Protocol for in vitro transcribing mRNAs with defined poly(A)-tail lengths and visualizing sequential PABP binding.

Quantifying the number of proteins that interact with mRNAs, in particular with poly(A) tails of mRNAs, is crucial for understanding gene regulation. Biochemical assays offer significant advantages for this purpose. Here, we present a protocol for synthesizing mRNAs with accurate, length-specific poly(A) tails through a PCR-based approach.

Long range segmentation of prokaryotic genomes by gene age and functionality.

Bacterial and archaeal genomes encompass numerous operons that typically consist of two to five genes. On larger scales, however, gene order is poorly conserved through the evolution of prokaryotes. Nevertheless, non-random localization of different classes of genes on prokaryotic chromosomes could reflect important functional and evolutionary constraints.

Biofilm Disruption from within: Light-Activated Molecular Drill-Functionalized Polymersomes Bridge the Gap between Membrane Damage and Quorum Sensing-Mediated Cell Death.

Bacterial biofilms represent an escalating global health concern with the proliferation of drug resistance and hospital-acquired infections annually. Numerous strategies are under exploration to combat biofilms and preempt the development of antibacterial resistance. Among these, mechanical disruption of biofilms and enclosed bacteria presents a promising avenue, aiming to induce membrane permeabilization and consequent lethal damage.

Positional Information-Based Organization of Surfactant Droplet Swarms Emerging from Competition Between Local and Global Marangoni Effects.

Positional information is key for particles to adapt their behavior based on their position in external concentration gradients, and thereby self-organize into complex patterns. Here, position-dependent behavior of floating surfactant droplets that self-organize in a pH gradient is demonstrated, using the Marangoni effect to translate gradients of surface-active molecules into motion. First, fields of surfactant microliter-droplets are generated, in which droplets floating on water drive local, outbound Marangoni flows upon dissolution of surfactant and concomitantly grow myelin filaments.

Putting a cap on the glycome: Dissecting human sialyltransferase functions.

Human glycans are capped with sialic acids and these nine-carbon sugars mediate many of the biological functions and interactions of glycans. Structurally diverse sialic acid caps mark human cells as self and they form the ligands for the Siglec immune receptors and other glycan-binding proteins. Sialic acids enable host interactions with the human microbiome and many human pathogens utilize sialic acids to infect host cells.

Getting a molecular grip on the half-lives of iminothioindoxyl photoswitches.

Visible-light-operated photoswitches are of growing interest in reversibly controlling molecular processes, enabling for example the precise spatiotemporal focusing of drug activity and manipulating the properties of materials. Therefore, many research efforts have been spent on seeking control over the (photo)physical properties of photoswitches, in particular the absorption maxima and the half-life. For photopharmacological applications, photoswitches should ideally be operated by visible light in at least one direction, and feature a metastable isomer with a half-life of 0.

Structure and fragmentation chemistry of the peptide radical cations of glycylphenylalanylglycine (GFG).

Herein, we explore the generation and characterization of the radical cations of glycylphenylalanylglycine, or [GFG]•+, formed via dissociative electron-transfer reaction from the tripeptide to copper(II) within a ternary complex. A comprehensive investigation employing isotopic labeling, infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations elucidated the details and energetics in formation of the peptide radical cations as well as their dissociation products. Unlike conventional aromatic-containing peptide radical cations that primarily form canonical π-radicals, our findings reveal that 75% of the population of the experimentally produced [GFG]•+ precursors are [GFα•G]+, where the radical resides on the middle α-carbon of the phenylalanyl residue.

Modulation of the isomerization of iminothioindoxyl switches by supramolecular confinement.

Here we present the formation of an iminothioindoxyl (ITI)⊂Cage complex that retains the photochemical properties of the photoswitch within a confined environment in water. At the same time, besides ultrafast switching inside the cage, the ITI photoswitch displays an intriguing bifurcation of the excited state isomerization pathway when encapsulated.

Origin of the Felkin-Anh(-Eisenstein) model: a quantitative rationalization of a seminal concept.

