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Synthesis of biocompatible gold nanoparticles for photothermal therapy by mineralization using peptides 査読あり
Shuhei Yoshida, Koki Yoshida, Yoshiki Shitamukai, Makoto Ozaki, Takaaki Tsuruoka, Kenji Usui
RSC Advances 15 48521 - 48528 2025年12月
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Current Trends in Liquid Chromatography-Mass Spectrometry Analysis of Small Interfering RNAs: A Short Review 査読あり
Hiroyuki Togawa, Takao Yamaguchi, Junji Kawakami, Satoshi Obika
Journal of Chromatography A 2025年11月
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Theoretical calculation of the amounts of nucleotide deletion impurities in oligonucleotides 査読あり
Yasunori Uchida, Tokuyuki Yoshida, Emi Saito, Hirokazu Nankai, Kaoru Karasawa, Chie Inagaki, Noriyuki Iwasaki, Daisuke Higo, Kentaro Takahara, Takashi Osawa, Takao Yamaguchi, Kosuke Ito, Junji Kawakami, Satoshi Obika, Takao Inoue
International Journal of Pharmaceutical 2025年11月
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Natsumi Ueda, Hayato Okazaki, Akihiro Mikuma, Ayane Kunieda, Soma Kawashima, Takeru Torii, Keiko Kawauchi, Masatake Matsuoka, Tomohiro Onodera, Norimasa Iwasaki, Koji Nagahama
16 8847 2025年10月
担当区分：最終著者, 責任著者
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Phase Separation of RX Repeat Peptides with Nucleic Acids
Sumit Shil, Mitsuki Tsuruta, Ryosuke Suzuki, Yoshiki Hashimoto, Takeru Torii, Shinya Taniguchi, Tomohiro Umetani, Keiko Kawauchi, Daisuke Miyoshi
Chemistry – An Asian Journal 2025年10月
出版者・発行元：Wiley
Abstract
Biomolecular liquid‐liquid phase separation (LLPS) plays a crucial role in organizing membraneless cellular compartments, which regulate a wide variety of cellular processes. A key molecular mechanism underlying LLPS of nucleic acids involves G‐quadruplex (G4) structures of DNA and RNA interacting with intrinsically disordered proteins, particularly arginine and glycine (RGG/RG) rich proteins. The role of arginine residues in LLPS has been studied extensively, whereas few studies have focused on the role of the another frequently occurring residues, glycine. Here, we systematically investigated the contribution of G residues by substituting them with alanine (A), proline (P), valine (V), and tyrosine (Y) residues, generating a series of RX repeat peptides. Turbidity and microscopy assays with DNA oligonucleotides forming G4, duplex, as well as random coil, showed that RP and RA‐peptides enhanced LLPS with G4 DNA, by comparing RG‐peptide. In contrast, RY promoted liquid‐solid phase separation (LSPS) with the G4 DNA, although it underwent LLPS with the random coil and duplex DNAs. In addition, RV‐peptide formed aggregates even in the absence of any DNA. These results demonstrate that side‐chain size, hydrophobicity, and aromaticity are critical factors for the LLPS and LSPS capability and selectivity with DNA forming various secondary structures. This study provides mechanistic insights into protein‐nucleic acid LLPS and LSPS and guides the rational design peptides to undergo LLPS but not LSPS with nucleic acids. -
Effects of molecular crowding on the structure, folding, stability, and catalysis of RNA 招待あり 査読あり 国際誌
Shu-Ichi Nakano
Subcellular Biochemistry, (Macro)Molecular Crowding (Springer) 109 155 - 185 2025年10月
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Effects of acid-mediated deamination of cytidine and 5-methylcytidine on solid-phase synthesis of oligonucleotides 査読あり
Yusuke Isono, Chihiro Karasugi, Takuya Akisawa, Takashi Osawa, Qin Ren, Michiaki Tatsuno, Fumi Ito, Takao Inoue, Junji Kawakami, Satoshi Obika, Masaki Shinoda
Tetrahedron 185 134840 - 134840 2025年10月
出版者・発行元：Elsevier BV
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Metal-organic framework-injectable hydrogel hybrid scaffolds promote accelerated angiogenesis for in vivo tissue engineering 査読あり
S. S. Islam, T. Dode, S. Kawashima, M. Fukuoka, T. Tsuruoka, K. Nagahama
RSC Adv. 15 32143 - 32154 2025年9月
担当区分：責任著者
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Functional analysis of histidine-dependent self-cleaving RNAs obtained by in vitro selection 査読あり
Nae Sakimoto, Shoichiro Tanaka, Riki Hatakenaka, Yoshie Yamaguchi-Miyazaki, Elisa Tomita-Sudo, Tomoka Akita, Taku Ishigaki, Shigenori Iwai, Junji Kawakami
ChemBioChem e202500411 2025年9月
担当区分：最終著者, 責任著者
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Metal–organic framework–injectable hydrogel hybrid scaffolds promote accelerated angiogenesis for in vivo tissue engineering 査読あり
Sobuj Shahidul Islam, Tatsuya Dode, Soma Kawashima, Myu Fukuoka, Takaaki Tsuruoka, Koji Nagahama
RSC Advances 15 32143 - 32154 2025年9月
担当区分：最終著者, 責任著者
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Hydrophilic ether-modified carboxybetaines: a molecular design approach for enzyme activation and stabilization 査読あり
