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  1. Article ; Online: Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids.

    Lee, Joon-Hwa / Katahira, Masato

    International journal of molecular sciences

    2022  Volume 23, Issue 10

    Abstract: Nucleic acids have essential roles in all biological processes related to genetic information, such as replication, transcription, translation, repair, and recombination [ ... ]. ...

    Abstract Nucleic acids have essential roles in all biological processes related to genetic information, such as replication, transcription, translation, repair, and recombination [...].
    MeSH term(s) Biophysics ; Nucleic Acids
    Chemical Substances Nucleic Acids
    Language English
    Publishing date 2022-05-23
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23105836
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  2. Article ; Online: Enhancing Bioethanol Production from Rice Straw through Environmentally Friendly Delignification Using Versatile Peroxidase.

    Teo, Kenneth Sze Kai / Kondo, Keiko / Khattab, Sadat Mohamed Rezk / Watanabe, Takashi / Nagata, Takashi / Katahira, Masato

    Journal of agricultural and food chemistry

    2024  Volume 72, Issue 5, Page(s) 2657–2666

    Abstract: Rice straw (RS), an agricultural residue rich in carbohydrates, has substantial potential for bioethanol production. However, the presence of lignin impedes access to these carbohydrates, hindering efficient carbohydrate-to-bioethanol conversion. Here, ... ...

    Abstract Rice straw (RS), an agricultural residue rich in carbohydrates, has substantial potential for bioethanol production. However, the presence of lignin impedes access to these carbohydrates, hindering efficient carbohydrate-to-bioethanol conversion. Here, we expressed versatile peroxidase (VP), a lignin-degrading enzyme, in
    MeSH term(s) Lignin/chemistry ; Oryza/chemistry ; Peroxidase/metabolism ; Carbohydrates/chemistry ; Peroxidases/metabolism ; Fermentation ; Hydrolysis
    Chemical Substances Lignin (9005-53-2) ; Peroxidase (EC 1.11.1.7) ; Carbohydrates ; Peroxidases (EC 1.11.1.-)
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 241619-0
    ISSN 1520-5118 ; 0021-8561
    ISSN (online) 1520-5118
    ISSN 0021-8561
    DOI 10.1021/acs.jafc.3c07998
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    In stock of ZB MED Cologne/Königswinter

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  3. Article ; Online: Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR.

    Eladl, Omar / Yamaoki, Yudai / Kondo, Keiko / Nagata, Takashi / Katahira, Masato

    International journal of molecular sciences

    2023  Volume 24, Issue 10

    Abstract: An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside ... ...

    Abstract An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside living cells. We examined an RNA aptamer for HIV-1 Tat (TA), which had been found to trap Tat and repress its function in living human cells. We first used in vitro NMR to examine the interaction between TA and a part of Tat containing the binding site for trans-activation response element (TAR). It was revealed that two U-A∗U base triples are formed in TA upon binding of Tat. This was assumed to be critical for strong binding. Then, TA in complex with a part of Tat was incorporated into living human cells. The presence of two U-A∗U base triples was also revealed for the complex in living human cells by in-cell NMR. Thus, the activity of TA in living human cells was rationally elucidated by in-cell NMR.
    MeSH term(s) Humans ; tat Gene Products, Human Immunodeficiency Virus/metabolism ; Aptamers, Nucleotide/chemistry ; HIV-1/metabolism ; Nucleic Acid Conformation ; Magnetic Resonance Spectroscopy ; RNA, Viral/genetics
    Chemical Substances tat Gene Products, Human Immunodeficiency Virus ; Aptamers, Nucleotide ; RNA, Viral
    Language English
    Publishing date 2023-05-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24109069
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  4. Article ; Online: Structural insights into the molecular mechanisms of substrate recognition and hydrolysis by feruloyl esterase from Aspergillus sydowii.

    Phienluphon, Apisan / Kondo, Keiko / Mikami, Bunzo / Nagata, Takashi / Katahira, Masato

    International journal of biological macromolecules

    2023  Volume 253, Issue Pt 5, Page(s) 127188

    Abstract: The depolymerization of lignocellulosic biomass is facilitated by feruloyl esterases (FAEs), which hydrolyze ester bonds between lignin and polysaccharides. Fungal FAEs belonging to subfamily (SF) 6 release precursors such as ferulic acid derivatives, ... ...

