Light-induced conformational change and product release in DNA repair by (6-4) photolyase

Proteins of the cryptochrome/photolyase family share high sequence similarities, common folds, and the flavin adenine dinucleotide (FAD) cofactor, but exhibit diverse physiological functions. Mammalian cryptochromes are essential regulatory components of the 24 h circadian clock, whereas (6-4) photolyases recognize and repair UV-induced DNA damage by using light energy absorbed by FAD. Despite increasing knowledge about physiological functions from genetic analyses, the molecular mechanisms and conformational dynamics involved in clock signaling and DNA repair remain poorly understood. The (6-4) photolyase, which has strikingly high similarity to human clock cryptochromes, is a prototypic biological system to study conformational dynamics of cryptochrome/photolyase family proteins. The entire light-dependent DNA repair process for (6-4) photolyase can be reproduced in a simple in vitro system. To decipher pivotal reactions of the common FAD cofactor, we accomplished time-resolved measurements of radical formation, diffusion, and protein conformational changes during light-dependent repair by full-length (6-4) photolyase on DNA carrying a single UV-induced damage. The (6-4) photolyase by itself showed significant volume changes after blue-light activation, indicating protein conformational changes distant from the flavin cofactor. A drastic diffusion change was observed only in the presence of both (6-4) photolyase and damaged DNA, and not for (6-4) photolyase alone or with undamaged DNA. Thus, we propose that this diffusion change reflects the rapid (50 μs time constant) dissociation of the protein from the repaired DNA product. Conformational changes with such fast turnover would likely enable DNA repair photolyases to access the entire genome in cells.     

Phase behavior of binary mixtures composed of ethylene carbonate and various organic solvents

Phase behaviors of the binary mixtures composed of ethylene carbonate (EC) and aliphatic alcohols, ω-phenyl alcohols, and alkylbenzenes were investigated. In addition, heat of solution of EC into these organic solvents was measured. The EC/methanol and EC/ethanol systems gave homogeneous solution at the temperature above their liquidus lines, while the mixtures of EC and alcohols with longer alkyl chain showed a miscibility gap in a liquid phase and provided the monotectic-type phase diagram. The liquid–liquid phase separation region expanded with the increase in the alkyl chain length. A similar phase behavior was also observed for the mixtures of EC and alkylbenzenes. On the other hand, the EC mixtures with ω-phenyl alcohols showed no miscibility gap in a liquid phase at least up to 4-phenylbutan-1-ol which has C4 alkyl chain intervening between phenyl and hydroxyl groups. This result demonstrates that both of the hydroxyl and phenyl groups act to facilitate the mixing of aliphatic compounds with EC. The phase behavior of these EC mixtures was analyzed applying the modified regular solution model in which the pair interaction energy was regarded as free energy. The model calculation with the use of heat of solution of EC at infinite dilution as the pair interaction enthalpy reproduced well both of the experimentally obtained liquidus line and mutual solubility curve as well as monotectic point.     

Synthesis of the proposed structure of phaeosphaeride A

The first total synthesis of the proposed structure of phaeosphaeride A has been achieved via six-membered-ring formation by means of an intramolecular vinyl-anion aldol reaction as the key step. This synthesis suggests a revised configurational assignment for phaeosphaeride A.     

A tandem reaction of organozinc reagent prepared from palladium-catalyzed umpolung method: diastereoselective formation of cyclohexene derivatives bearing three adjacent stereocenters

In the presence of a palladium catalyst, treatment of γ-acyloxy-α,β-unsaturated ketone with bis(iodozincio)methane caused umpolung of π-allylpalladium to give a zinc dienolate. Thus formed zinc species afforded a cyclohexene derivative via a self-condensation reaction. It is noteworthy that the three adjacent stereogenic centers were created in a single process with quite high diastereoselectivity.     

