Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA

The sulfoindocyanine Cy3 is one of the most commonly used fluorescent dyes in the investigation of the structure and dynamics of nucleic acids by means of fluorescence methods. In this work, we report the fluorescence and photophysical properties of Cy3 attached covalently to single-stranded and duplex DNA. Steady-state and time-resolved fluorescence techniques were used to determine fluorescence quantum yields, emission lifetimes, and fluorescence anisotropy decays. The existence of a transient photoisomer was investigated by means of transient absorption techniques. The fluorescence quantum yield of Cy3 is highest when attached to the 5' terminus of single-stranded DNA (Cy3-5' ssDNA), and decreases by a factor of 2.4 when the complementary strand is annealed to form duplex DNA (Cy3-5' dsDNA). Substantial differences were also observed between the 5'-modified strands and strands modified through an internal amino-modified deoxy uridine. The fluorescence decay of Cy3 became multiexponential upon conjugation to DNA. The longest lifetime was observed for Cy3-5' ssDNA, where about 50% of the decay is dominated by a 2.0-ns lifetime. This value is more than 10 times larger than the fluorescence lifetime of the free dye in solution. These observations are interpreted in terms of a model where the molecule undergoes a trans-cis isomerization reaction from the first excited state. We observed that the activation energy for photoisomerization depends strongly on the microenvironment in which the dye is located. The unusually high activation energy measured for Cy3-5' ssDNA is an indication of dye-ssDNA interactions. In fact, the time-resolved fluorescence anisotropy decay of this sample is dominated by a 2.5-ns rotational correlation time, which evidences the lack of rotational freedom of the dye around the linker that separates it from the terminal 5' phosphate. The remarkable variations in the photophysical properties of Cy3-DNA constructs demonstrate that caution should be used when Cy3 is used in studies employing DNA conjugates.     

Single-laboratory validation of the biosense direct competitive enzyme-linked immunosorbent assay (ELISA) for determination of domoic acid toxins in shellfish

Method validation was conducted for an enzyme-linked immunosorbent assay (ELISA) for the determination of domoic acid (DA) toxins, known to give amnesic shellfish poisoning (ASP) symptoms, in shellfish. The calibration curve range of the assay is approximately 10-260 pg/mL, with a dynamic working range for DA toxins in shellfish from 0.01 to at least 250 mg/kg. The ASP ELISA showed no significant cross-reactivity to structural analogs, and proved to be robust to deliberate alterations of the optimal running conditions. The shellfish matrix effects observed with mussels, oysters, and scallops were eliminated by diluting shellfish extracts 1:200 prior to analysis, leading to a limit of detection at 0.003 mg/kg. Thirteen blank shellfish homogenates were spiked with certified mussel material containing DA to levels in the range of 0.1-25 mg DA/kg, and analyzed in quadruplicate on 3 different days. The relative standard deviation (RSD) under intra-assay repeatability conditions ranged from 6.5 to 13.1%, and under interassay repeatability conditions the RSD ranged from 5.7 to 13.4%, with a mean value of 9.3%. The recoveries ranged from 85.5 to 106.6%, with a mean recovery of 102.2%. A method comparison was conducted with liquid chromatography with ultraviolet detection, using naturally contaminated scallop samples (n = 27) with DA levels at 0-244 mg/kg. The overall correlation coefficient was 0.960 and the slope of the regression was 1.218, indicating a good agreement between the methods.     

Enantioanalysis of bisoprolol in human plasma with a macrocyclic antibiotic HPLC chiral column using fluorescence detection and solid phase extraction

A sensitive, enantioselective, high-performance liquid chromatographic (HPLC) method was developed and validated to determine S-(-)- and R-(+)-bisoprolol in human plasma. Baseline resolution was achieved using the teicoplanin macrocyclic antibiotic chiral stationary phase (CSP) known as Chirobiotic T with a polar ionic mobile phase (PIM) consisting of methanol-glacial acetic acid-triethylamine (100 : 0.02 : 0.025, v/v/v) at a flow rate of 1.5 ml/min and fluorescence detection set at 275 nm for excitation and 305 nm for emission. All analyses with S-(-)-atenolol as the internal standard were conducted at ambient temperature. The assay involved the use of a solid-phase extraction procedure for human plasma samples prior to HPLC analysis. The C18 cartridge gave good recovery rates for both enantiomers without any interference. The method was validated over the range of 20-200 ng/ml for each enantiomer concentration. Recovery rates for S-(-)- and R-(+)-bisoprolol enantiomers were in the range of 95-102%. The method proved to be precise (within-run precision expressed as % RSD ranged from 1.0-6.2% and between-run precision ranged from 0.9-6.7%) and accurate (within-run accuracies expressed as percentage error ranged from 0.2-4.8% and between-run accuracies ranged from 0.3-1.7%). The limit of quantitation and limit of detection for each enantiomer in human plasma were 20 and 5 ng/ml, respectively.     