    Abstract The depolymerization of lignocellulosic biomass is facilitated by feruloyl esterases (FAEs), which hydrolyze ester bonds between lignin and polysaccharides. Fungal FAEs belonging to subfamily (SF) 6 release precursors such as ferulic acid derivatives, attractive for biochemical production. Among these, Aspergillus sydowii FAE (AsFaeE), an SF6 FAE, exhibits remarkable activity across various substrates. In this study, we conducted X-ray crystallography and kinetic analysis to unravel the molecular mechanisms governing substrate recognition and catalysis by AsFaeE. AsFaeE exhibits a typical α/β-hydrolase fold, characterized by a catalytic triad of serine, aspartate, and histidine. Comparative analysis of substrate-free, ferulic acid-bound, and sinapic acid-bound forms of AsFaeE suggests a conformational change in the loop covering the substrate-binding pocket upon binding. Notably, Pro158 and Phe159 within this loop cover the phenolic part of the substrate, forming three layers of planar rings. Our structure-based functional mutagenesis clarifies the roles of the residues involved in substrate binding and catalytic activity. Furthermore, distinct substrate-binding mechanisms between AsFaeE and other studied FAEs are identified. This investigation offers the initial structural insights into substrate recognition by SF6 FAEs, equipping us with structural knowledge that might facilitate the design of FAE variants capable of efficiently processing a wider range of substrate sizes.
    MeSH term(s) Hydrolysis ; Kinetics ; Carboxylic Ester Hydrolases/chemistry ; Substrate Specificity
    Chemical Substances feruloyl esterase (EC 3.1.1.73) ; ferulic acid (AVM951ZWST) ; Carboxylic Ester Hydrolases (EC 3.1.1.-)
    Language English
    Publishing date 2023-09-30
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2023.127188
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Fluoride Ion in Alcohols: Isopropanol vs Hexafluoroisopropanol.

    Yoneda, Nozomi / Iyama, Haruka / Nagata, Takashi / Katahira, Masato / Ishii, Yoshiki / Tada, Kohei / Matsumoto, Kazuhiko / Hagiwara, Rika

    The journal of physical chemistry letters

    2024  Volume 15, Issue 6, Page(s) 1677–1685

    Abstract: The utility of alcohol as a hydrogen bonding donor is considered a providential avenue for moderating the high basicity and reactivity of the fluoride ion, typically used with large cations. However, the practicality of alcohol-fluoride systems in ... ...

    Abstract The utility of alcohol as a hydrogen bonding donor is considered a providential avenue for moderating the high basicity and reactivity of the fluoride ion, typically used with large cations. However, the practicality of alcohol-fluoride systems in reactions is hampered by the limited understanding of the pertinent interactions between the OH group and F
    Language English
    Publishing date 2024-02-05
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c03619
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  6. Article ; Online: Detection of interaction between an RNA aptamer and its target compound in living human cells using 2D in-cell NMR.

    Eladl, Omar / Yamaoki, Yudai / Kondo, Keiko / Nagata, Takashi / Katahira, Masato

    Chemical communications (Cambridge, England)

    2022  

    Abstract: We introduced an isotopically labeled RNA aptamer for HIV-1 Tat prepared ... ...

    Abstract We introduced an isotopically labeled RNA aptamer for HIV-1 Tat prepared by
    Language English
    Publishing date 2022-12-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d2cc05576g
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  7. Article ; Online: Detection of parallel and antiparallel DNA triplex structures in living human cells using in-cell NMR.

    Sakamoto, Tomoki / Yamaoki, Yudai / Nagata, Takashi / Katahira, Masato

    Chemical communications (Cambridge, England)

    2021  Volume 57, Issue 52, Page(s) 6364–6367

    Abstract: We introduced oligodeoxynucleotides (ODNs) that form parallel and antiparallel triplex structures in vitro into living human cells and recorded their in-cell NMR spectra. Observation of landmark signals for triplex structures proved for the first time ... ...