Photoemission study on the valence band of a β-FeSi2 thin film using synchrotron radiation

Resonant and constant-initial state photoemission spectroscopies using synchrotron radiation were applied to investigate the valence-band electronic structure of a semi-conducting β-type iron-disilicide (β-FeSi(2)) thin film. The results clearly indicated that the component elements, iron (Fe) and silicon (Si), contribute differently to the valence band features; the Fe 3d orbitals mainly concentrate in the top region of the valence band while the Si 3s and 3p orbitals spread over the wide region of the valence band. The β-FeSi(2) thin film showed a typical p-type semi-conducting nature with a work function of 4.78 eV. The β-FeSi(2) film showed the Fe M(1)VV Auger lines around the kinetic energy of 88 eV. It would be expected from these observations that there exist strong interactions between iron and silicon atoms in the β-FeSi(2) film resulting in orbital mixing and band formation.     

Diastereoselective hydroformylation of 2,5-cyclohexadienyl-1-carbinols with catalytic amounts of a reversibly bound directing group

A phosphinite plays a role as a reversibly bound directing group for the regio- and diastereoselective hydroformylation of 2,5-cyclohexadienyl-1-carbinols. Of the two alkene functions only one was functionalized through hydroformylation to form a synthetically attractive quaternary carbon center leaving the second alkene function for potential further functionalization.     

Synthesis of the ABC ring system of Jiadifenin via Pd-catalyzed cyclizations

An efficient route toward the central ABC system of jiadifenin has been developed using two key Pd-catalyzed cyclizations. A protic solvent-activated Mizoroki-Heck reaction was used to construct the C(9) quaternary carbon and the A ring. A cascading Tsuji-Trost cyclization/lactonization sequence was employed to establish the BC ring system and the C(5,6) stereochemistry.     

A new method for aromatic difluoromethylation: copper-catalyzed cross-coupling and decarboxylation sequence from aryl iodides

A new methodology for aromatic difluoromethylation is described. Aryl iodides reacted with α-silyldifluoroacetates upon treatment with copper catalyst in DMSO or DME to give the corresponding aryldifluoroacetates in moderate to good yields. The subsequent hydrolysis of aryldifluoroacetates and KF-promoted decarboxylation afforded a variety of difluoromethyl aromatics.     

Thermo-responsive polymer brushes as intelligent biointerfaces: preparation via ATRP and characterization

PIPAAm-brush grafted glass substrates with various graft densities and chain lengths were prepared via surface-initiated ATRP. Temperature-dependent physicochemical properties of the surfaces were characterized by means of ATR/FT-IR spectroscopy, XPS, AFM, and contact angle measurements. ATRP conditions influence the amount of grafted PIPAAm and the surface wettability and roughness of the substrate. Fibronectin adsorption and EC adhesion increased with decreasing density of PIPAAm brushes. EC adhesion was diminished with increasing PIPAAm graft length. Thus, the preparation of PIPAAm brush surface with various graft densities and chain lengths using the surface-initiated ATRP is an effective method for modulating thermo-responsive properties of surfaces.     

Use of the MALDI BioTyper system with MALDI–TOF mass spectrometry for rapid identification of microorganisms

In a clinical diagnosis microbiology laboratory, the current method of identifying bacterial isolates is based mainly on phenotypic characteristics, for example growth pattern on different media, colony morphology, Gram stain, and various biochemical reactions. These techniques collectively enable great accuracy in identifying most bacterial isolates, but are costly and time-consuming. In our clinical microbiology laboratory, we prospectively assessed the ability of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI–TOF MS) to identify bacterial strains that were routinely isolated from clinical samples. Bacterial colonies obtained from a total of 468 strains of 92 bacterial species isolated at the Department of Clinical Laboratory at Chiba University were directly placed on target MALDI plates followed by addition of CHCA matrix solution. The plates were then subjected to MALDI–TOF MS measurement and the microorganisms were identified by pattern matching with the libraries in the BioTyper 2.0 software. Identification success at the species and genus levels was 91.7% (429/468) and 97.0% (454/468), respectively. MALDI–TOF MS is a rapid, simple, and high-throughput proteomic technique for identification of a variety of bacterial species. Because colony-to-colony differences and effects of culture duration on the results are minimal, it can be implemented in a conventional laboratory setting. Although for some pathogens, preanalytical processes should be refined, and the current database should be improved to obtain more accurate results, the MALDI–TOF MS based method performs, in general, as well as conventional methods and is a promising technology in clinical laboratories.