Exploring base-pair-specific optical properties of the DNA stain thiazole orange

Double-stranded DNA offers multiple binding sites to DNA stains. Measurements of noncovalently bound dye-nucleic acid complexes are, necessarily, measurements of an ensemble of chromophores. Thus, it is difficult to assign fluorescence properties to base-pair-specific binding modes of cyanine dyes or, vice versa, to obtain information about the local environment of cyanines in nucleic acids by using optical spectroscopy. The feasibility to stain DNA and simultaneously probe local perturbations by optical spectroscopy would be a valuable asset to nucleic acid research. So-called FIT probes (forced intercalation probes) were used to pinpoint the location of the DNA stain thiazole orange (TO) in PNADNA duplexes. A detailed analysis of the base-pair dependence of optical properties is provided and enforced binding of TO is compared with "classical" binding of free TO-PRO1. UV-visible absorbance, circular dichroism (CD) and fluorescence spectroscopy, and melting-curve analyses confirmed site-specific TO intercalation. Thiazole orange exhibited base-specific responses that are not observed in noncovalent dye-nucleic acid complexes, such as an extraordinary dependence of the TO extinction coefficient (+/-60 % variation of the averaged epsilon(max) of 57,000 M(-1) cm(-1)) on nearest-neighbor base pairs. TO signals hybridization, as shown by increases in the steady-state fluorescence emission. Studies of TO fluorescence lifetimes in FIT-PNA and in DNADNA and PNADNA complexes highlighted four different fluorescence-decay processes that may be closed or opened in response to matched or single-mismatched hybridization. A very fast decay process (0.04-0.07 ns) and a slow decay process (2.33-3.95 ns) provide reliable monitors of hybridization, and the opening of a fast decay channel (0.22-0.48 ns) that resulted in an attenuation of the fluorescence emission is observed upon the formation of mismatched base pairs.     

Coordination compounds of N,N′-olefin functionalized imidazolin-2-ylidenes

N-Heterocyclic carbene ligands (NHC) were metalated with Pd(OAc)₂ or [Ni(CH₃CN)₆](BF₄)₂ by in situ deprotonation of imidazolium salts to give the N-olefin functionalized biscarbene complexes [MX₂(NHC)₂] 3-7 (3: M = Pd, X = Br, NHC = 1,3-di(3-butenyl)imidazolin-2-ylidene; 4: M = Pd, X = Br, NHC = 1,3-di(4-pentenyl)imidazolin-2-ylidene; 5: M = Pd, X = I, NHC = 1,3-diallylimidazolin-2-ylidene; 6: M = Ni, X = I, NHC = 1,3-diallylimidazolin-2-ylidene; 7: M = Ni, X = I, NHC = 1-methyl-3-allylimidazolin-2-ylidene). Molecular structure determinations for 4-7 revealed that square-planar complexes with cis (5) or trans (4, 6, 7) coordination geometry at the metal center had been obtained. Reaction of nickelocene with imidazolium bromides afforded the η⁵-cyclopentadienyl (η⁵-Cp) monocarbene nickel complexes [NiBr(η⁵-Cp)(NHC)] 8 and 9 (8: NHC = 1-methyl-3-allylimidazolin-2-ylidene; 9: NHC = 1,3-diallylimidazolin-2-ylidene). The bromine abstraction in complexes 8 and 9 with silver tetrafluoroborate gave complexes [NiBr(η⁵-Cp)(η³-NHC)] 10 and 11. The X-ray structure analysis of 10 and 11 showed a trigonal-pyramidal coordination geometry at the nickel(II) center and coordination of one N-allyl substituent.     