An end theorem for stratified spaces

We show that a manifold-stratified space X is the interior of a compact manifold-stratified space with boundary if and only if X is tame-ended and a K-theoretic obstruction γ_*(X) vanishes. The obstruction γ_*(X) is a localization of Quinn's mapping cylinder neighborhood obstruction. The main results are Theorem 1.6 and Theorem 1.7 below. In particular, this explains when a G-manifold is the interior of a compact G-manifold with boundary. One of our methods is a new transversality theorem, Theorem 1.16. Oblatum 30-VI-1996 & 21-X-1997 / Published online: 14 January 1999     

Morphology and electrical properties of pulsed-laser deposited Bi2Sr2CaCu2O8+δ films on vicinal substrates

Thin films of Bi₂Sr₂CaCu₂O_8+δ have been grown on vicinal (001) SrTiO₃ substrates by pulsed-laser deposition. Transmission electron microscopy (TEM) and X-ray diffraction reveal well ordered films with the c axis of the film parallel with the c axis of the substrate for miscut angles up to θ_S≈15°. TEM also reveals the step-like film morphology due to step-flow growth. The in-plane and out-of-plane resistivities are independent of film thickness within the range 20–300 nm and agree quite well with Bi₂Sr₂CaCu₂O_8+δ single-crystal data. Received:15 May 2000 / Accepted:17 May 2000 / Published online: 9 August 2000     

Naturally Available Flavonoid Aglycones as Potential Antiviral Drug Candidates against SARS-CoV-2

Flavonoids are important secondary plant metabolites that have been studied for a long time for their therapeutic potential in inflammatory diseases because of their cytokine-modulatory effects. Five flavonoid aglycones were isolated and identified from the hydrolyzed aqueous methanol extracts of Anastatica hierochuntica L., Citrus reticulata Blanco, and Kickxia aegyptiaca (L.) Nabelek. They were identified as taxifolin (1), pectolinarigenin (2), tangeretin (3), gardenin B (4), and hispidulin (5). These structures were elucidated based on chromatographic and spectral analysis. In this study, molecular docking studies were carried out for the isolated and identified compounds against SARS-CoV-2 main protease (Mpro) compared to the co-crystallized inhibitor of SARS-CoV-2 Mpro (α-ketoamide inhibitor (KI), IC₅₀ = 66.72 µg/mL) as a reference standard. Moreover, in vitro screening against SARS-CoV-2 was evaluated. Compounds 2 and 3 showed the highest virus inhibition with IC₅₀ 12.4 and 2.5 µg/mL, respectively. Our findings recommend further advanced in vitro and in vivo studies of the examined isolated flavonoids, especially pectolinarigenin (2), tangeretin (3), and gardenin B (4), either alone or in combination with each other to identify a promising lead to target SARS-CoV-2 effectively. This is the first report of the activity of these compounds against SARS-CoV-2.     

Influence of molar mass of polymer on the solvent activity for binary system of poly N-vinylcaprolactam and water

The water activity in aqueous solution of poly N-vinyl caprolactam with different molecular weights is measured by isopiestic method at T = 308.15 K. The results show that water activity and vapour pressure of poly N-vinylcaprolactam solution increases with increasing the molecular weight. The Flory-Huggins model, the modified Flory-Huggins model and Freed Flory-Huggins equation + NRTL model are used for correlation of the experimental solvent activity. It is found that the Freed Flory-Huggins + NRTL model is better than the others.     

Systems-based decomposition schemes for the approximate solution of multi-term fractional differential equations

We give a comparison of the efficiency of three alternative decomposition schemes for the approximate solution of multi-term fractional differential equations using the Caputo form of the fractional derivative. The schemes we compare are based on conversion of the original problem into a system of equations. We review alternative approaches and consider how the most appropriate numerical scheme may be chosen to solve a particular equation.     

Effect of surfactant and solvent properties on the stacking behavior of non-aqueous suspensions of organically modified clays

Montmorillonite clay was treated with quaternary ammonium surfactants with 1-3 long chains of 10-18 carbons to form organoclays which can be suspended in non-aqueous solvents. The effects of surfactant chain length, number of long chains, and the properties of the solvent on the colloidal behavior of the surfactant coated clay plates were studied using small-angle X-ray scattering. The scattering data were modeled using a one-dimensional aggregation theory to describe the stacking of the clay plates. The plates self-organize into stacks with a reproducible basal spacing in the range of 30-50 A, and for each surfactant, the basal spacing falls into one of two preferred distances. We interpret this by considering that the surfactant layer on the clay has two strata, one being the polar near-clay headgroup region and the other the nonpolar alkane chain region. Polar solvents will swell the polar stratum preferentially while nonpolar solvents will swell the nonpolar stratum of the surfactant. As the nonpolar stratum is larger than the polar one, the nonpolar solvents increase the basal spacing between the clay plates more than the polar solvents. The number of long chains on the surfactant does not have an effect on the basal spacing, as the density of surfactant molecules on the surface is low enough to allow the unimpeded swelling of the chains. The one-dimensional aggregation theory can be used to determine the number of plates in a stack, but the effect of changing clay particle size or concentration is not as great as would be expected from this theory. This may be due to the formation of large-scale structures in the suspensions which prevent a true equilibrium stack size being attained.