RNA Ligation for Mono and Dually Labeled RNAs

Labeled RNAs are invaluable probes for investigation of RNA function and localization. However, mRNA labeling remains challenging. Here, we developed an improved method for 3′-end labeling of in vitro transcribed RNAs. We synthesized novel adenosine 3′,5′-bisphosphate analogues modified at the N6 or C2 position of adenosine with an azide-containing linker, fluorescent label, or biotin and assessed these constructs as substrates for RNA labeling directly by T4 ligase or via postenzymatic strain-promoted alkyne-azide cycloaddition (SPAAC). All analogues were substrates for T4 RNA ligase. Analogues containing bulky fluorescent labels or biotin showed better overall labeling yields than postenzymatic SPAAC. We successfully labeled uncapped RNAs, NAD-capped RNAs, and 5′-fluorescently labeled m⁷Gp₃A_m-capped mRNAs. The obtained highly homogenous dually labeled mRNA was translationally active and enabled fluorescence-based monitoring of decapping. This method will facilitate the use of various functionalized mRNA-based probes.     

Reaction of N-(Benzyloxycarbonyl)aminobenzyl-phosphonous Acid with Ethyl Orthoformate

Reaction of N-(benzyloxycarbonyl)aminobenzylphosphonous acid with ethyl orthoformate afforded two major products diethyl N-(benzyloxycarbonyl)aminobenzylphosphhite and ethyl (diethoxymethyl)[N-(benzyloxy-carbonyl)aminobenzyl]phosphmate, a product of addition of phosphonous acid to orthoformate.     

Alkylation of Potassium 1-(N-Benzyloxycarbonylamino)alkylphosphonates and Phosphinates in the Presence of 18-Crown-6

During past several years we have been engaged in the synthesis of phosphono peptides, peptide analogues with phosphonic acid replacing C-terminal or N-terminal carboxylate moiety. These compounds are of interest not only because of their promise of direct practical applications^1,2 but also as a source of information about mechanisms of enzymatic reactions. ^1,3–5 Esters of N-blocked 1 -aminoalkylphosphonic and phosphinic acids are popularly used as starting substrates in multistep syntheses of phosphono peptides.^6–9 Although several methods for their preparation have been described ^6,10–13 the search for the new and useful methods of their synthesis is still in progress. In this paper we report that the use of complexes of potassium 1-(N- benzyloxycarbonylamiuo)alkylphosphonates and phosphates with 18-crown-6 as nucleophiles in the reaction with alkyl halides afforded the desired esters in good yields.     

Atomic Hydrogen Induced Chemical Vapor Deposition of Silicon Oxycarbide Thin Films Derived from Diethoxymethylsilane Precursor

Amorphous silicon oxycarbide (a-SiOC:H) films produced by remote plasma RPCVD from diethoxymethylsilane (DEMS) were characterized in terms of their basic properties related to the coatings deposited using conventional plasma enhanced PECVD method. The effect of substrate temperature (T_S) on the growth rate, chemical composition, structure, and properties of resulting a-SiOC:H films is reported. Film growth is an adsorption-controlled process, wherein two mechanisms can be distinguished with a transition at about T_S=70°C. Depending on the temperature, films of different nature can be obtained, from polymer-like to highly crosslinked material with C-Si-O network. The chemical structure of a-SiOC:H films was characterized by FTIR, ¹³C and ²⁹Si solid-state NMR, and X-ray photoelectron spectroscopes. The a-SiOC:H films were also characterized in terms of their density, refractive index, surface morphology, conformality of coverage, hardness, adhesion to a substrate, and friction coefficient. The films were found to be morphologically homogeneous materials exhibiting good conformality of coverage and small surface roughness. Their refractive index exhibits anomalous effect revealing a minimum value at T_S=125°C. Due to their exceptional physical properties a-SiOC:H films produced by RPCVD from DEMS precursor seems to be useful as potential dielectric materials or coatings for various encapsulation applications.     

Optimization of CuW alloy electrodeposition towards high-tungsten content

With the help of the factorial design of experiments, optimization of the deposition of the CuW alloy was successfully done. The important deposition parameters were identified as pH, current density, and—the most important one—copper ion concentration. All of them were examined in their wide ranges. Under optimal conditions, in a citrate bath, with copper ion concentration of 1.0 mM, at current density of −100 mA cm⁻² and at pH ca. 8.3, the alloy layer had the highest tungsten content (circa 30 wt.%), satisfactory adhesion and a smooth and crackless morphology. The structure of the electrodeposited alloy can be described as an amorphous solid solution of Cu in W with built-in Cu nanocrystals.