Three Small Molecule Entities (MPK18, MPK334 and YAK308) with Activity against Haemonchus contortus In Vitro

Due to widespread multi-drug resistance in parasitic nematodes of livestock animals, there is an urgent need to discover new anthelmintics with distinct mechanisms of action. Extending previous work, here we screened a panel of 245 chemically-diverse small molecules for anti-parasitic activity against Haemonchus contortus—an economically important parasitic nematode of livestock. This panel was screened in vitro against exsheathed third-stage larvae (xL3) of H. contortus using an established phenotypic assay, and the potency of select compounds to inhibit larval motility and development assessed in dose-response assays. Of the 245 compounds screened, three—designated MPK18, MPK334 and YAK308—induced non-wildtype larval phenotypes and repeatedly inhibited xL3-motility, with IC₅₀ values of 45.2 µM, 17.1 µM and 52.7 µM, respectively; two also inhibited larval development, with IC₅₀ values of 12.3 µM (MPK334) and 6.5 µM (YAK308), and none of the three was toxic to human liver cells (HepG2). These findings suggest that these compounds deserve further evaluation as nematocidal candidates. Future work should focus on structure–activity relationship (SAR) studies of these chemical scaffolds, and assess the in vitro and in vivo efficacies and safety of optimised compounds against adults of H. contortus.     

The Influence of Weakly Coordinating Cations on the O−H⋅⋅⋅O− Hydrogen Bond of Silanol-Silanolate Anions

The reaction of a saline phosphazenium hydroxide hydrate with siloxanes led to a novel kind of silanol-silanolate anions. The weakly coordinating behavior of the cation renders the formation of silanol-silanolate hydrogen bonds possible, which otherwise suffer from detrimental silanolate–oxygen cation interactions. We investigated the influence of various weakly coordinating cations on silanol-silanolate motifs, particularly with regard to different cation sizes. While large cations favor the formation of intramolecular hydrogen bonds resulting in cyclic structures, the less bulky tetramethyl ammonium cation encourages the formation of polyanionic silanol-silanolate chains in the solid state.     

Controlling Spin-Correlated Radical Pairs with Donor–Acceptor Dyads: A New Concept to Generate Reduced Metal Complexes for More Efficient Photocatalysis

One-electron reduced metal complexes derived from photoactive ruthenium or iridium complexes are important intermediates for substrate activation steps in photoredox catalysis and for the photocatalytic generation of solar fuels. However, owing to the heavy atom effect, direct photochemical pathways to these key intermediates suffer from intrinsic efficiency problems resulting from rapid geminate recombination of radical pairs within the so-called solvent cage. In this study, we prepared and investigated molecular dyads capable of producing reduced metal complexes via an indirect pathway relying on a sequence of energy and electron transfer processes between a Ru complex and a covalently connected anthracene moiety. Our test reaction to establish the proof-of-concept is the photochemical reduction of ruthenium(tris)bipyridine by the ascorbate dianion as sacrificial donor in aqueous solution. The photochemical key step in the Ru-anthracene dyads is the reduction of a purely organic (anthracene) triplet excited state by the ascorbate dianion, yielding a spin-correlated radical pair whose (unproductive) recombination is strongly spin-forbidden. By carrying out detailed laser flash photolysis investigations, we provide clear evidence for the indirect reduced metal complex generation mechanism and show that this pathway can outperform the conventional direct metal complex photoreduction. The further optimization of our approach involving relatively simple molecular dyads might result in novel photocatalysts that convert substrates with unprecedented quantum yields.     

Synthesis,Photophysics and PDT Evaluation of Mono‐, Di‐, Tri‐ and Hexa‐PEG Chlorins for Pointsource Photodynamic Therapy

Pointsource photodynamic therapy (PSPDT) is a newly developed fiber optic method aimed at the delivery of photosensitizer, light and oxygen to a diseased site. Because of a need for developing photosensitizers with desirable properties for PSPDT, we have carried out a synthetic, photophysical and phototoxicity study on a series of PEGylated sensitizers. Chlorin and pheophorbide sensitizers were readily amenable to our synthetic PEGylation strategy to reach triPEG and hexaPEG galloyl pheophorbides and mono‐, di‐, triPEG chlorins. On screening these PEG sensitizers, we found that increasing the number of PEG groups, except for hexaPEGylation, increases phototoxicity. We found that three PEG groups but not less or more were optimal. Of the series tested, a triPEG gallyol pheophorbide and a triPEG chlorin were the most efficient at generating singlet oxygen, and produced the highest phototoxicity and lowest dark toxicity to Jurkat cells. A detailed kinetic analysis of the PEGylated sensitizers in solution and cell culture and media is also presented. The data provide us with steps in the development of PSPDT to add to the PDT tools we have in general.     

