Search Results 1-20 of 1478

  • Self-powered RNA nanomachine driven by metastable structure

    Shungo Kobori , Yoko Nomura , Yohei Yokobayashi

    … Many non-coding and regulatory RNA elements have evolved to exploit transient or metastable structures that emerge during transcription to control complex folding pathways or to encode dynamic functions. … However, efforts to engineer synthetic RNA devices have mostly focused on the thermodynamically stable structures. … In this work, we designed a short RNA sequence that adopts a robust metastable structure when transcribed by an RNA polymerase. …

    Nucleic Acids Research 47(11), 6007-6014, 2019-05-11


  • 5′-Terminal stem-loop of carnation ringspot virus RNA1 is required for the efficient amplification of viral RNAs

    Kaido Masanori , Nagano Hideaki , Omote Kazunori , Takano Yoshitaka , Mise Kazuyuki , Okuno Tetsuro

    … Overall RNA sequences of these viruses were similar, but PV-0097 and PV-21 contained additional nucleotides at the 5′ end of RNA1. … Stem-loop structures were predicted in the 5′-terminal region of PV-0097 and PV-21 RNA1 but not in 1.30 RNA1. …

    Virus Research (265), 138-142, 2019-05


  • The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism

    岩崎 憲治 , Nai-Chi Chen , Masato Yoshimura , Naoyuki Miyazaki , Hong-Hsiang Guan , Phimonphan Chuankhayan , Chien-Chih Lin , Shao-Kang Chen , Pei-Ju Lin , Yen-Chieh Huang , Kenji IWASAKI , Atsushi Nakagawa , Sunney I. Chan , Chun-Jung Chen

    … The viral capsid structure determines viral assembly and host specificity during infections. … Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. … The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; …

    Communications Biology (2), 72, 2019-02


  • Recent Progress of Targeted G-Quadruplex-Preferred Ligands Toward Cancer Therapy

    Asamitsu Sefan , Obata Shunsuke , Yu Zutao , Bando Toshikazu , Sugiyama Hiroshi

    … A G-quadruplex (G4) is a well-known nucleic acid secondary structure comprising guanine-rich sequences, and has profound implications for various pharmacological and biological events, including cancers. … To date, a large variety of DNA/RNA G4 ligands have been developed by a number of laboratories. … As protein-targeting drugs face similar situations, G-quadruplex-interacting drugs displayed low selectivity to the targeted G-quadruplex structure. …

    Molecules 24(3), 2019-01-24


  • Localization of BCR-ABL to Stress Granules Contributes to Its Oncogenic Function

    Kashiwagi Sayaka , Ohba Yusuke , Fujioka Yoichiro , Kondo Takeshi , Satoh Aya O. , Yoshida Aiko , Fujioka Mari , Sasajima Hitoshi , Amano Maho , Teshima Takanori

    … BCR-ABL-positive granules were not colocalized with any markers for membrane-bound organelles but were colocalized with HSP90a, a component of RNA granules. …

    Cell Structure and Function 44(2), 195-204, 2019


  • X-Ray Crystallographic Structure of <i>Hericium erinaceus</i> Ribonuclease, RNase He1 in Complex with Zinc

    Kobayashi Hiroko , Sangawa Takeshi , Takebe Katsuki , Motoyoshi Naomi , Itagaki Tadashi , Suzuki Mamoru

    … Its RNA degrading activity is strongly inhibited by Zn<sup>2+</sup>, similar to other T1 family RNases. … Here, we determined the three-dimensional X-ray crystal structure of RNase He1 in complex with Zn, which revealed that Zn binding most likely prevents substrate entry into the active site due to steric hindrance. …

    Biological and Pharmaceutical Bulletin 42(12), 2054-2061, 2019


  • Prediction of the secondary structure of short DNA aptamers

    Afanasyeva Arina , Nagao Chioko , Mizuguchi Kenji

    … However, to understand the structure-function relationships of aptamers, robust structure modeling tools are necessary. … Several such tools have been developed and extensively tested, although most of them target various forms of biological RNA. …

