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.     

Influence of bromoalkyloxy side chain on mesomorphic behavior in heterocyclic 7-(4-bromoalkyloxy)-3-(4′-decyloxyphenyl)-4H- 1-benzopyran-4-ones

A new homologous series of isoflavone-based ethers,7-(4-bromoalkyloxy)-3-(4’-decyloxyprienyl)-4H-1-benzopyran-4-ones were synthesized and characterized.The mesomorphic properties of all homologues were investigated by differential scanning calorimetry(DSC) and polarizing optical microscopy(POM).Enantiotropic smectic A(SmA) phase was observed for all homologues.The structure-property study was carried out by comparing the mesomorphic behavior of the homologues with those previously reported analogues.The bromine atom from the alkyloxy side chain of the benzene ring fused to the heterocyclic moiety was found to be capable of changing the mesomorphic properties.     

Synthesis and structure of dawson polyoxometalate-based, multifunctional, inorganic-organic hybrid compounds: organogermyl complexes with one terminal functional group and organosilyl analogues with two terminal functional groups

Four novel multifunctional polyoxometalate (POM)-based inorganic-organic hybrid compounds, [α(2)-P(2)W(17)O(61){(RGe)}](7-) (Ge-1, R(1) = HOOC(CH(2))(2(-)) and Ge-2, R(2) = H(2)C═CHCH(2(-))) and [α(2)-P(2)W(17)O(61){(RSi)(2)O}](6-) (Si-1, R(1) and Si-2, R(2)), were prepared by incorporating organic chains having terminal functional groups (carboxylic acid and allyl groups) into monolacunary site of Dawson polyoxoanion [α(2)-P(2)W(17)O(61)](10-). In these POMs, new modification of the terminal functional groups was attained by introducing organogermyl and organosilyl groups. Dimethylammonium salts of the organogermyl complexes, (Me(2)NH(2))(7)[α(2)-P(2)W(17)O(61)(R(1)Ge)]·H(2)O MeN-Ge-1 and (Me(2)NH(2))(7)[α(2)-P(2)W(17)O(61)(R(2)Ge)]·4H(2)O MeN-Ge-2, were obtained as analytically pure crystals, in 22.8% and 55.3% yields, respectively, by stoichiometric reactions of [α(2)-P(2)W(17)O(61)](10-) with separately prepared Cl(3)GeC(2)H(4)COOH in water, and H(2)C═CHCH(2)GeCl(3) in a solvent mixture of water/acetonitrile. Synthesis and X-ray structure analysis of the Dawson POM-based organogermyl complexes were first successful. Dimethylammonium salts of the corresponding organosilyl complexes, (Me(2)NH(2))(6)[α(2)-P(2)W(17)O(61){(R(1)Si)(2)O}]·4H(2)O MeN-Si-1 and (Me(2)NH(2))(6)[α(2)-P(2)W(17)O(61){(R(2)Si)(2)O}]·6H(2)O MeN-Si-2, were also obtained as analytically pure crystalline crystals, in 17.1% and 63.5% yields, respectively, by stoichiometric reactions of [α(2)-P(2)W(17)O(61)](10-) with NaOOC(CH(2))(2)Si(OH)(2)(ONa) and H(2)C═CHCH(2)Si(OEt)(3). These complexes were characterized by elemental analysis, thermogravimetric and differential thermal analyses (TG/DTA), FTIR, solid-state ((31)P) and solution ((31)P, (1)H, and (13)C) NMR, and X-ray crystallography.     

Linking Conformational Flexibility and Kinetics: Catalytic 1,4‐Type Friedel–Crafts Reactions of Phenols Utilizing 1,3‐Diamine‐Tethered Guanidine/Bisthiourea Organocatalysts

Herein, we present details of our conformationally flexible, 1,3‐diamine‐tethered guanidine/bisthiourea organocatalysts for chemo‐, regio‐, and enantioselective 1,4‐type Friedel–Crafts reactions of phenols. These organocatalysts show a unique stereo‐discrimination governed by the differential activation entropy (ΔΔS^≠), rather than by the differential activation enthalpy (ΔΔH^≠). Extensive kinetic analyses using Eyring plots for a series of guanidine/bisthiourea organocatalysts revealed the key structural motif in the catalysts associated with a large magnitude of differential activation entropy (ΔΔS^≠). A plausible guanidine–thiourea cooperative mechanism for the enantioselective Friedel–Crafts reaction is proposed.     

Change of concentrations of trace elements and protein contents in the liver of zinc deficient mice

The concentrations of essential trace elements and proteins in cytosolic fraction of hepatic cells of mice fed with Zn-deficient diet (Zn-def, mice) and control were determined by ICP-MS and BCA protein assay method, respectively, after division into forty fractions by gel filtration chromatography. The concentrations of zinc and proteins decreased in the 14–17th fractions of Zn-def, mice, whereas cobalt concentrations increased in the 14, 17, and 18th fractions. However, no significant differences were found on the gel after SDS-PAGE for the 12–21st fractions, although the BCA protein assay date showed the decrease of protein amounts in 13–15th fractions of Zn-def. mice.     

CpRuIIPF6/quinaldic acid-catalyzed chemoselective allyl ether cleavage. A simple and practical method for hydroxyl deprotection

A cationic CpRu(II) complex in combination with quinaldic acid shows high reactivity and chemoselectivity for the catalytic deprotection of hydroxyl groups protected as allyl ethers. The catalyst operates in alcoholic solvents without the need for any additional nucleophiles, satisfying the practical requirements of operational simplicity, safety, and environmental friendliness. The wide applicability of this deprotection strategy to a variety of multifunctional molecules, including peptides and nucleosides, may provide new opportunities in protective group chemistry. [structure: see text]     

Intramolecular Benzyne–Phenolate [4+2] Cycloadditions

An intramolecular benzyne–phenolate [4+2] cycloaddition is reported. Benzyne precursors, having vicinal halogen‐sulfonate functionalities, linked with a phenol(ate) by various tether groups undergo efficient intramolecular [4+2] cycloaddition by treatment with either Ph₃MgLi or nBuLi for halogen–metal exchange to form various benzobarrelenes.     

Highly (Z)-selective hydrosilylation of terminal alkynes catalyzed by a diphosphinidenecyclobutene-coordinated ruthenium complex: application to the synthesis of (Z,Z)-bis(2-bromoethenyl)arenes

[reaction: see text] Complex 1 bearing a diphosphinidenecyclobutene ligand (DPCB-OMe) catalyzes highly stereoselective hydrosilylation of diethynylarenes with HSiMe2Ph to afford (Z,Z)-bis(2-silylethenyl)arenes. Treatment of the hydrosilylation products with N-bromosuccinimide causes bromodesilylation in a stereospecific manner, giving (Z,Z)-bis(2-bromoethenyl)arenes in high geometrical purity (>98%).