Quantum chemical calculations were carried out to quantitatively understand the origin of the Felkin-Anh(-Eisenstein) model, widely used to rationalize the π-facial stereoselectivity in the nucleophilic addition reaction to carbonyl groups directly attached to a stereogenic center. To this end, the possible approaches of cyanide to both ()-2-phenylpropanal and ()-3-phenylbutan-2-one have been explored in detail. With the help of the activation strain model of reactivity and the energy decomposition analysis method, it is found that the preference for the Felkin-Anh addition is mainly dictated by steric factors which manifest in a less destabilizing strain-energy rather than, as traditionally considered, in a lower Pauli repulsion.

Noncovalent Interactions Steer the Formation of Polycyclic Aromatic Hydrocarbons.

Aromatic molecules play an important role in the chemistry of astronomical environments such as the cold interstellar medium (ISM) and (exo)planetary atmospheres. The observed abundances of (polycyclic) aromatic hydrocarbons such as benzonitrile and cyanonaphthalenes are, however, highly underestimated by astrochemical models. This demonstrates the need for more experimentally verified reaction pathways.

Infrared Spectroscopic Characterization of Early 4d Transition Metal Carbene Cations, ZrCH and NbCH.

IR multiple-photon dissociation (IRMPD) action spectroscopy is combined with quantum chemical calculations to examine the [M,C,2H] species for the early 4d metals, M = Zr and Nb. These ions were formed by reacting laser ablated M ions with cyclopropane (-CH) in a molecular beam apparatus. Both IRMPD spectra exhibit one major band near 700 cm and a second weaker band at about twice that wavenumber, more evident when irradiated in focus.

Effect of Preparation Methods on the Interface of LiBH/SiO Nanocomposite Solid Electrolytes.

Nanocomposites of complex metal hydrides and oxides are promising solid state electrolytes. The interaction of the metal hydride with the oxide results in a highly conducting interface layer. Up until now it has been assumed that the interface chemistry is independent of the nanoconfinement method.

Quantifying Organic Cation Ratios in Metal Halide Perovskites: Insights from X-ray Photoelectron Spectroscopy and Nuclear Magnetic Resonance Spectroscopy.

The employment of metal halide perovskites (MHPs) in various optoelectronic applications requires the preparation of thin films whose composition plays a crucial role. Yet, the composition of the MHP films is rarely reported in the literature, partly because quantifying the actual organic cation composition cannot be done with conventional characterization methods. For MHPs, NMR has gained popularity, but for films, tedious processes like scratching several films are needed.

With or without a co-solvent? highly efficient ultrafast phenanthrenequinone-electron rich alkene (PQ-ERA) photoclick reactions.

The light-induced photocycloaddition of 9,10-phenanthrenequinone (PQ) with electron-rich alkenes (ERA), known as the PQ-ERA reaction, is a highly attractive photoclick reaction characterized by its operational simplicity and high biocompatibility. One essential aspect of photoclick reactions is their high rate, however the limited solubility of PQs often requires the use of a co-solvent. Evaluating the effect of different co-solvents on the PQ-ERA reaction and their influence on the reaction rate, we discovered that sulfur-containing compounds, in particular the frequently used solubilizing co-solvent DMSO, quench the triplet state of the PQ.

Zero-Point-Energy Driven Isotopic Exchange of the [HO] anion Probed by Mid-Infrared Action Spectroscopy.

We present the first observation of vibrational transitions in the [HO] anion, an intermediate in the anion-molecule reaction of water, HO, and hydride, H, using a laser-induced isotopic H/D exchange reaction action spectroscopy scheme applied to anions. The observed bands are assigned as the fundamental and first overtone of the HO-H vibrational stretching mode, based on anharmonic calculations within the vibrational perturbation theory and vibrational configuration interaction. Although the DO·D species has the lowest energy, our experiments confirm the DO·H isotope to be a sink of the H/D exchange reaction.

The nature of metallophilic interactions in closed-shell d-d metal complexes.

We have quantum chemically analyzed the closed-shell d-d metallophilic interaction in dimers of square planar [M(CO)X] complexes (M = Ni, Pd, Pt; X = Cl, Br, I) using dispersion-corrected density functional theory at ZORA-BLYP-D3(BJ)/TZ2P level of theory. Our purpose is to reveal the nature of the [X(CO)M]⋯[M(CO)X] bonding mechanism by analyzing trends upon variations in M and X. Our analyses reveal that the formation of the [M(CO)X] dimers is favored by an increasingly stabilizing electrostatic interaction when the M increases in size and by more stabilizing dispersion interactions promoted by the larger X.

