Limitations of the Clausius‐Mossotti function used in dielectrophoresis and electrical impedance studies of biomacromolecules

Dielectrophoresis (DEP) studies have progressed from the microscopic scale of cells and bacteria, through the mesoscale of virions to the molecular scale of DNA and proteins. The Clausius‐Mossotti function, based on macroscopic electrostatics, is invariably employed in the analyses of all these studies. The limitations of this practice are explored, with the conclusion that it should be abandoned for the DEP study of proteins and modified for native DNA. For macromolecular samples in general, a DEP theory that incorporates molecular‐scale interactions and the influence of permanent dipoles is more appropriate. Experimental ways to test these conclusions are proposed.     

Synthesis,spectral investigation and development of tetrahedral copper(II) complexes as artificial metallonucleases and antimalarial agents

Seven new copper(II) complexes of type [Cu(A)(L)]?H₂O (A = sparfloxacin, ciprofloxacin, levofloxacin, gatifloxacin, pefloxacin, ofloxacin, norfloxacin; L = 5‐[(3‐chlorophenyl)diazenyl]‐4‐hydroxy‐1,3‐thiazole‐2(3H)‐thione) were synthesized and characterized using elemental and thermogravimetric analyses, and electronic, electron paramagnetic resonance (EPR), Fourier transform infrared and liquid chromatography–mass spectroscopies. Tetrahedral geometry around copper is assigned in all complexes using EPR and electronic spectral analyses. All complexes were investigated for their interaction with herring sperm DNA utilizing absorption titration (K_b = 1.27–3.13 × 10⁵ M^?1) and hydrodynamic volume measurement studies. The studies suggest the classical intercalative mode of DNA binding. The cleavage reaction on pUC19 DNA was monitored by agarose gel electrophoresis. The results indicate that the Cu(II) complexes can more effectively promote the cleavage of plasmid DNA. The superoxide dismutase mimic activity of the complexes was evaluated by nitroblue tetrazolium assay, and the complexes catalysed the dismutation of superoxide at pH = 7.8 with IC₅₀ values in the range 0.597–0.900 μM. The complexes were screened for their in vitro antibacterial activity against five pathogenic bacteria. All the complexes are good cytotoxic agents and show LC₅₀ values ranging from 5.559 to 11.912 µg ml^?1. All newly synthesized Cu(II) complexes were also evaluated for their in vitro antimalarial activity against Plasmodium falciparum strain (IC₅₀ = 0.62–2.0 µg ml^?1). Copyright © 2015 John Wiley & Sons, Ltd.     

Ratiometric Detection of microRNA Using Hybridization Chain Reaction and Fluorogenic Silver Nanoclusters

miRNA (miR)-155 is a potential biomarker for breast cancers. We aimed at developing a nanosensor for miR-155 detection by integrating hybridization chain reaction (HCR) and silver nanoclusters (AgNCs). HCR serves as an enzyme-free and isothermal amplification method, whereas AgNCs provide a built-in fluorogenic detection probe that could simplify the downstream analysis. The two components were integrated by adding a nucleation sequence of AgNCs to the hairpin of HCR. The working principle was based on the influence of microenvironment towards the hosted AgNCs, whereby unfolding of hairpin upon HCR has manipulated the distance between the hosted AgNCs and cytosine-rich toehold region of hairpin. As such, the dominant emission of AgNCs changed from red to yellow in the absence and presence of miR-155, enabling a ratiometric measurement of miR with high sensitivity. The limit of detection (LOD) of our HCR-AgNCs nanosensor is 1.13 fM in buffered solution. We have also tested the assay in diluted serum samples, with comparable LOD of 1.58 fM obtained. This shows the great promise of our HCR-AgNCs nanosensor for clinical application.     

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.     

Nano-sized Cu(II) and Zn(II) complexes and their use as a precursor for synthesis of CuO and ZnO nanoparticles: A study on their sonochemical synthesis,characterization, and DNA-binding/cleavage,anticancer, and antimicrobial activities

Two new divalent copper (C1) and zinc (C2) chelates having the formulae [M(PIMC)₂] (where M = Cu(II), Zn(II) and PIMC = Ligand [(E)-3-(((3-hydroxypyridin-2-yl)imino)methyl)-4H-chromen-4-one] were obtained and characterized by several techniques. Structures and geometries of the synthesized complexes were judged based on the results of alternative analytical and spectral tools supporting the proposed formulae. IR spectral data confirmed the coordination of the ligands to the copper and zinc centers as monobasic tridentate in the enol form. Thermal analysis, UV-Vis spectra and magnetic moment confirmed the geometry around the copper center to be tetrahedral, square pyramidal and octahedral. Study of the binding ability of the synthesized compounds with Circulating tumor DNA (CT-DNA) bas been evaluated applying UV-Vis spectral titration and viscosity measurements. The copper and zinc oxides were achieved from the copper and zinc nano-particles structures Schiff base complexes as the raw material after calcination for 5 hr at 600°C. On the other hand, synthesized of C1 and C2 NPs were used as suitable precursors to the preparation of CuO and ZnO NPs. Finally, the synthesized of the two complexes exhibited enhanced activity against the tested bacterial (Staphylococcus aureus and Escherichia Coli) and fungal strains (Candida albicans and Aspergillus fumigatus) as compared to HPIMC. Among all these synthesized compounds, C1 exhibits good cleaving ability compared to other newly synthesized C2.     

A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson–Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15–25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35–90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.     

