Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA

Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.     

Alkylsulfanylphenyl derivatives of cytosine and 7-deazaadenine nucleosides, nucleotides and nucleoside triphosphates: synthesis, polymerase incorporation to DNA and electrochemical study

Aqueous Suzuki–Miyaura cross‐coupling reactions of halogenated nucleosides, nucleotides and nucleoside triphosphates derived from 5‐iodocytosine and 7‐iodo‐7‐deazaadenine with methyl‐, benzyl‐ and tritylsufanylphenylboronic acids gave the corresponding alkylsulfanylphenyl derivatives of nucleosides and nucleotides. The modified nucleoside triphosphates were incorporated into DNA by primer extension by using Vent(exo‐) polymerase. The electrochemical behaviour of the alkylsulfanylphenyl nucleosides indicated formation of compact layers on the electrode. Modified nucleotides and DNA with incorporated benzyl‐ or tritylsulfanylphenyl moieties produced signals in [Co(NH₃)₆]³⁺ ammonium buffer, attributed to the Brdi?ka catalytic response, depending on the negative potential applied. Repeated constant current chronopotentiometric scans in this medium showed increased Brdi?ka catalytic response, which suggests the deprotection of the alkylsulfanyl derivatives to free thiols under the conditions.     

pH buffer assessment and Pitzer��s equations

Traceable measurement of the quantity pH in media outside the limits of the recent IUPAC recommendation requires an alternative to the Bates?CGuggenheim convention. The Pitzer??s approach to ion interactions is widely appraised and offers a suitable approach to the estimation of single-ion activity coefficients. For this purpose, the underlying electrolyte data need to be consistent and the uncertainty in existing Pitzer??s data needs to be assessed. Such an assessment is attempted in this study for pH in potassium acetate buffer medium. The re-evaluation of Pitzer??s data from potassium nitrate data revealed inconsistencies and wide uncertainty margins. The uncertainty contribution from binary Pitzer??s parameters to an assessment of pH in seawater resulted in an uncertainty in pH of about 0.03 (95% confidence interval). This contribution has to be taken into account in the overall uncertainty budget. Lack of appropriate data for other pH buffer systems (e.g., phosphate buffers) is noted.     

Stability for Lie–Trotter products for some operator matrix semigroups

Coupled systems of linear differential equations in Banach spaces can be often handled by the theory of C₀-semigroups of operator matrices. We study the stability of Lie–Trotter products of such matrix semigroups, and present three classes of examples (abstract delay equations, abstract inhomogeneous equations, abstract dynamic boundary value problems) and some open problems. This survey is based on the papers [1], [2] and [5], to which we refer the interested reader for more details and extensive bibliographical information. (© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Experimental study of Fe–C–O based system below 1000 °C

The paper deals with the study of phase transformation temperatures of Fe (Fe–C–O) based metallic alloys. Six model alloys with graded carbon and oxygen content were used for experimental investigation. Low-temperature region (<1000 °C) was the investigated area. Phase transformation temperatures were obtained using Differential thermal analysis and Setaram Setsys 18_TM laboratory system. Controlled heating was conducted at the rates of 2, 4, 7, 10, 15, 20 °C min^?1. Region of eutectoid transformation (Fe_α(C) + Fe₃C → Fe_γ(C)), alpha–gamma (Fe_α(C) → Fe_γ(C)) and transformation Fe_α(O) + Fe_0.92O → Fe_γ(O) + Fe_0.92O was studied. New original data (phase transformation temperatures) were obtained in this study. The relationship between shift of phase transformation temperatures and chemical composition (mainly carbon and oxygen content) is investigated in this paper. To achieve good approximation to the equilibrium conditions, the extrapolation of the obtained phase transformation temperatures to the zero heating rate was performed. The influence of experimental conditions (heating rate) on temperatures of phase transformations was studied as well. Comparison of the obtained experimental data with the data presented in the accessible literature and IDS calculations (Solidification Analysis Package) was carried out. It follows from literature search that there is a lack of thermo-physical and thermo-dynamical data on Fe–C–O system.     

Anatase–rutile transformation at the synthesis of rutile pigments (Ti,Cr,Nb)O2 and their color properties

Synthesis of rutile pigments is based on solid state reaction and on Hedvall effect, i.e., phase transformation from anatase to rutile. Therefore, it is important to know the thermal behavior of these compounds (the temperature of this change). The goal was to prepare rutile pigments of type Ti_1?3xCr_xNb_2xO_2+x/2 by conventional solid state method from titanium dioxide TiO₂ (AV-01, anatase), to determine an influence of composition (x = 0, 0.05, 0.10, 0.20, 0.30, 0.50) and calcination temperature (850; 900; 950; 1,000; 1,050; 1,100; 1,150 °C) on color properties of these compounds and to analyze other starting compounds of titanium (hydrated anatase paste TiO₂·nH₂O, titanyl sulfate dihydrate TiOSO₄·2H₂O (VKR 611), hydrated sodium titanium oxide paste Na₂Ti₄O₉·nH₂O) and their reaction mixtures for x = 0.05 by simultaneous TG–DTA analysis. According to the highest chroma C of color, the optimal conditions for synthesis of these pigments are concentration x = 0.05 and calcination temperature 1,050 °C and higher. It was observed that initial temperature 760–830 °C is needful for a formation of rutile structure. This temperature is the lowest for hydrated Na₂Ti₄O₉ paste (760 °C) and similar for other starting compounds of titanium.     

