) ^t Bu)₁₆(H₂O)₄] (3), whose preparation remained elusive by direct replacement of the acetate groups of Mn₁₂Ac (1). Complex 3 bearing open-shell radical units, was prepared to increase the total spin number of its ground state, and consequently, to increase T _B , with the expectation that the radical ligands may couple ferromagnetically with the Mn₁₂ core. Unfortunately, magnetic measurements of complex 3 revealed that the sixteen radical carboxylate ligands interact antiferromagnetically with the Mn₁₂ core to yield a S = 2 magnetic ground state. Corresponding author. E-mail: vecianaj@icmab.es Received March 27, 2002; accepted May 2, 2002     

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.     

Solvato Modulation of the Magnetic Memory in Isotopically Enriched Erbium Polyoxometalate

Single-Molecule Magnet (SMM) property is by essence molecular, while commonly measured in solid crystalline state. Solvent crystallization molecules are usually neglected in the analysis and interpretation of solid-state properties. The solvation/desolvation process in the polyoxometalate(POM)-based Na₉[Er(W₅O₁₈)₂] ⋅ 35 H₂O SMM demonstrates that the dehydrated form relaxes more than 1000 times faster than the initial state, while the rehydration process allows the quasi complete recovering of the initial magnetic behaviour. This dehydration process is monitored by thermogravimetric analysis (TGA) and temperature-dependent X-ray powder diffraction, and rationalized by periodic quantum chemical calculations evidencing the tremendous role of the labile water molecules in the stability of the edifice. Ab-initio calculations highlight that sodium ions localization in the structure drive the magnetic responses. Isotopic enrichment with nuclear spin free (¹⁶⁶Er, I=0) Er^III ions shows that the relaxation dynamics in the quantum regime depends on the nuclear spin.     

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.     

Observing Confined Local Oxygen-induced Reversible Thiol/Disulfide Cycle with a Protein Nanopore

Disulfide bonds play an important role in thiol-based redox regulation. However, owing to the lack of analytical tools, little is known about how local O₂ mediates the reversible thiol/disulfide cycle under protein confinement. In this study, a protein-nanopore inside a glove box is used to control local O₂ for single-molecule reaction, as well as a single-molecule sensor for real-time monitoring of the reversible thiol/disulfide cycle. The results demonstrate that the local O₂ molecules in protein nanopores could facilitate the redox cycle of disulfide formation and cleavage by promoting a higher fraction of effective reactant collisions owing to nanoconfinement. Further kinetic calculations indicate that the negatively charged residues near reactive sites facilitate proton-involved oxygen-induced disulfide cleavage under protein confinement. The unexpectedly strong oxidation ability of confined local O₂ may play an essential role in cellular redox signaling and enzyme reactions.     

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.