2'-O,4'-C-aminomethylene-bridged nucleic acid modification with enhancement of nuclease resistance promotes pyrimidine motif triplex nucleic acid formation at physiological pH

Due to the instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex-formation-based strategies in vivo, such as gene expression regulation, genomic DNA mapping, and gene-targeted mutagenesis. To this end, we investigated the thermodynamic and kinetic effects of our previously reported chemical modification, 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNA(NC)) modification of triplex-forming oligonucleotide (TFO), on triplex formation at physiological pH. The thermodynamic analyses indicated that the 2',4'-BNA(NC) modification of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold. The number and position of the 2',4'-BNA(NC) modification in TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity and the increased degree of hydration of the 2',4'-BNA(NC)-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant. Kinetic data demonstrated that the observed increase in the binding constant by the 2',4'-BNA(NC) modification resulted mainly from the considerable decrease in the dissociation rate constant. The TFO stability in human serum showed that the 2',4'-BNA(NC) modification significantly increased the nuclease resistance of TFO. Our results support the idea that the 2',4'-BNA(NC) modification of TFO could be a key chemical modification to achieve higher binding affinity and higher nuclease resistance in the triplex formation under physiological conditions, and may lead to progress in various triplex-formation-based strategies in vivo.     

Polymerization of liposomes composed of diene-containing lipids by radical initiators. II. Polymerization of monodiene-type lipids as liposomes

1-Palmitoyl-2(2,4-octadecadienoyl)-sn-glycero-3-phosphocholine (POPC), a polymerizable lipid that contains one diene group in only a 2-acyl chain, was polymerized as liposome in an aqueous medium. Polymerization was initiated by water-insoluble azobisisobutyronitrile (AIBN), or water-soluble azobis(2-amidinopropane) dihydrochloride (AAPD). AIBN was mixed with monomeric lipids, and the mixture was dispersed in an aqueous medium by sonication to prepare AIBN-containing monomeric lipid liposomes. On the other hand, AAPD was simply added to the liposome suspension. The POPC liposomes were easily polymerized by the addition of AAPD, a water-soluble radical initiator, but few were polymerized by AIBN. The results suggested that the diene group in the 2-acyl chain was in an aqueous phase and, therefore, easily polymerized by a water-soluble radical initiator. The polymerized POPC liposomes were revealed to be more stable than those of monomeric ones because the scattered-light intensity from the polymerized POPC liposome suspension changed a little by the addition of Triton X-100. For only the polymerized ones, the liposome structure was confirmed by TEM after addition of an excess amount of Triton X-100.     

Pair Distribution Function from Liquid Jet Nanoparticle Suspension using Femtosecond X-ray Pulses

X-ray scattering data measured on femtosecond timescales at the SACLA X-ray Free Electron Laser (XFEL) facility on a suspension of HfO₂ nanoparticles in a liquid jet were used for pair distribution function (PDF) analysis. Despite a non-optimal experimental setup resulting in a modest Q_max of ~8 Å⁻¹, a promising PDF was obtained. The main features were reproduced when comparing the XFEL PDF to a PDF obtained from data measured at the PETRA III synchrotron light source. Refining structural parameters such as unit cell dimension and particle size from the XFEL PDF provided reliable values. Although the reachable Q_max limited the obtainable information, the present results indicate that good quality PDFs can be obtained on femtosecond timescales if the experimental conditions are further optimized. The study therefore encourages a new direction in ultrafast structural science where structural features of amorphous and disordered systems can be studied.     

Imaging of Oral SCC Cells by Raman Micro-Spectroscopy Technique

We used Raman micro-spectroscopy technique to analyze the molecular changes associated with oral squamous cell carcinoma (SCC) cells in the form of frozen tissue. Previously, Raman micro-spectroscopy technique on human tissue was mainly based on spectral analysis, but we worked on imaging of molecular structure. In this study, we evaluated the distribution of four components at the cell level (about 10 μm) to describe the changes in protein and molecular structures of protein belonging to malignant tissue. We analyzed ten oral SCC samples of five patients without special pretreatments of the use of formaldehyde. We obtained cell level images of the oral SCC cells at various components (peak at 935 cm⁻¹: proline and valine, 1004 cm⁻¹: phenylalanine, 1223 cm⁻¹: nucleic acids, and 1650 cm⁻¹: amide I). These mapping images of SCC cells showed the distribution of nucleic acids in the nuclear areas; meanwhile, proline and valine, phenylalanine, and amide I were detected in the cytoplasm areas of the SCC cells. Furthermore, the peak of amide I in the cancer area shifts to the higher wavenumber side, which indicates the α-helix component may decrease in its relative amounts of protein in the β-sheet or random coil conformation. Imaging of SCC cells with Raman micro-spectroscopy technique indicated that such a new observation of cancer cells is useful for analyzing the detailed distribution of various molecular conformation within SCC cells.     

Cation complexation with p-tert-butylcalix[5]arene pentacarboxylic acid derivative: an allosteric regulation of the first metal ion for stepwise extraction of the second ion

A calix[5]arene based solvent extraction reagent 3, appending carboxylic acid groups at the lower rim, has been developed and its complexation behavior towards some transition metal ions has been studied. The host 3 can selectively and quantitatively extract Pb(II) ions above pH 1.8 while other divalent ions such as Cu(II), Zn(II), Co(II), Ni(II) are extracted quantitatively only above pH 3.0. The outstanding Pb(II) selectivity of 3 comes from the size fit complementarity effect of the Pb(II) ion in the calix[5]arene cavity. One molecule of 3 extracts two Pb(II) ions in a stepwise manner. The first Pb(II) ion is extracted into the deep cavity of the calix[5]arene defined by phenoxy oxygen atoms. The first complexed Pb(II) ion acts as a template to bring the host into a cone conformation and induces a positive allosteric effect for the extraction of the second Pb(II) ion at an oxygen rich coordinating site composed of carboxyl groups. Both the Pb(II) ions are extracted through an ion exchange mechanism and the electroneutral complex in the organic phase is formed by the release of an equivalent number of hydrogen ions into aqueous solution. The loaded Pb(II) is easily back-extracted from Pb(II)-complexed 3 using dilute acid solution.     

Morphology control of tungsten nanorods grown by glancing angle RF magnetron sputtering under variable argon pressure and flow rate

Morphologically novel tungsten nanorods (WNRs) with the co-existence of two crystalline phases, α-W (thermodynamically stable) and β-W, were fabricated by glancing angle RF magnetron sputtering technique under various Ar pressures and flow rates. For these nanorods, a significant variation in their morphology and surface roughness was observed. These structures could be useful in a wide range of applications such as field emission, robust superhydrophobic coatings, energy, and medicine.     

Oxygen-rich Ti1−xO2 pillar growth at a gold nanoparticle–TiO2 contact by O2 exposure

In-situ gas-injection transmission electron microscopy revealed that a pillar grew at the edge of the interface of a gold nanoparticle and a TiO₂ substrate during exposure to O₂ gas at 100 Pa. The pillar was found to have a titanium-deficient chemical composition of Ti_1 ? xO₂ (x > 0) by electron energy loss spectroscopy (EELS). The spectra showed a chemical shift of oxygen and titanium ions to have ionic states of Ti³⁺ and O^y? (y < 3/2). The formation of the Ti_1 ? xO₂ at the contact edge of gold–Ti_1 ? xO₂ interface is discussed from the perspective of an O₂ affinity, which plays an important role in CO oxidation process of supported gold particle.