    Abstract We introduced oligodeoxynucleotides (ODNs) that form parallel and antiparallel triplex structures in vitro into living human cells and recorded their in-cell NMR spectra. Observation of landmark signals for triplex structures proved for the first time that parallel and antiparallel triplex structures are formed in living human cells.
    MeSH term(s) DNA/analysis ; DNA/metabolism ; HeLa Cells ; Humans ; Magnetic Resonance Spectroscopy ; Microscopy, Confocal ; Nucleic Acid Conformation ; Oligonucleotides/chemistry ; Oligonucleotides/metabolism
    Chemical Substances Oligonucleotides ; triplex DNA ; DNA (9007-49-2)
    Language English
    Publishing date 2021-06-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d1cc01761f
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  8. Article: Detection of parallel and antiparallel DNA triplex structures in living human cells using in-cell NMR

    Sakamoto, Tomoki / Yamaoki, Yudai / Nagata, Takashi / Katahira, Masato

    Chemical communications. 2021 June 29, v. 57, no. 52

    2021  

    Abstract: We introduced oligodeoxynucleotides (ODNs) that form parallel and antiparallel triplex structures in vitro into living human cells and recorded their in-cell NMR spectra. Observation of landmark signals for triplex structures proved for the first time ... ...

    Abstract We introduced oligodeoxynucleotides (ODNs) that form parallel and antiparallel triplex structures in vitro into living human cells and recorded their in-cell NMR spectra. Observation of landmark signals for triplex structures proved for the first time that parallel and antiparallel triplex structures are formed in living human cells.
    Keywords DNA ; humans ; oligodeoxyribonucleotides
    Language English
    Dates of publication 2021-0629
    Size p. 6364-6367.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d1cc01761f
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  9. Article: Recent progress of in-cell NMR of nucleic acids in living human cells.

    Yamaoki, Yudai / Nagata, Takashi / Sakamoto, Tomoki / Katahira, Masato

    Biophysical reviews

    2020  Volume 12, Issue 2, Page(s) 411–417

    Abstract: The inside of living cells is highly crowded with biological macromolecules. It has long been considered that the properties of nucleic acids and proteins, such as their structures, dynamics, interactions, and enzymatic activities, in intracellular ... ...

    Abstract The inside of living cells is highly crowded with biological macromolecules. It has long been considered that the properties of nucleic acids and proteins, such as their structures, dynamics, interactions, and enzymatic activities, in intracellular environments are different from those under in vitro dilute conditions. In-cell NMR is a robust and powerful method used in the direct measurement of those properties in living cells. However, until 2 years ago, in-cell NMR was limited to Xenopus laevis oocytes due to technical challenges of incorporating exogenous nucleic acids. In the last 2 years, in-cell NMR spectra of nucleic acid introduced into living human cells have been reported. By use of the in-cell NMR spectra of nucleic acids in living human cells, the formation of hairpin structures with Watson-Crick base pairs, and i-motif and G-quadruplex structures with non-Watson-Crick base pairs was demonstrated. Others investigated the mRNA-antisense drug interactions and DNA-small compound interactions. In this article, we review these studies to underscore the potential of in-cell NMR for addressing the structures, dynamics, and interactions of nucleic acids in living human cells.
    Language English
    Publishing date 2020-03-06
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-020-00664-x
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  10. Article: Observation of nucleic acids inside living human cells by in-cell NMR spectroscopy.

    Yamaoki, Yudai / Nagata, Takashi / Sakamoto, Tomoki / Katahira, Masato

    Biophysics and physicobiology

    2020  Volume 17, Page(s) 36–41

    Abstract: The intracellular environment is highly crowded with biomacromolecules such as proteins and nucleic acids. Under such conditions, the structural and biophysical features of nucleic acids have been thought to be different from ... ...

    Abstract The intracellular environment is highly crowded with biomacromolecules such as proteins and nucleic acids. Under such conditions, the structural and biophysical features of nucleic acids have been thought to be different from those
    Language English
    Publishing date 2020-05-26
    Publishing country Japan
    Document type Journal Article
    ISSN 2189-4779
    ISSN 2189-4779
    DOI 10.2142/biophysico.BSJ-2020006
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