Versatile Inclusion Behaviour of a Dinitrocalix[4]arene Having Two Ester Pendants – Preparation and X-ray Crystal Structures of Complexes

An upper-rim dinitro-substituted calix[4]arene possessing two lower-rim ethyl ester pendant groups (1) has been shown to form solid inclusion compounds with acetone (1:1) (1a), DMF (1:1) (1b), DMSO (1:1) (1c) and n-BuOH (2:1) (1d). X-ray crystal structures of the four complexes 1a–d are reported and comparatively discussed, including isostructurality calculations. Although the solid-state conformation of the dinitrocalix[4]arene moiety, stabilized by two intramolecular O–H…O bonds, is maintained in the four inclusion compounds, and all four co-crystals have similar unit cell dimensions and identical space group symmetries, only three of them (1a–c) are homostructural. Depending on the nature of the guest molecule, either the upper or the lower rim site of the calixarene is involved in the complexation, demonstrating either cavitate- or clathrate-type of supramolecular interactions, respectively. Moreover, due to the different guest recognition modes, the calixarene host in 1d is rotated through a non-crystallographic virtual rotation of 180° within the unit cell, in relation to the host molecules in each of the other three homostructural compounds 1a–c, thus giving rise to supramolecular morphotropism – to our knowledge the first case ever described.     

High-resolution monolithic columns—a new tool for effective and quick separation

This work describes a comparison of three types of commercial high-performance liquid chromatography silica monolithic columns with different inner diameters and generations of monolithic sorbent: a “classic” monolithic column, the first generation (Onyx? monolithic C₁₈, 100 mm?×?4.6 mm, Phenomenex); a “narrow” monolithic column for fast separation at lower flow rates (Chromolith® Performance RP-18e, 100 mm?×?3 mm, Merck); and a recently introduced “high-resolution” monolithic column, the next generation (Chromolith® HighResolution RP-18e, 100 mm?×?4.6 mm, Merck). Separation efficiency (number of theoretical plates, height equivalent to a theoretical plate and van Deemter curves), working pressure, the symmetry factor and resolution were critical aspects of the comparison in the case of the separation of ascorbic acid, paracetamol and caffeine. The separations were performed under isocratic conditions with a mobile phase consisting of 10:90 (v/v) acetonitrile–phosphoric acid (pH 2.80). Detailed comparison of the newest-generation monolithic column (Chromolith® HighResolution) with the previously introduced monolithic sorbents was performed and proved the advantages of the Chromolith® HighResolution column.

Optimization in multidimensional gas chromatography applying quantitative analysis via a stable isotope dilution assay

Trace level analyses in complex matrices benefit from heart-cut multidimensional gas chromatographic (MDGC) separations and quantification via a stable isotope dilution assay. Minimization of the potential transfer of co-eluting matrix compounds from the first dimension (¹D) separation into the second dimension separation requests narrow cut-windows. Knowledge about the nature of the isotope effect in the separation of labeled and unlabeled compounds allows choosing conditions resulting in at best a co-elution situation in the ¹D separation. Since the isotope effect strongly depends on the interactions of the analytes with the stationary phase, an appropriate separation column polarity is mandatory for an isotopic co-elution. With 3-alkyl-2-methoxypyrazines and an ionic liquid stationary phase as an example, optimization of the MDGC method is demonstrated and critical aspects of narrow cut-window definition are discussed.

Critical investigation of the substituent distribution in the polymer chains of hydroxypropyl methylcelluloses by (LC-)ESI-MS

Three hydroxypropyl methylcellulose samples (HPMC1–3, DS_Me?=?1.45, 1.29, and 1.36; MS_HP?=?0.28, 0.46, and 0.84) were analyzed with respect to their methyl and hydroxypropyl substitution pattern in the polymer chains. Ionization yield of HPMC oligomers in electrospray ionization ion trap mass spectrometry (ESI-IT-MS) is strongly influenced by the hydroxypropyl pattern. Therefore, a sample derivatization procedure, as well as suitable measurement conditions that enable relative quantification were elaborated. Analysis was performed by negative ESI-IT-MS after per(deutero)methylation, partial depolymerization, and reductive amination with m-aminobenzoic acid. Measurement parameters like solvent, trap drive, and voltages of the ion transportation unit were studied with regard to the suitability for quantitative evaluation. Using direct infusion of the samples, strong influence of trap drive and octopole settings was observed. Optimized measurement conditions were used for the determination of the HP pattern of the permethylated samples by direct infusion. The methyl pattern was determined from the perdeuteromethylated samples by high-performance liquid chromatography–electrospray tandem mass spectrometry. For HPMC1, substituents were both found to fit the random distribution model. The other two samples showed pronounced heterogeneity which could be interpreted in more detail by extracting methyl subpatterns depending on the number of HP groups.