Papers -
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Functional analysis of histidine-dependent self-cleaving RNAs obtained by in vitro selection Reviewed
Nae Sakimoto, Shoichiro Tanaka, Riki Hatakenaka, Yoshie Yamaguchi-Miyazaki, Elisa Tomita-Sudo, Tomoka Akita, Taku Ishigaki, Shigenori Iwai, Junji Kawakami
ChemBioChem e202500411 2025.9
Authorship：Last author, Corresponding author
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Metal–organic framework–injectable hydrogel hybrid scaffolds promote accelerated angiogenesis for in vivo tissue engineering Reviewed
Sobuj Shahidul Islam, Tatsuya Dode, Soma Kawashima, Myu Fukuoka, Takaaki Tsuruoka, Koji Nagahama
RSC Advances 15 32143 - 32154 2025.9
Authorship：Last author, Corresponding author
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Nanocomposite thin layers of in situ-embedded bismuth nanoparticles in a polymer matrix: synthesis and size-dependent thermal properties Reviewed
Takaya Kawakami, Yohei Takashima, Takaaki Tsuruoka, Kensuke Akamatsu
Chem. Lett. 54 upaf172 2025.9
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Hydrophilic ether-modified carboxybetaines: a molecular design approach for enzyme activation and stabilization Reviewed
Takuma Aoki, Koki Takagi, Yuichi Nakagawa, Kazuya Koumoto
Bulletin of the Chemical Society of Japan 98 uoaf075 2025.8
Authorship：Last author, Corresponding author
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Sobuj Shahidul Islam,Tatsuya Dode,Soma Kawashima,Myu Fukuoka,Takaaki Tsuruoka andKoji Nagahama
Gels 11 ( 7 ) 514 2025.7
Authorship：Last author, Corresponding author
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MOFs—Combining Fully Synthetic Injectable Hydrogel Scaffolds Exhibiting Higher Skeletal Muscle Regenerative Efficiency than Matrigel Reviewed
S. S. Islam, T. Dode, S. Kawashima, M. Fukuoka, T. Tsuruoka, K. Nagahama
Gles 11 514 2025.7
Authorship：Corresponding author
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Dynamic Remodeling of Mechano-Sensing Complexes in Suspended Fibroblast Cell-Sheets Under External Mechanical Stimulus Reviewed International journal
Madoka Suzuki, Keiko Kawauchi, Hiroaki Machiyama, Hiroaki Hirata, Shin'ichi Ishiwata, Hideaki Fujita
Biotechnology and Bioengineering 122 ( 7 ) 1929 - 1940 2025.7
DOI： 10.1002/bit.28996
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Comprehensive analysis of stability and variability of DNA minimal i-motif structures Invited Reviewed
K. Ashida, A. Kitabayashi, K. Nishiyama, and S. Nakano
Molecules 30 1831 2025.4
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One-Pot Synthesis and Immobilization of Gold Nanoparticles Using Peptidyl Microbeads Reviewed International journal
Shuhei Yoshida, Koki Yoshida, Taichi Isozaki, Maho Oura, Makoto Ozaki, Takaaki Tsuruoka, Kenji Usui
Molecules 30 1689 2025.4
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.
DOI： 10.3390/molecules30081689
Other Link： https://www.mdpi.com/1420-3049/30/8/1689
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Three- and four-stranded nucleic acid structures and their ligands. International journal
Yoshiki Hashimoto, Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi, Daisuke Miyoshi
RSC chemical biology 6 ( 4 ) 466 - 491 2025.4
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 Invited Reviewed
Ryosuke Suzuki, Mitsuki Tsuruta, Sumit Shil, Kosei Morohashi, Keiko Kawauchi, Daisuke Miyoshia
Polymer J. 57 931 - 940 2025.4
Authorship：Corresponding author
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One-Pot Synthesis and Immobilization of Gold Nanoparticles Using Peptidyl Microbeads Reviewed
Shuhei Yoshida, Koki Yoshida, Taichi Isozaki, Maho Oura, Makoto Ozaki, Takaaki Tsuruoka, Kenji Usui
Molecules 2025.4
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Tendon Tissue Regeneration With Cell Orientation Using an Injectable Alginate-Cell Cross-linked Gel Reviewed
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 2025.3
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The role of cytosine methylation in regulating the topology and liquid-liquid phase separation of DNA G-quadruplexes. International journal
Mitsuki Tsuruta, Sumit Shil, Shinya Taniguchi, Keiko Kawauchi, Daisuke Miyoshi
Chemical science 16 ( 10 ) 4213 - 4225 2025.3
Aberrant expansion of GGGGCC DNA repeats that form G-quadruplexes (G4) is the main cause of amyotrophic lateral sclerosis (ALS). Expanded GGGGCC repeats induce liquid-liquid phase separation (LLPS) through their interaction with cellular proteins. Furthermore, GGGGCC expansion induces cytosine methylation (mC). Previous studies have shown that even slight chemical modifications of RNAs and proteins can drastically affect their LLPS ability, yet the relationship between LLPS and epigenetic DNA modifications like mC remains unexplored. As a model system, we investigated the effects of mC on LLPS induced by GGGGCC repeat DNAs and show for the first time that mC suppresses LLPS by altering the topology of G4 from being parallel to antiparallel.