    Biophysics and Physicobiology 16(0), 287-294, 2019


  • Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments

    Ekimoto Toru , Kokabu Yuichi , Oroguchi Tomotaka , Ikeguchi Mitsunori

    … To avoid overfitting, only the two parameters are adjusted for an entire structure ensemble. … To verify the developed method, theoretical SAXS profiles for various proteins, DNA/RNA, and a protein-RNA complex are compared with both experimental profiles and theoretical profiles obtained by the all-atom representation. …

    Biophysics and Physicobiology 16(0), 377-390, 2019


  • Methodological improvements for the analysis of domain movements in large biomolecular complexes

    Veevers Ruth , Hayward Steven

    … As more structures of large biomolecules in different functional states become available as experimental techniques for structure determination advance, there is a need to develop methods to understand the conformational changes that occur. … The new stand-alone, platform-independent implementation, DynDom6D, can analyse biomolecules comprising protein, DNA and RNA, and employs an alignment method to automatically achieve the required equivalence of atoms in the two structures.</p> …

    Biophysics and Physicobiology 16(0), 328-336, 2019


  • Expression and function of exportin 6 in full-grown and growing porcine oocytes

    ONUMA Asuka , FUJIOKA Yoshie A. , FUJII Wataru , SUGIURA Koji , NAITO Kunihiko

    … In this study, we assessed the expression and effects of exportin 6 on meiotic resumption in porcine oocytes after cloning porcine exportin 6 cDNA and carrying out overexpression and expression inhibition by mRNA and antisense RNA injection, respectively. … In contrast, exportin 6 was absent from the growing oocytes, which are meiotically incompetent and maintain the germinal-vesicle structure in the long term; …

    Journal of Reproduction and Development 65(5), 407-412, 2019


  • Identification of 15 New Bypassable Essential Genes of Fission Yeast

    Takeda Aoi , Saitoh Shigeaki , Ohkura Hiroyuki , Sawin Kenneth E. , Goshima Gohta

    … we also identified multiple genes regulating RNA processing. …

    Cell Structure and Function 44(2), 113-119, 2019


  • Study at the Kool Lab in Stanford University —Chemical Biology of Nucleic Acid—  [in Japanese]

    Tahara Yuki

    … In particular, biochemical applications/material sciences with synthetic nucleic acids, DNA and RNA have growth potential, and they are one of the most attactive fields. … This article describes the chemical biology tool with fluorescent DNA probe for detection of 8-oxoguanine DNA glycosylase activity, and the structure-activity relationships of the inhibitors by synthesizing a broad range of analogues. …

    Journal of Synthetic Organic Chemistry, Japan 77(7), 724-731, 2019


  • Anti-RelA siRNA-Encapsulated Flexible Liposome with Tight Junction-Opening Peptide as a Non-invasive Topical Therapeutic for Atopic Dermatitis

    Ibaraki Hisako , Kanazawa Takanori , Kurano Takumi , Oogi Chihiro , Takashima Yuuki , Seta Yasuo

    … <p>Small interfering RNA (siRNA) has been proposed as a novel treatment for atopic dermatitis (AD) because it suppresses sequence-specific mRNA expression. … The 1,2-dioleoyl-<i>sn</i>-glycero-3-phosphoethanolamine (DOPE)/cholesteryl hemisuccinate (CHEMS) liposome was chosen as a carrier for siRNA because of its highly flexible structure and permeability. …

    Biological and Pharmaceutical Bulletin 42(7), 1216-1225, 2019


  • Human keratinocyte HaCaT cells form aggregates containing Ras-GAP SH3 domain-binding proteins in the cytoplasm in response to a low dose of teniposide

