Modified alpha-beta chimeric oligoDNA bearing a multi-conjugate of 2,2-bis(hydroxymethyl)propionic acid-anthraquinone-polyamine exhibited improved and stereo-nonspecific triplex-forming ability

Novel alpha-beta chimeric oligonucleotides bearing a propionic acid derivative of an anthraquinone-polyamine conjugate in the "linker" region sequence-specifically formed a substantially stable alternate-stranded triplex with dsDNA almost regardless of the stereochemistry of the derivative.     

An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in Streptomyces

Carquinostatin A (CQS), a potent neuroprotective substance, is a unique carbazole alkaloid with both an ortho‐quinone function and an isoprenoid moiety. We identified the entire gene cluster responsible for CQS biosynthesis in Streptomyces exfoliatus through heterologous production of CQS and gene deletion. Biochemical characterization of seven CQS biosynthetic gene products (CqsB1–7) established the total biosynthetic pathway of CQS. Reconstitution of CqsB1 and CqsB2 showed that the synthesis of the carbazole skeleton involves CqsB1‐catalyzed decarboxylative condensation of an α‐hydroxyl‐β‐keto acid intermediate with 3‐hydroxybutyryl‐ACP followed by CqsB2‐catalyzed oxidative cyclization. Based on crystal structures and mutagenesis‐based biochemical assays, a detailed mechanism for the unique deprotonation‐initiated cyclization catalyzed by CqsB2 is proposed. Finally, analysis of the substrate specificity of the biosynthetic enzymes led to the production of novel carbazoles.     

An Unusual Skeletal Rearrangement in the Biosynthesis of the Sesquiterpene Trichobrasilenol from Trichoderma

The skeletons of some classes of terpenoids are unusual in that they contain a larger number of Me groups (or their biosynthetic equivalents such as olefinic methylene groups, hydroxymethyl groups, aldehydes, or carboxylic acids and their derivatives) than provided by their oligoprenyl diphosphate precursor. This is sometimes the result of an oxidative ring‐opening reaction at a terpene‐cyclase‐derived molecule containing the regular number of Me group equivalents, as observed for picrotoxan sesquiterpenes. In this study a sesquiterpene cyclase from Trichoderma spp. is described that can convert farnesyl diphosphate (FPP) directly via a remarkable skeletal rearrangement into trichobrasilenol, a new brasilane sesquiterpene with one additional Me group equivalent compared to FPP. A mechanistic hypothesis for the formation of the brasilane skeleton is supported by extensive isotopic labelling studies.     

Reversible mechanochromic luminescence of [(C6F5Au)2(mu-1,4-diisocyanobenzene)

Reversible mechanochromic luminescence of [(C6F5Au)2(mu-1,4-diisocyanobenzene)] is reported. Grinding of the complex induced a photoluminescent color change, which was restored by exposure to a solvent. This cycle was repeated 20 times with no color degradation in the emissions. Their optical properties, X-ray crystallographic analysis, IR, and XRD measurements strongly suggested that the change in the molecular arrangement is responsible for this mechanochromic property. Intermolecular aurophilic bondings presumably play a key role in the altered emission.     

Crystal structure of friction-transferred poly(2,5-dioctyloxy-1,4-phenylenevinylene)

Poly(2,5-dioctyloxy-1,4-phenylenevinylene) (DOPPV) was found to form a highly oriented film by a friction-transfer technique. Structural investigation of friction-transferred DOPPV was studied by means of polarized ultraviolet-visible (UV-vis) absorption spectroscopy, polarized photoluminescence (PL) spectroscopy, and synchrotron-sourced grazing incident X-ray diffraction (GIXD) analysis. The polarized UV-vis absorption and PL spectra indicate clear axial alignment. DOPPV backbones in friction-transferred film are highly aligned along the drawing direction of the friction-transfer. Further information of the molecular arrangement in friction-transferred DOPPV film was investigated by both the out-of-plane and the in-plane GIXD analyses with synchrotron source. The DOPPV molecules in friction-transferred films were perfectly arranged three-dimensionally: the backbones aligned along the drawing direction of friction-transfer, the alkyl side chains lay in the film plane, and the planar backbones were arranged parallel to the film surface. Additionally, two neighboring DOPPV molecules along the direction of inter-backbones separation by alkyl side chains were found to be shifted with respect to one another by the mean distance of half of a monomeric repeat.     

