Exploring the Minimal RNA Substrate of Flexizymes

Flexizymes are tRNA acylation ribozymes that have been successfully used to facilitate genetic code reprogramming. They are capable of charging acid substrates onto various tRNAs and tRNA analogues. However, their minimal RNA substrate has not been investigated. Here we have designed fluorescently labeled short RNAs corresponding to the four, three, and two bases (4bRNA, 3bRNA, 2bRNA) at the tRNA 3′-end and explored the minimal RNA substrate of flexizymes, dFx and eFx. 3bRNA was the observed minimal RNA substrate of the flexizymes, but the efficiency of acylation of this short RNA was two to three times lower than that of 4bRNA. The efficiency of acylation of 4bRNA was comparable with that of the microhelix, a 22-base RNA conventionally used as a tRNA analogue for analyzing acylation efficiency. We also compared the efficiencies of acylation of the microhelix and 4bRNA with various acid substrates. Thanks to the short length of 4bRNA, its acyl-4bRNA products exhibited larger mobility shifts in gel electrophoresis than those exhibited by acyl-microhelix products with every substrate tested. This indicated that 4bRNA was an ideal RNA substrate for analyzing the efficiency of acylation by flexizymes.     

Study of Cuprate Superconductivity Using the Particle Number Conserving Bogoliubov-de Gennes Equations: ARPES and STS Images From Surface Plus Bulk Layers Model

Journal of Superconductivity and Novel Magnetism - We theoretically study the superconductivity in hole-doped cuprate superconductors by employing a model composed of surface and bulk CuO $$_2$$...     

Soluble network polymers based on trifluoropropyl-substituted open-cage silsesquioxane: Synthesis,properties, and application for surface modifiers

Fluorinated completely condensed polyhedral oligomeric silsesquioxanes (F-CC-POSSs) are widely utilized as surface modifiers for polymeric materials because of their polyhedral and fluorine-rich structures, which generate polymers with lower surface energies under molecular-level control. In contrast, their derivatives, fluorinated incompletely condensed or open-cage POSSs (F-IC-POSSs), have similarly intriguing structures, but their utilization for polymer synthesis remains undeveloped. Herein, fluorinated network polymers were prepared based on a 3,3,3-trifluoropropyl-substituted IC-POSSs via hydrosilylation polymerization with isobutyl- and phenyl-substituted IC-POSS under optimized conditions. In addition to their good thermal stability and tunable refractive indices, these polymers exhibited solution processability and their casting films showed excellent optical transparency, indicating their potential for constructing fluorinated polymers. Their utilization as surface modifiers was examined by addition to poly(methylmethacrylate) (PMMA) films. Intriguingly, modified PMMA films with 2.0 and 0.5 wt% addition showed similar hydrophobicity and surface energies to the films prepared with only fluorinated network polymers.     

Polypropylene plasticization and photodegradation with a TiO2/poly(ethylene oxide)/methyl linoleate paint photocatalyst system

The photodegradation of polypropylene (PP) film was performed by a TiO₂/polyethylene oxide (PEO)/plant oil paint photocatalyst system. The photodegradation underwent two stages of development as follows: Initially PP reacted with linoleic acid radical originated from the photoreaction of plant oil component. Second, the linoleic acid graft‐polymer was decomposed, and then PP chain scission was caused. The process was studied using methyl linoleate (ML) in detail. The melting point of the 24 h‐photodegraded PP slightly decreased, and those of the 48 h‐ and 96 h‐ones drastically did as compared with the pristine PP. The crystallinity (χ_c) decreased at the 48 h photodegradation time and drastically increased at the 96 h one. The 24 h‐photodegraded PP showed the 77% Young's modulus, 88% tensile strength, and 103% strain at break values to those of the pristine PP. The ML graft‐polymerization and decomposition brought about the PP plasticizing and chemi‐crystallization, causing the PP degradation. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 39909.     

Combinatorial Measurement of CDKN1A/p21 and KIF20A Expression for Discrimination of DNA Damage-Induced Clastogenicity

In vitro mammalian cytogenetic tests detect chromosomal aberrations and are used for testing the genotoxicity of compounds. This study aimed to identify a supportive genomic biomarker could minimize the risk of misjudgments and aid appropriate decision making in genotoxicity testing. Human lymphoblastoid TK6 cells were treated with each of six DNA damage-inducing genotoxins (clastogens) or two genotoxins that do not cause DNA damage. Cells were exposed to each compound for 4 h, and gene expression was comprehensively examined using Affymetrix U133A microarrays. Toxicogenomic analysis revealed characteristic alterations in the expression of genes included in cyclin-dependent kinase inhibitor 1A (CDKN1A/p21)-centered network. The majority of genes included in this network were upregulated on treatment with DNA damage-inducing clastogens. The network, however, also included kinesin family member 20A (KIF20A) downregulated by treatment with all the DNA damage-inducing clastogens. Downregulation of KIF20A expression was successfully confirmed using additional DNA damage-inducing clastogens. Our analysis also demonstrated that nucleic acid constituents falsely downregulated the expression of KIF20A, possibly via p16 activation, independently of the CDKN1A signaling pathway. Our results indicate the potential of KIF20A as a supportive biomarker for clastogenicity judgment and possible mechanisms involved in KIF20A downregulation in DNA damage and non-DNA damage signaling networks.     

Terpendole E and its Derivative Inhibit STLC‐ and GSK‐1‐Resistant Eg5

Terpendole E is first natural product found to inhibit mitotic kinesin Eg5, but its inhibitory mechanism remains to be revealed. Here, we report the effects of terpendole E and 11ketopaspaline (a new natural terpendole E analogue) on the Eg5–microtubule interaction and in several Eg5 mutants. 11‐Ketopaspaline is a shunt product from terpendole E, and it shows potent inhibitory activity against the microtubule‐stimulated ATPase activity of Eg5. Unlike other Eg5 inhibitors, such as S‐trityl‐L ‐cysteine (STLC) and GSK‐1, both terpendole E and 11‐ketopaspaline only partially inhibited Eg5–microtubule interaction. Furthermore, terpendole E and 11‐ketopaspaline inhibited several Eg5 mutants that are resistant to STLC (Eg5^D130A, Eg5^L214A) or GSK‐1 (Eg5^I299F, Eg5^A356T), but with the same extent of inhibition against wild‐type Eg5. Because Eg5^D130A and Eg5^L214A show cross‐resistance to most known Eg5 inhibitors, which bind the L5 loop, these results suggest that terpendole E and its analogues have a different binding site and/or inhibitory mechanism to those for L5 loop‐binding type Eg5 inhibitors.