     

Erratum to: “Comparative studies of Pd, Ru, Ni, Cu/ZnAl2O4 catalysts for the water gas shift reaction”

The original version of the article was published in Cent. Eur. J. Chem. 11(6) (2013) pp. 912–919. Unfortunately, the original version of this article contains a mistake in the Acknowledgement section. It should be written as “Partially financed from grant number 0680/B/H03/2011/40 and gratefully acknowledged. Pawe? Mierczyński is a participant of START Programme.”     

Magnetic resonance study of annealed and rinsed N-doped TiO2 nanoparticles

Nanoparticles of nitrogen-modified TiO₂ (N-doped TiO₂) calcined at 300°C and 350°C, have been prepared with and without water rinsing. Samples were characterized by x-ray diffractrometry (XRD) and optical spectroscopy. The electron paramagnetic resonance (EPR) spectra from centers involving oxygen vacancies were recorded for all samples. These could be attributed to paramagnetic surface centers of the hole type, for example to paramagnetic oxygen radicals O^?, O₂ ^? etc. The concentration of these centers increased after water rising and it further increased for samples annealed at higher temperature. Additionally, for samples calcined at 300°C, and calcined at 350°C and rinsed, the EPR spectra evidenced the presence of magnetic clusters of Ti³⁺ ions. The photocatalytic activity of samples was studied towards phenol decomposition under unltraviolet-visible (UV-Vis) irradiation. It was found that, in comparison to the starting materials, the rinsed materials showed increased photocatalytic activity towards phenol oxidation. The light absorption (UV-Vis/DRS) as well as surface Fourier transform infrared/diffuse reflectance spectroscopy (FTIR/DR) studies confirmed a significantly enhanced light absorption and the presence of nitrogen groups on the photocatalysts surfaces, respectively. A significant increase of concentration of paramagnetic centers connected with oxygen vacancies after water rising has had an essential influence on increasing their photocatalytic activity.      

Comparative studies of Pd, Ru, Ni, Cu/ZnAl2O4 catalysts for the water gas shift reaction

The activity of monometallic Pd, Ru, Ni and Cu catalysts supported on spinel ZnAl₂O₄ for water gas shift reaction (WGS) was investigated. The physicochemical properties of each catalyst was studied by XRD, TPR, BET and chemisorption methods. The highest activity was obtained for Cu/ZnAl₂O₄ among the catalysts tested. The activation process carried out in a reducing atmosphere 5%H₂-95%Ar in the case of Cu/ZnAl₂O₄ system lead to the catalytic activity improvement. In the case of copper catalysts, the water gas shift reaction proceeded by the redox surface mechanism between Cu⁰/Cu⁺. The PdZn alloy formation after reduction at 350°C was shown.      

Coffee-ring effects in laser desorption/ionization mass spectrometry

This report focuses on the heterogeneous distribution of small molecules (e.g. metabolites) within dry deposits of suspensions and solutions of inorganic and organic compounds with implications for chemical analysis of small molecules by laser desorption/ionization (LDI) mass spectrometry (MS). Taking advantage of the imaging capabilities of a modern mass spectrometer, we have investigated the occurrence of “coffee rings” in matrix-assisted laser desorption/ionization (MALDI) and surface-assisted laser desorption/ionization (SALDI) sample spots. It is seen that the “coffee-ring effect” in MALDI/SALDI samples can be both beneficial and disadvantageous. For example, formation of the coffee rings gives rise to heterogeneous distribution of analytes and matrices, thus compromising analytical performance and reproducibility of the mass spectrometric analysis. On the other hand, the coffee-ring effect can also be advantageous because it enables partial separation of analytes from some of the interfering molecules present in the sample. We report a “hidden coffee-ring effect” where under certain conditions the sample/matrix deposit appears relatively homogeneous when inspected by optical microscopy. Even in such cases, hidden coffee rings can still be found by implementing the MALDI-MS imaging technique. We have also found that to some extent, the coffee-ring effect can be suppressed during SALDI sample preparation.