Functionalized Silver-Ion-Mediated α-dC/β-dC Hybrid Base Pairs with Exceptional Stability: α-d-5-Iodo-2′-Deoxycytidine and Its Octadiynyl Derivative in Metal DNA

Silver-mediated α-dC–Ag⁺–β-dC hybrid base pairs decorated with 5-iodo- or 5-octadiynyl residues are well accommodated in duplex DNA. A strong T_m increase and favorable thermodynamic data for duplex DNA were observed after addition of silver ions. The phenomenon is particularly obvious when both nucleobases of the base pairs are functionalized. Neither the position of the base pair, nor the type of 5-substituent had a negative influence. On the contrary, functionalization of conventional silver-mediated β-dC–Ag⁺–β-dC homo base pairs showed a negative impact induced by the bulky substituents. To this end, cytosine modified 12-mer oligodeoxynucleotides were prepared by solid-phase synthesis employing new α-anomeric 2′-deoxycytidine phosphoramidites. A multigram scale synthesis was developed for 5-iodo-α-d -2′-deoxycytidine ( 1 ) employing the direct glycosylation of cytosine with Hoffer's α-d -halogenose followed by separation of anomeric DMT nucleosides. Regarding base-pair stability and functionalization silver-mediated α/β-dC hybrid base pairs were found to be superior to β/β-dC homo pairs. According to their extraordinary properties, they might find applications in DNA diagnostics, material science, or nanotechnology.     

Simultaneous quantification of leukotrienes and hydroxyeicosatetraenoic acids in cell culture medium using liquid chromatography/tandem mass spectrometry

Leukotrienes (LTs) and hydroxyeicosatetraenoic acids (HETEs) are important bioactive lipid mediators that participate in various pathophysiological processes. To advance understanding of the mechanisms that regulate these mediators in physiological and pathological processes, an analytical method using liquid chromatography/tandem mass spectrometry for the simultaneous quantification of LTB₄, LTC₄, LTD₄, LTE₄, 5‐HETE_, 8‐HETE, 12‐HETE and 15‐HETE in cell culture media was developed. A Supel?‐Select HLB solid‐phase extraction cartridge was used for sample preparation. The compounds were separated on a C₁₈ column using gradient elution with acetonitrile–water–formic acid (20:80:0.1, v/v/v) and acetonitrile–formic acid (100:0.1, v/v). The calibration curves of LTB₄, LTD₄, LTE₄ and HETEs were linear in the range of 0.025–10 ng/mL, and the calibration curve of LTC₄ was linear in the range of 0.25–10 ng/mL. Validation assessment showed that the method was highly reliable with good accuracy and precision. The stability of LTs and HETEs was also investigated. Using the developed method, we measured LTs and HETEs in the culture supernatant of the human mast cell line HMC‐1. The present method could facilitate investigations of the mechanisms that regulate the production, release and signaling of LTs and HETEs. Copyright © 2014 John Wiley & Sons, Ltd.     

A novel LC–MS/MS method for the determination of ziritaxestat in rat plasma and its pharmacokinetic study

Ziritaxestat is a first-in-class autotoxin inhibitor. The purpose of this study was to develop a liquid chromatography/electrospray ionization tandem mass spectrometric (LC–MS/MS) method for the determination of ziritaxestat in rat plasma. The plasma sample was deproteinated using acetonitrile and then separated on an Acquity BEH C₁₈ column with water containing 0.1% formic acid and acetonitrile as mobile phase, which was delivered at 0.4 ml/min. Ziritaxestat and the internal standard (crizotinib) were quantitatively monitored with precursor-to-product transitions of m/z 589.3 > 262.2 and m/z 450.1 > 260.2, respectively. The total running time was 2.5 min. The method showed excellent linearity over the concentration range 0.5–2000 ng/ml, with correlation coefficient >0.9987. The extraction recovery was >82.09% and the matrix effect was not significant. Inter- and intra-day precisions (RSD) were <11.20% and accuracies were in the range of −8.50–7.45%. Ziritaxestat was demonstrated to be stable in rat plasma under the tested conditions. The validated LC–MS/MS method was successfully applied to study the pharmacokinetic profiles of ziritaxestat in rat plasma after intravenous and oral administration. Pharmacokinetic results demonstrated that ziritaxestat displayed a short half-life (~3 h) and low bioavailability (20.52%).     

Metabolic Profiling of Amino Acids by Liquid Chromatography–Tandem Mass Spectrometry (LC–MS) to Characterize the Significance of Glutamine in Triple-Negative Breast Cancer (TNBC)

Triple-negative breast cancer (TNBC) is considered to be aggressive based on its low overall survival and disease-free rates. Currently, there is no molecular-targeted therapy. The identification of a suitable biomarker is still a research focus for TNBC at the present time. Amino acid metabolism fulfills multiple important physiological roles in humans. Their metabolic abnormalities have been reported in numerous cancer studies and amino acid pathways may also be chemotherapeutic targets. This study reports the profiling analysis of amino acids in TNBC and non-TNBC cell lines for detecting biomarkers based on the strategy of N-phosphorylation labeling with liquid chromatography–tandem mass spectrometry (LC–MS). Glutamine (Gln) was found to be significantly down-regulated in TNBC cells because it was largely absorbed and consumed in the TNBC cell lines. These results indicate faster proliferation of TNBC and higher consumption of glutamine to meet the material and energy demand, suggesting its potential role in TNBC progression. Hence, glutamine may be regarded as a biomarker and Gln-targeted approaches may become a new therapeutic strategies for TNBC.