Rheological and DSC studies of mixtures of gellan gum and konjac glucomannan

The interaction between gellan gum (GELL) and konjac glucomannan (KGM) with and without sodium chloride, potassium chloride, calcium chloride and magnesium chloride has been monitored using mechanical spectroscopy and differential scanning calorimetry (DSC). The rheological results indicated that the synergism occurred at sufficient low temperatures where individual helices of GELL molecules were sufficiently aggregated. With progressive addition of monovalent cations, storage shear modulus G' and loss shear modulus G” for mixtures gradually increased, and not only the helix-coil transition temperature of GELL molecules in mixtures but also the sol-gel transition temperature for mixtures shifted to higher temperatures with increasing concentration of salts. Moreover, in the presence of sufficient monovalent cations, mixtures formed an elastic gel with large thermal hysteresis. In the presence of divalent cations, the synergistic interaction was promoted up to a certain concentration, however, with more progressive addition of divalent cations, the main structure formed by aggregates of GELL helices would be smaller, so that mixtures could not form a gel in the presence of excessive divalent cations. DSC results indicated that the intermolecular binding complexes between GELL and KGM molecules would not occur, but KGM markedly influenced the disorder-order transition of GELL molecules. We have suggested that KGM was attached to the surface of large aggregates of GELL helices, and since cations promote GELL self-aggregation by a screening effect, the synergistic interaction between GELL and KGM was promoted with increasing concentration of salts. However, excessive divalent cations formed various aggregates of GELL helices with different thermal stabilities, so that the phase-separation in GELL/KGM mixtures was promoted in the presence of excessive divalent cations.     

Compressed Corannulene in a Molecular Cage

Self‐assembled coordination cages can be employed as a molecular press, where the bowl‐shaped guest corannulene (C₂₀H₁₀) is significantly flattened upon inclusion within the hydrophobic cavity. This is demonstrated by the pairwise inclusion of corannulene with naphthalene diimide as well as by the dimer inclusion of bromocorannulene inside the box‐like host. The compressed corannulene structures are unambiguously revealed by single‐crystal X‐ray analysis.     

Single nucleotide polymorphism detection method by temperature-gradient affinity chromatography using a single-stranded oligo-DNA coupled column

We developed an affinity chromatographic method for simple single nucleotide polymorphism (SNP) detection by use of a single-stranded DNA-coupled column and temperature gradient elution, utilizing the difference in thermal stability between hybridized double-stranded DNAs with and without mismatched base-pairs in the course of temperature gradient elution. We studied experimentally and theoretically the elution behavior of DNAs with and without SNPs in this chromatography and proposed a numerical calculation method based on a thermodynamic dissociation model. The effects of the column volume, flow rate of eluent and heating rate of the column on elution profiles were clarified. For designing DNA ligands, mismatched base-pair positions favorable for detection of SNPs were also explored by use of hybridized DNAs coding a part of the human TP53 gene.     

Two distinct pathways for essential metabolic precursors for isoprenoid biosynthesis

Isoprenoids are a diverse group of molecules found in all organisms, where they perform such important biological functions as hormone signaling (e.g., steroids) in mammals, antioxidation (e.g., carotenoids) in plants, electron transport (e.g., ubiquinone), and cell wall biosynthesis intermediates in bacteria. All isoprenoids are synthesized by the consecutive condensation of the five-carbon monomer isopentenyl diphosphate (IPP) to its isomer, dimethylallyl diphosphate (DMAPP). The biosynthetic pathway for the formation of IPP from acetyl-CoA (i.e., the mevalonate pathway) had been established mainly in mice and the budding yeast Saccharomyces cerevisiae. Curiously, most prokaryotic microorganisms lack homologs of the genes in the mevalonate pathway, even though IPP and DMAPP are essential for isoprenoid biosynthesis in bacteria. This observation provided an impetus to search for an alternative pathway to synthesize IPP and DMAPP, ultimately leading to the discovery of the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate pathway. This review article focuses on our significant contributions to a comprehensive understanding of the biosynthesis of IPP and DMAPP.