Imaging of RNA in bacteria with self-ligating quenched probes

We report on the application of a new class of oligonucleotide reporter probes, QUAL probes, that "light up" when a nucleophilic phosphorothioate probe binds adjacent to a dabsyl-quenched probe. These self-ligating DNA probes were used for sequence-specific detection of 16S rRNA in Escherichia coli cells. Strong fluorescence was observed only when the phosphorothioate and quenched dabsyl probes bind side-by-side on a 16S rRNA target. The results demonstrate the use of QUAL probes to detect specific RNA sequences in bacterial cells without enzymes and without washing steps.     

Quantitative evaluation of stress distribution in bulk polymer samples through the comparison of mechanical behaviors between giant single‐crystal and semicrystalline samples of poly(trans‐1,4‐diethyl muconate)

The Raman shift and crystallite modulus were measured under the application of tensile force for a giant single crystal and a series of uniaxially oriented semicrystalline samples of poly(trans‐1,4‐diethyl muconate) (polyEMU). The apparent Raman shift factor α^app or a vibrational frequency shift per 1 GPa tensile stress was higher for the semicrystalline samples with lower crystallinity or lower bulk modulus. The apparent crystallite modulus E or Young's modulus along the chain axis in the crystalline region was not constant but varied remarkably between the giant single crystal and semicrystalline samples. A systematic change in α^app and E among the polyEMU samples with different preparation history could be interpreted quantitatively on the basis of a mechanical series parallel model consisting of crystalline and amorphous phases. The origin of different E and α^app was speculated to be a stress concentration on the taut‐tie chain contained as a parallel crystalline component in the mechanical model. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 444–453, 2003     

Programmable DNA translation system using cross-linked DNA mediators

The information of template DNA strands was converted into the specific sequences in a programmable way by following the mediation of cross-linked DNAs.     

Lipid-soluble and water-soluble arsenic compounds in blubber of ringed seal (Pusa hispida)

High concentrations of arsenic were observed in the blubber of ringed seals (Pusa hispida) in our previous study. To better understand the arsenic accumulation in blubber of marine mammals, arsenicals in the blubber of ringed seal were characterized using high performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC–ICPMS). The most predominant water-soluble arsenical in the blubber was dimethylarsinic acid (DMA), in spite of the predominance of arsenobetaine in other tissues. Lipid-soluble fraction was hydrolyzed under mild (tetraethylammonium hydroxide (TEAH) hydrolysis) and strong (NaOH hydrolysis) conditions, and then an aliquot of hydrolysate was injected onto HPLC–ICPMS. Both TEAH-labile and TEAH-stable/NaOH-labile lipid-soluble fractions contained precursors of DMA. These results suggest that the blubber might be the pool of DMA and DMA-containing precursors in ringed seals.     

Energy transfer reaction of cationic porphyrin complexes on the clay surface: effect of sample preparation method

Photochemical energy transfer of non-aggregated cationic porphyrins on an anionic-type clay (Smecton SA) surface was investigated. The efficiency of energy transfer and excited-state quenching in the absence of energy transfer were evaluated at various loading levels of porphyrin on the clay surface and were found to be significantly affected by the loading level. As the latter increased, both energy transfer efficiency and excited-state quenching increased. Judging from the dependency of energy-transfer efficiency on the porphyrin loading level, a partially clustered structure, but without aggregation, of porphyrins on the clay surface is proposed.     

Induction of a remarkable conformational change in a human telomeric sequence by the binding of naphthyridine dimer: inhibition of the elongation of a telomeric repeat by telomerase

The binding of a dimeric form of the 2-amino-1,8-naphthyridine derivative (naphthyridine dimer) to a human telomeric sequence, TTAGGG, was investigated by UV melting, CD spectra, and CSI-MS measurements. Both the 9-mer d(TTAGGGTTA) and the 15-mer d(TTAGGGTTAGGGTTA) showed apparent melting temperatures (T(m)) of 45.6 and 63.6 degrees C, respectively, in the presence of naphthyridine dimer (30 microM) in sodium cacodylate buffer (50 mM, pH 7.0) containing 100 mM NaCl. The CD spectra at 235 and 255 nm of the 9-mer increased in intensity accompanied with strong induced CDs at 285 and 340 nm upon complex formation with naphthyridine dimer. UV titration of the binding of naphthyridine dimer to the 9-mer at 320 nm showed a hypochromism of the spectra. A Scatchard plot of the data showed the presence of multiple binding sites with different association constants. Cold spray ionization mass spectrometry of the complex between naphthyridine dimer and the 9-mer clearly showed that one to three molecules of the ligand bound to the dimer duplex of the 9-mer. Telomeric repeat elongation assay showed that the binding of naphthyridine dimer to the telomeric sequence inhibits the elongation of the sequence by telomerase.     

Synthesis of well‐defined block copolymer composed of flexible amphiphilic poly(ethylene glycol) and hydrophobic liquid crystalline segments by living coordination polymerization of allene derivatives and its application to thin film with perpendicularly oriented cylindrical nanostructure

A block copolymer composed of a flexible polar poly(ethylene glycol) (PEG) and a less polar liquid crystalline poly(allene) segments is prepared by the living coordination polymerization of an allene derivative possessing trans‐azobenzene‐containing mesogenic substituent by the use of a π‐allylnickel macroinitiator bearing PEG segment. The thin film of the block copolymer is prepared by the spin coating of its solution onto mica or silicon wafer which proves to possess perpendicularly oriented nanocylindrical microphase separated structures as supported by the differential calorimetric, polarized optical microscopic, grazing‐incidence small‐angle X‐ray scattering, transmission electron microscope, and atomic force microscope measurements.