Effect of Alkynyl Group on Reactivity in Photoaffinity Labeling with 2-Thienyl-Substituted α-Ketoamide

Minimalist photo-reactive probes, which consist of a photo-reactive group and a tag for detection of target proteins, are useful tools in chemical biology. Although several diazirine-based and aryl azide-based minimalist probes are available, no keto-based minimalist probe has yet been reported. Here we describe minimalist probes based on a 2-thienyl-substituted α-ketoamide bearing an alkyne group on the thiophene ring. The 3-alkyne probe showed the highest photo-affinity labeling efficiency.     

Revisiting the Rate-Limiting Step of the ANS–Protein Binding at the Protein Surface and Inside the Hydrophobic Cavity

8-Anilino-1-naphthalenesulfonic acid (ANS) is used as a hydrophobic fluorescence probe due to its high intensity in hydrophobic environments, and also as a microenvironment probe because of its unique ability to exhibit peak shift and intensity change depending on the surrounding solvent environment. The difference in fluorescence can not only be caused by the microenvironment but can also be affected by the binding affinity, which is represented by the binding constant (K). However, the overall binding process considering the binding constant is not fully understood, which requires the ANS fluorescence binding mechanism to be examined. In this study, to reveal the rate-limiting step of the ANS–protein binding process, protein concentration-dependent measurements of the ANS fluorescence of lysozyme and bovine serum albumin were performed, and the binding constants were analyzed. The results suggest that the main factor of the binding process is the microenvironment at the binding site, which restricts the attached ANS molecule, rather than the attractive diffusion-limited association. The molecular mechanism of ANS–protein binding will help us to interpret the molecular motions of ANS molecules at the binding site in detail, especially with respect to an equilibrium perspective.     

ESR and calculations on electronic structure of phenalenyl and phenalenyl derivative radicals

Calculations on electronic structure of the perinaphthenyl radical and phenalenyl derivative radicals responsible for the composition of the ESR spectrum of marine diesel under heating were performed to obtain support for the experimental ESR results. The parameters calculated were the hyperfine coupling constants (A), which were then used for comparison with the experimental data. The energy‐minimized structures were obtained using the density functional theory method. In all cases, the symmetry system was taken into account in theoretical calculations. The differences between experimental and theoretical values were below 7% for nearest hydrogens in molecules, named hyperfine coupling constant A (first neighbors) and 18% for farthest hydrogens atoms named hyperfine coupling constants A′ (second neighbors), for all structures analyzed. Copyright © 2014 John Wiley & Sons, Ltd.     

Carbon fibers prepared from tailored reversible‐addition‐fragmentation transfer copolymerization‐derived poly(acrylonitrile)‐co‐poly(methylmethacrylate)

Reversible‐addition fragmentation‐transfer (RAFT) polymerization of acrylonitrile (AN) was performed with 2‐(2‐cyano‐2‐propyl‐dodecyl)trithiocarbonate as RAFT agent and azobis(isobutyronitrile) as initiator. Linear polyacrylonitrile (M_n = 133,000 g/mol, PDI = 1.34) was prepared within 7 h in 86% isolated yield. High‐yield copolymerization with methyl methacrylate (MMA) was performed and copolymerization parameters were determined according to Kelen and Tüdös at 90 °C in ethylene carbonate yielding r_AN = 0.2 and r_MMA = 0.42. The molecular weights, polydispersity indices (PDIs), and MMA content of the copolymer were adjusted in a way that precursor fibers could be prepared via wet spinning. These precursor fibers had round cross‐sections and a dense morphology, showing tenacities of 40–50 cN/tex and elastic moduli of 900–1000 cN/tex at a fineness of 1 dtex and an elongation of 13–17%. Precursor fibers were oxidatively stabilized and then carbonized at different temperatures. A maximum tensile strength of 2.5 GPa was reached at 1350 °C. Thermal analysis, infrared and Raman spectroscopy, wide‐angle X‐ray scattering, scanning electron microscopy, and tensile testing were used to characterize the resulting carbon fibers. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 1322–1333     

Control of the Orientation and Photoinduced Phase Transitions of Macrocyclic Azobenzene

Photoinduced phase transitions caused by photochromic reactions bring about a change in the state of matter at constant temperature. Herein, we report the photoinduced phase transitions of crystals of a photoresponsive macrocyclic compound bearing two azobenzene groups ( 1 ) at room temperature on irradiation with UV (365 nm) and visible (436 nm) light. The trans/trans isomer undergoes photoinduced phase transitions (crystal–isotropic phase–crystal) on UV light irradiation. The photochemically generated crystal exhibited reversible phase transitions between the crystal and the mesophase on UV and visible light irradiation. The molecular order of the randomly oriented crystals could be increased by irradiating with linearly polarized visible light, and the value of the order parameter was determined to be ?0.84. Heating enhances the thermal cis‐to‐trans isomerization and subsequent cooling returned crystals of the trans/trans isomer.     

The existence of a 2‐factor in K1, n‐free graphs with large connectivity and large edge‐connectivity

In this article, we study the existence of a 2‐factor in a K_{1, n}‐free graph. Sumner [J London Math Soc 13 (1976), 351–359] proved that for n?4, an (n?1)‐connected K_{1, n}‐free graph of even order has a 1‐factor. On the other hand, for every pair of integers m and n with m?n?4, there exist infinitely many (n?2)‐connected K_{1, n}‐free graphs of even order and minimum degree at least m which have no 1‐factor. This implies that the connectivity condition of Sumner's result is sharp, and we cannot guarantee the existence of a 1‐factor by imposing a large minimum degree. On the other hand, Ota and Tokuda [J Graph Theory 22 (1996), 59–64] proved that for n?3, every K_{1, n}‐free graph of minimum degree at least 2n?2 has a 2‐factor, regardless of its connectivity. They also gave examples showing that their minimum degree condition is sharp. But all of them have bridges. These suggest that the effects of connectivity, edge‐connectivity and minimum degree to the existence of a 2‐factor in a K_{1, n}‐free graph are more complicated than those to the existence of a 1‐factor. In this article, we clarify these effects by giving sharp minimum degree conditions for a K_{1, n}‐free graph with a given connectivity or edge‐connectivity to have a 2‐factor. Copyright © 2010 Wiley Periodicals, Inc. J Graph Theory 68:77‐89, 2011     

Theory of phase dynamics in intrinsic Josephson junctions with multigap superconducting layers

We construct a theory of dynamical behavior in intrinsic Josephson junction stacks with multigap superconducting layers. The theory predicts the existence of two kinds of phase modes, one of which is the Josephson-plasma mode and other of which is the Leggett’s mode. We discuss a cooperative phenomena induced by inter-band Josephson coupling in addition to capacitive and inductive couplings between the superconducting layers.     

Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.