DOI： 10.1039/d4sc06959e
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Three- and four-stranded nucleic acid structures and their ligands Invited Reviewed
Yoshiki Hashimoto, Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi, and Daisuke Miyoshi
RSC Chemical Biology 6 466 - 491 2025.3
Authorship：Corresponding author
DOI： 10.1039/D4CB00287C
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ケミカルバイオロジーの冒険（１２） 核酸を標的とした低分子・中分子化合物 Invited
堂野主税、勝田陽介、三好大輔
現代化学 648 32 - 39 2025.2
Authorship：Last author
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Roles of Loop Region in Folding Kinetics and Transcription Inhibition of DNA G-Quadruplexes Reviewed
64 609 - 619 2025.2
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Development of a New Structural Transformation Reaction in Cr-Based MOFs Induced by Fluoride Reviewed
Shintaro Tanaka, Ryoya Miyata, Reon Teramoto, Junya Sugimoto, Takaaki Tsuruoka, Kensuke Akamatsu, Yohei Takashima
Chem. Asian J e202401717 2025.2
Authorship：Last author, Corresponding author
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Development of detection system for lead ions in mixture solutions using UV-Vis measurements with peptide immobilized microbeads Reviewed International journal
Shuhei Yoshida, Koki Yoshida, Yoshio Hamada, Takaaki Tsuruoka, Kenji Usui
Scientific Reports 15 3249 2025.1
Environmental pollution caused by heavy metals are problems worldwide. In particular, pollution and poisoning by lead ions (Pb2+) continue to be common and serious problems. Hence, there is a need for a widely usable method to easily detect Pb2+ from solutions containing organic materials from environmental water such as seas, ponds, etc. Here, we established a system to easily detect Pb2+ from such mixture solutions using Pb2+ binding peptide immobilized beads (peptidyl beads) and ultraviolet (UV) absorption measurements. This method could detect Pb2+ at low concentrations equivalent to inductively coupled plasmon-atomic emission spectroscopy (ICP-AES). Using the detected values to create a calibration curve, it was found that there was a positive correlation between the concentration of Pb2+ and absorbance, which also made it possible to quantify sub-µM Pb2+ in the solutions. Furthermore, Pb2+ was detected and quantified under mixed conditions of environmental water such as seas, rivers, and ponds. This method is expected to become a versatile and easy-to-use Pb2+ detection method for end-users worldwide.
DOI： 10.1038/s41598-025-86082-z
Other Link： https://www.nature.com/articles/s41598-025-86082-z
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Complex and Non-sequential Current Signatures of a β-Hairpin Peptide Confined in a Nanopore International coauthorship International journal
Misa Yamaji, Mauro Chinappi, Blasco Morozzo della Rocca, Kenji Usui, Ryuji Kawano
Analytical Chemistry 97 2044 - 2051 2025.1
Publisher：American Chemical Society (ACS)
Nanopore sensing is widely used for single-molecule detection, originally applied to nucleic acids and now extended to protein sensing. Our study focuses on the complex conformational changes of peptides in nanopores, which may have implications for peptide fingerprinting and protein identification. Specifically, we investigated the interaction of a β-hairpin peptide (SV28) within an α-hemolysin (αHL) nanopore. Our experiments revealed that SV28 is captured via dielectrophoresis and exhibits long dwell times within the nanopore, leading to multiple current blockade levels. Unlike DNA hairpins, the peptide showed non-sequential transitions among four distinct blockade levels. This complex behavior indicates that the peptide dynamics in nanopores cannot be simply modeled along a single reaction coordinate. Our findings provide insights into peptide-nanopore interactions, which are potentially useful for developing nanopore-based peptide identification technologies.