Takuma Aoki, Koki Takagi, Yuichi Nakagawa, Kazuya Koumoto
Bulletin of the Chemical Society of Japan 98 uoaf075 2025年8月
担当区分：最終著者, 責任著者
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Sobuj Shahidul Islam,Tatsuya Dode,Soma Kawashima,Myu Fukuoka,Takaaki Tsuruoka andKoji Nagahama
Gels 11 ( 7 ) 514 2025年7月
担当区分：最終著者, 責任著者
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MOFs—Combining Fully Synthetic Injectable Hydrogel Scaffolds Exhibiting Higher Skeletal Muscle Regenerative Efficiency than Matrigel 査読あり
S. S. Islam, T. Dode, S. Kawashima, M. Fukuoka, T. Tsuruoka, K. Nagahama
Gles 11 514 2025年7月
担当区分：責任著者
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Madoka Suzuki, Keiko Kawauchi, Hiroaki Machiyama, Hiroaki Hirata, Shin'ichi Ishiwata, Hideaki Fujita
Biotechnology and Bioengineering 122 ( 7 ) 1929 - 1940 2025年7月
DOI： 10.1002/bit.28996
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Comprehensive analysis of stability and variability of DNA minimal i-motif structures 招待あり 査読あり
K. Ashida, A. Kitabayashi, K. Nishiyama, and S. Nakano
Molecules 30 1831 2025年4月
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One-Pot Synthesis and Immobilization of Gold Nanoparticles Using Peptidyl Microbeads 査読あり 国際誌
Shuhei Yoshida, Koki Yoshida, Taichi Isozaki, Maho Oura, Makoto Ozaki, Takaaki Tsuruoka, Kenji Usui
Molecules 30 1689 2025年4月
Gold nanoparticles (AuNPs) have surface plasmon resonance (SPR) and catalytic activity that are not found in bulk gold and have been studied in various fields. Among these, immobilization of AuNPs on various solid-phase substrates is known to produce stable catalytic activity and specific SPRs and research on the immobilization of AuNPs has been conducted actively. However, the conventional method requires the preparation and immobilization of AuNPs in separate processes, making it difficult to prepare immobilized AuNPs in a one-pot process. In this study, we attempted to synthesize and immobilize AuNPs using peptidyl beads, which are microbeads having immobilized a peptide capable of reducing gold ions. We successfully reduced Au ions from 0.5 to 1000 µM of HAuCl4 and immobilized them on peptidyl beads in the form of AuNPs. The immobilized AuNPs have a constant particle size independent of the HAuCl4 concentration. Furthermore, the peptidyl beads with AuNPs have catalytic activity. The quantity of the AuNPs on the peptidyl beads and, subsequently, the catalytic reaction rate of the sample, could be controlled. This study would also be expected to be applied to the immobilization of metallic nanomaterials other than AuNPs by modifying the peptide sequence.
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Three- and four-stranded nucleic acid structures and their ligands. 国際誌
Yoshiki Hashimoto, Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi, Daisuke Miyoshi
RSC chemical biology 6 ( 4 ) 466 - 491 2025年4月
Nucleic acids have the potential to form not only duplexes, but also various non-canonical secondary structures in living cells. Non-canonical structures play regulatory functions mainly in the central dogma. Therefore, nucleic acid targeting molecules are potential novel therapeutic drugs that can target 'undruggable' proteins in various diseases. One of the concerns of small molecules targeting nucleic acids is selectivity, because nucleic acids have only four different building blocks. Three- and four-stranded non-canonical structures, triplexes and quadruplexes, respectively, are promising targets of small molecules because their three-dimensional structures are significantly different from the canonical duplexes, which are the most abundant in cells. Here, we describe some basic properties of the triplexes and quadruplexes and small molecules targeting the triplexes and tetraplexes.
DOI： 10.1039/d4cb00287c
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Liquid-liquid phase separation induced by i-motif DNA under molecular crowding conditions 招待あり 査読あり
Ryosuke Suzuki, Mitsuki Tsuruta, Sumit Shil, Kosei Morohashi, Keiko Kawauchi, Daisuke Miyoshia
Polymer J. 57 931 - 940 2025年4月
担当区分：責任著者
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One-Pot Synthesis and Immobilization of Gold Nanoparticles Using Peptidyl Microbeads 査読あり
Shuhei Yoshida, Koki Yoshida, Taichi Isozaki, Maho Oura, Makoto Ozaki, Takaaki Tsuruoka, Kenji Usui
Molecules 2025年4月
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Tendon Tissue Regeneration With Cell Orientation Using an Injectable Alginate-Cell Cross-linked Gel 査読あり
Jun Yamaguchi, Kentaro Homan, Tomohiro Onodera, Masatake Matsuoka, Shoutaro Arakawa, Natsumi Ueda, Nana Kawate, Takayuki Nonoyama, Yoshinori Katsuyama, Koji Nagahama, Mitsuru Saito, Norimasa Iwasaki
The American Journal of Sports Medicine 2025年3月