Efficient DNA strand displacement by a W-shaped nucleoside analogue (WNA-βT) containing an ortho-methyl-substituted phenyl ring

Molecules that can target duplex DNA with sequence selectivity have the potential to be useful tools in genomic research and also as therapeutic agents. Homopurine-homopyrimidine stretches in duplex DNA can be recognized by homopurine or homopyrimidine TFOs (triplex-forming oligonucleotides) through the formation of triplex DNA. We have previously developed bicyclic nucleoside analogues (WNAs) for the formation of stable triplexes in the formation of stable antiparallel triplexes containing a TA or a CG interrupting site. In this study, we investigated the effects on triplex DNA formation of ortho-, meta-, and para-methyl substituent groups on the aromatic ring of the WNA analogue. It was found that the homopurine TFO containing meta- and para-methyl-substituted WNA-βT (mMe-WNA-βT, pMe-WNA-βT) stabilized triplexes containing a TA interrupting site or a GC site, respectively. Interestingly, the ortho-methyl-substituted WNA-βT (oMe-WNA-βT) efficiently promoted DNA strand displacement to form the TFO/pyrimidine duplex. A detailed investigation showed that the duplex was in the antiparallel orientation and that its formation took place prior to triplex formation with the need for a magnesium cation. NOESY measurements indicated a significant difference in the rotation flexibilities of the phenyl rings of WNA-βTs: that is, the conformation of the ortho-methylated phenyl ring was stable in a temperature-independent manner. It was speculated that the initial formation of a ternary complex was followed by strand displacement and then the formation of the TFO/pyrimidine duplex together with the TFO(2)/pyrimidine triplex formation during the early stage, and that the equilibrium shifted to the triplex during the later stage. Although the detailed role is still uncertain, the fixed phenyl ring of oMe-WNA-βT might play a role in the displacement reaction.     

Diagnosis of Desmoplastic Reaction by Immunohistochemical Analysis,in Biopsy Specimens of Early Colorectal Carcinomas,Is Efficacious in Estimating the Depth of Invasion

The aim of our study was to evaluate the diagnosis of desmoplastic reaction (DR) by immunostaining for α-smooth muscle actin (αSMA) and desmin, for predicting the depth of submucosal invasion in biopsy specimens of early colorectal carcinomas (CRCs). Thirty-eight cases of non-pedunculated early CRCs were included in this study. Positive for DR was defined as αSMA-positive and desmin-negative stroma in the CRC. The depth of submucosal invasion was measured in endoscopically or surgically resected specimens and the lesions were subsequently divided into two groups: Group A (carcinoma in situ/intramucosal carcinoma and submucosal invasive carcinoma with a depth <1000 μm) and Group B (submucosal invasion with a depth ≥1000 μm). Twenty-one cases were DR-positive and 17 were DR-negative. No statistical significance was found between the DR with regard to tumor size, location and histological type. All DR-positive cases belonged to Group B whereas 14 (82.4%) DR-negative lesions belonged to Group A (p < 0.001). The sensitivity, specificity, positive and negative predictive values and accuracy of DR positivity for diagnosis of Group B were 87.5%, 100%, 100%, 82.4% and 92.1%, respectively. Conclusively, detection of DR in biopsy specimens with ancillary immunohistochemistry (αSMA/desmin) would help in preoperative diagnosis for the depth of submucosal invasion of early CRC.     

A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle

We developed a method of predicting the tertiary structuresof seven transmembrane helical proteins in triangle latticemodels, assuming that the configuration of helices is stabilizedby polar interactions. Triangle lattice models having 12 or11 nearest neighbor pairs were used as general templates ofa seven-helix system, then the orientation angles of all heliceswere varied at intervals of 15°. The polar interaction energyfor all possible positions of each helix was estimated usingthe calculated polar indices of transmembrane helices. An automatedsystem was constructed and applied to bacteriorhodopsin, a typicalmembrane protein with seven transmembrane helices. The predictedoptimal and actual structures were similar. The top 100 predictedhelical configurations indicated that the helix-triangle, CFG,occurred at the highest frequency. In fact, this helix-triangleof bacteriorhodopsin forms an active proton-pumping site, suggestingthat the present method can identify functionally importanthelices in membrane proteins. The possibility of studying thestructure change of bacteriorhodopsin during the functionalprocess by this method is discussed, and may serve to explainthe experimental structures of photointermediate states.     

Arc Plasma Processing of Pt and Pd Catalysts Supported on γ-Al2O3 Powders

Direct deposition of Pt and Pd nanoparticles onto γ-Al₂O₃ powders was studied by using a pulsed arc plasma process under vacuum to use them as an automotive catalyst. As deposited Pt catalyst exhibited a higher metal dispersion and thus a higher catalytic activity for CO oxidation, compared to the conventional Pt/Al₂O₃ prepared by wet impregnation. In contrast, Pd/Al₂O₃ prepared by the arc plasma method was less active because of its metallic state of Pd with a lower dispersion. A weak interaction between precious metals and γ-Al₂O₃ is not enough for thermal stabilization of as deposited nanoparticles during ageing in a stream of 10% H₂O in air at 900 °C.     

Identification of Physiological and Toxic Conformations in Aβ42 Aggregates

Aggregation of the 42‐residue amyloid β‐protein (Aβ42) plays a crucial role in the pathogenesis of Alzheimer's disease (AD). Despite numerous structural studies on Aβ aggregates, the relationship between tertiary structure and toxicity remains unclear. Our proline scanning and solid‐state NMR studies suggested that aggregates both of wild‐type Aβ42 and of E22K‐Aβ42 (one of the mutants related to cerebral amyloid angiopathy) contain two conformers: a major one with a turn at positions 25 and 26, and a minor one with a turn at positions 22 and 23. To identify the toxic conformer, the derivative Aβ42‐lactam(22K–23E), in which the side chains at positions 22 and 23 were covalently linked, was synthesized as a minor conformer surrogate, along with Aβ42‐lactam(25K–26E) as a major conformer surrogate. The Aβ42‐lactam(22K–23E) showed stronger aggregation, neurotoxicity, radical generation, and oligomerization than wild‐type Aβ42, whereas in Aβ42‐lactam(25K–26E) were weak. The transition from the physiological conformation with a turn at positions 25 and 26 to the toxic conformation with a turn at positions 22 and 23 might be a key event in the pathogenesis of AD.