Controlling Reactivity through Spin Manipulation: Steric Bulkiness of Peroxocobalt(III) Complexes.

The intrinsic relationship between spin states and reactivity in peroxocobalt(III) complexes was investigated, specifically focusing on the influence of steric modulation on supporting ligands. Together with the previously reported [Co(TBDAP)(O)] (), which exhibits spin crossover characteristics, two peroxocobalt(III) complexes, [Co(MDAP)(O)] () and [Co(ADDAP)(O)] (), bearing pyridinophane ligands with distinct -substituents such as methyl and adamantyl groups, were synthesized and characterized. By manipulating the steric bulkiness of the -substituents, control of spin states in peroxocobalt(III) complexes was demonstrated through various physicochemical analyses.

Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry.

The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is often a bottleneck. Here, we report on the interface between a continuous stirred-tank reactor, in which an immobilized enzymatic network made of 12 enzymes is compartmentalized, and an ion mobility-mass spectrometer.

Laboratory infrared spectra and fragmentation chemistry of sulfur allotropes.

Sulfur is one of six life-essential elements, but its path from interstellar clouds to planets and their atmospheres is not well known. Astronomical observations in dense clouds have so far been able to trace only 1 percent of cosmic sulfur, in the form of gas phase molecules and volatile ices, with the missing sulfur expected to be locked in a currently unidentified form. The high sulfur abundances inferred in icy and rocky solar system bodies indicate that an efficient pathway must exist from volatile atomic sulfur in the diffuse interstellar medium to some form of refractory sulfur.

Simulating the Motion Underlying the Mechanism of Thioredoxin Reductase.

Thioredoxin reductase (TrxR) is an essential antioxidant in most cells; it reduces thioredoxin (Trx) and several more substrates, utilizing NADPH. However, the enzyme's internal active site is too small to accommodate the Trx substrate. Thus, TrxR evolved a disulfide shuttle that can carry reducing equivalents from the active site to the docking site of thioredoxin on the enzyme surface.

Liquid crystals from curved colloidal rods: waves, twists and more.

The curvature of elongated microscopic building blocks plays a crucial role on their self-assembly into orientationally ordered phases. While rod-like molecules form a handful of liquid crystal (LC) phases, curved or banana-shaped molecules show more than fifty phases, with fascinating physical properties, such as chirality or polarity. Despite the fundamental and technological importance of these so-called 'banana-shaped liquid crystals', little is known about their microscopic details at the single-molecule level.

How Droplets Can Accelerate Reactions─Coacervate Protocells as Catalytic Microcompartments.

ConspectusCoacervates are droplets formed by liquid-liquid phase separation (LLPS) and are often used as model protocells-primitive cell-like compartments that could have aided the emergence of life. Their continued presence as membraneless organelles in modern cells gives further credit to their relevance. The local physicochemical environment inside coacervates is distinctly different from the surrounding dilute solution and offers an interesting microenvironment for prebiotic reactions.

Myelin Surfactant Assemblies as Dynamic Pathways Guiding the Growth of Electrodeposited Copper Dendrites.

Self-organization of inorganic matter enables bottom-up construction of materials with target shapes suited to their function. Positioning the building blocks in the growth process involves a well-balanced interplay of the reaction and diffusion. Whereas (supra)molecular structures have been used to template such growth processes, we reasoned that molecular assemblies can be employed to actively create concentration gradients that guide the deposition of solid, wire-like structures.

Magnon-phonon Fermi resonance in antiferromagnetic CoF.

Understanding spin-lattice interactions in antiferromagnets is a critical element of the fields of antiferromagnetic spintronics and magnonics. Recently, coherent nonlinear phonon dynamics mediated by a magnon state were discovered in an antiferromagnet. Here, we suggest that a strongly coupled two-magnon-one phonon state in this prototypical system opens a novel pathway to coherently control magnon-phonon dynamics.