Angular tolerance of Shack-Hartmann wavefront sensors with microaxicons

Wavefront sensing under nonparaxial conditions was studied with Shack-Hartmann setups based on arrays of microaxicons. The robustness of the generated pseudonondiffracting subbeams against tilt and axial displacement was demonstrated for ultraflat Gaussian- and inverse-Gaussian-shaped elements in transmission and reflection. To characterize slight aberrations and to identify optimum parameter fields, spatial moments of intensity profiles were analyzed with high sensitivity. Reflective design enables for wavefront sensing at oblique incidence as necessary for low-feedback detection and phase diagnostics of ultrashort pulses.     

Electronic properties of neutral dyes in the channels of zeolite L: a combined spectroscopic and quantum chemical study

Three low molecular weight model compounds for poly(phenylene-ethynylene)s were inserted into the channels of zeolite L by using gas phase insertion. The absorption and emission spectra in solution and dye/zeolite L are reported. Two compounds show emission properties in zeolite L comparable to that in solution. In contrast, the bipyridine containing compound shows a red shift toward longer excitation wavelengths. Matrix rank analysis of the emission spectra gave three contributing species. Quantum chemical calculations provide different conformations depending on the Si/Al distribution of the framework and the extraframework cations and attached protons.     

A direct and simple method of coupling matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) to thin-layer chromatography (TLC) for the analysis of phospholipids from egg yolk

Although the most important application of matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) is "proteomics," there is growing evidence that this soft ionization method is also useful for phospholipid (PL) analysis. Although all PLs are detectable by MALDI-TOF MS, some lipid classes, particularly those with quaternary amines such as phosphatidylcholines (PCs), are more sensitively detected than others, and these suppress the signals of less sensitively detected PLs when complex mixtures are analyzed. Therefore, a separation of the total organic extract into individual lipid classes is necessary. As MALDI uses a solid sample, the direct evaluation of thin-layer chromatography (TLC) plates is possible. We report here on a method of directly coupling MALDI-TOF MS and TLC that can be easily implemented on commercially available MALDI-TOF devices. A total extract of hen egg yolk is used as a simple PL mixture to demonstrate the capabilities of this method. It will be shown that "clean" spectra without any major contributions from fragmentation products and matrix peaks can be obtained, and that this approach is even sensitive enough to detect the presence of PLs at levels of less than 1% of the total extract.     

Multiparticle moves in acceptance rate optimized monte carlo

Molecular Dynamics (MD) and Monte Carlo (MC) based simulation methods are widely used to investigate molecular and nanoscale structures and processes. While the investigation of systems in MD simulations is limited by very small time steps, MC methods are often stifled by low acceptance rates for moves that significantly perturb the system. In many Metropolis MC methods with hard potentials, the acceptance rate drops exponentially with the number of uncorrelated, simultaneously proposed moves. In this work, we discuss a multiparticle Acceptance Rate Optimized Monte Carlo approach (AROMoCa) to construct collective moves with near unit acceptance probability, while preserving detailed balance even for large step sizes. After an illustration of the protocol, we demonstrate that AROMoCa significantly accelerates MC simulations in four model systems in comparison to standard MC methods. AROMoCa can be applied to all MC simulations where a gradient of the potential is available and can help to significantly speed up molecular simulations. © 2015 Wiley Periodicals, Inc.