    Qiu Wenzhe , Arimoto-Matsuzaki Kyoko , Kitamura Masami , Hata Yutaka

    … Cells arethought to survive stress by utilizing SGs as theplatform of RNA triage. … In sum, we have unexpectedly found anovel cytoplasmic structure containing G3BP thatis distinct from SG. …

    Journal of Medical and Dental Sciences 66(2), 23-30, 2019

    IR  J-STAGE 

  • Activated sludge microbial communities of a chemical plant wastewater treatment facility with high-strength bromide ions and aromatic substances

    Zhao Yan-Jie , Sato Yuya , Inaba Tomohiro , Aoyagi Tomo , Hori Tomoyuki , Habe Hiroshi

    … <p>The prokaryotic and eukaryotic microbial communities of activated sludge in a chemical plant wastewater treatment facility, processing relatively oligotrophic wastewater containing aromatic compounds and high-strength bromide ions, were characterized by high-throughput sequencing of rRNA genes based on DNA and RNA extracts. … The microbial community structure was distinct from those previously reported from domestic wastewater treatment plants. …

    The Journal of General and Applied Microbiology 65(2), 106-110, 2019


  • Calculation of Eddy Current Loss on Rotor Surface of Field-Winding type Claw-Pole Motor based on Reluctance Network Analysis

    Ichikawa Y. , Nakamura K.

    … <p>  A field-winding type claw-pole motor has a three-dimensional complicated structure. … In a previous paper, three-dimensional relcutance network anaysis (RNA) model of the claw-pole motor was proposed and the validity of the proposed model is proved by comparing with the results of torque characteristics obtained from finite element method (FEM). … This paper presents a method for calculating eddy current loss on the rotor surface of the claw-pole motor based on RNA.</p> …

    Transaction of the Magnetics Society of Japan Special Issues 3(1), 64-68, 2019


  • Long Noncoding RNA LINC00202 Promotes Tumor Progression by Sponging miR-3619-5p in Retinoblastoma

    Yan Guigang , Su Yi , Ma Zhao , Yu Lianzhi , Chen Ning

    … Luciferase reporter assay was applied to examine RNA stability, and RNA pulldown assays were used to detect interaction between lncRNA and microRNA (miRNA). …

    Cell Structure and Function 44(1), 51-60, 2019


  • MiR-187-3p Enhances Propranolol Sensitivity of Hemangioma Stem Cells

    Liu Chao , Zhao Zeliang , Ji Zhidong , Jiang Yanyan , Zheng Jiawei

    … Luciferase reporter assay and biotin RNA pull down assay were used to detect the interaction between miR-187-3p and the targeted gene. …

    Cell Structure and Function 44(1), 41-50, 2019


  • PUM2 Promotes Glioblastoma Cell Proliferation and Migration via Repressing BTG1 Expression

    Wang Yuanyu , Sun Weili , Yang Jiankai , Yang Liang , Li Chen , Liu Hongjiang , Liu Xiaopeng , Jiao Baohua

    … <p>PUM2, an RNA binding protein, is known to promote stem cell proliferation via repressing expressions of cell cycle genes. … RNA pull-down assay and RNA immunoprecipitation assay were used to test the interaction between PUM2 and BTG1 3'UTR. … RNA pull-down assay and RNA immunoprecipitation assay show PUM2 binds to BTG1 3'UTR directly. …

    Cell Structure and Function 44(1), 29-39, 2019


  • Antiviral Mechanism of Action of Epigallocatechin-3-O-gallate and Its Fatty Acid Esters

    Kaihatsu Kunihiro , Yamabe Miyuki , Ebara Yasuhito

    … Epigallocatechin-3-O-gallate (EGCG) is the major catechin component of green tea (Cameria sinensis), and is known to possess antiviral activities against a wide range of DNA viruses and RNA viruses. … According to the relationships between structure and antiviral activity of catechin derivatives, the 3-galloyl and 5'-OH group of catechin derivatives appear critical to antiviral activities. …

    Molecules 23(10), 2475, 2018-09-27


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