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A Comparative Study on the Relative Quantification of Oligonucleotide Impurities Using Several Different Types of Liquid Chromatography-Mass Spectrometers at Analytical Facilities of Multiple Institutions Reviewed
Ryutaro Takamine, Takao Yamaguchi, Kenji Hirose, Mitsuaki Sekiguchi, Kaoru Karasawa, Noriyuki Iwasaki, Kentaro Takahara, Hiroshi Sezaki, Yoshihiro Hayakawa, Hiroyuki Togawa, Takashi Okubo, Hiroo Nagano, Amane Sakurai, Nae Sakimoto, Elisa Tomita-Sudo, Tokuyuki Yoshida, Takao Inoue, Satoshi Obika, Junji Kawakami
Pharmaceutical and Medical Device Regulatory Science 57 ( 3 ) 2026.6
Authorship：Last author, Corresponding author
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Cy3-Conjugated Biocompatible Polymer Nanoparticles for Long-Term Mitochondrial Imaging Reviewed
ChemBioChem ChemBioChem Research Article Full Access Cy3-Conjugated Biocompatible Polymer Nanoparticles for Long-Term Mitochondrial Imaging Souma Kawashima, Mitsuo Inui, Izumi Takaba, Haruka Taniguchi, Koji Nagahama
ChemBioChem 27 ( 8 ) e70323 2026.4
Authorship：Last author, Corresponding author
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Development of a Microwave-Assisted Method for Enhancing the Cellular Uptake of Arginine-Rich Peptides
Fumihiro Kayamori, Momo Hirata, Takuto Kariya, Yonejiro Arimoto, Ryuji Osawa, Mami Ishikawa, Tamaki Endoh, Nobuhiro Nakanishi, Kenji Usui
Processes 14 ( 3 ) 497 2026.1
Cell-penetrating peptides (CPPs) have been extensively explored as tools for the intracellular delivery of diverse molecular cargoes. Although substantial progress has been made in elucidating their uptake mechanisms and sequence-dependent functions, limitations in cellular internalization efficiency remain a major challenge, hindering their broader biomedical application. To address this issue, the present study investigated whether microwave (MW) irradiation at 2.45 GHz can enhance CPP-mediated delivery. Using confocal laser scanning microscopy and fluorescence spectroscopy, we examined the effects of MW irradiation on the cellular uptake of arginine-rich peptides. Our results suggested that MW irradiation enhanced the cellular uptake of the peptides. These findings imply that CPP-mediated delivery assisted by MW irradiation is an effective method for improving intracellular transport and may open new avenues for the development of advanced drug delivery systems.
DOI： 10.3390/pr14030497
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Investigation of the physicochemical and functional properties of poly(2-methacryloyloxyethyl phosphorylcholine)-conjugated aptamers. International journal
Seojung Cho, Jumpei Morimoto, Yutaro Saito, Yukiko Nagai, Asuka Sakata, Keitaro Yoshimoto, Mitsuki Tsuruta, Daisuke Miyoshi, Shinsuke Sando
Biomaterials science 14 ( 1 ) 232 - 239 2026.1
Polymer conjugation is a common strategy to improve the pharmacokinetics of aptamers, yet its effects on aptamer properties are incompletely understood. Poly(ethylene glycol) (PEG) is the most widely used polymer for this purpose, but concerns about anti-PEG immune responses have prompted interest in alternative polymers. We previously reported that conjugation with the zwitterionic polymer poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) significantly prolongs the circulation time of a DNA aptamer while avoiding anti-PEG antibody recognition. In this study, we evaluated the physicochemical and functional consequences of PMPC conjugation of aptamers. Biophysical analyses suggested that the secondary structure and target-binding affinity of the aptamer were preserved, while functional consequences upon PMPC conjugation varied with the targets. The activity of a membrane receptor-targeting aptamer partially decreased, likely due to spatial constraints around the cell membrane, while RB005, targeting soluble activated coagulation factor IX, retained its full activity. In addition, PMPC conjugation significantly prolonged the in vivo plasma retention of RB005. By elucidating the effects of PMPC on aptamer properties and introducing another example that further supports the general applicability of PMPC conjugation in enhancing aptamer pharmacokinetics, these findings support PMPC as a promising alternative to PEG.
DOI： 10.1039/d5bm01078k
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Current Trends in Liquid Chromatography-Mass Spectrometry Analysis of Small Interfering RNAs: A Short Review Reviewed
Hiroyuki Togawa, Takao Yamaguchi, Junji Kawakami, Satoshi Obika
Journal of Chromatography A 1766 466550 2026.1
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Theoretical calculation of the amounts of nucleotide deletion impurities in oligonucleotides Reviewed
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 687 126364 2026.1
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Effects of N–1-mer impurities in antisense oligonucleotides on the target RNA suppression Reviewed
Tomoka Akita, Elisa Tomita-Sudo, Renshin Sano, Nae Sakimoto, Shigenori Iwai, Hirokazu Nankai, Satoshi Obika, Takao Inoue, Junji Kawakami
Nucleic Acid Therapeutics 2026
Authorship：Last author, Corresponding author
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Position-dependent stabilization of DNA/RNA duplexes by site-specific incorporation of LNA nucleosides Reviewed
Elisa Tomita-Sudo, Tomoka Akita, Nae Sakimoto, Saori Tahara-Takamine, Renshin Sano, Shigenori Iwai, Junji Kawakami
Journal of Nucleic Acids 2026
Authorship：Last author, Corresponding author
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Synthesis of Biocompatible Gold Nanoparticles for Photothermal Therapy by Mineralization Using Peptides Reviewed
Shuhei Yoshida, Koki Yoshida, Yoshiki Shitamukai, Makoto Ozaki, Takaaki Tsuruoka, Kenji Usui
RSC Advances 15 48521 - 48528 2025.12
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Phase Separation of RX Repeat Peptides with Nucleic Acids. International journal
Sumit Shil, Mitsuki Tsuruta, Ryosuke Suzuki, Yoshiki Hashimoto, Takeru Torii, Shinya Taniguchi, Tomohiro Umetani, Keiko Kawauchi, Daisuke Miyoshi
Chemistry, an Asian journal 20 ( 23 ) e00805 2025.12
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.
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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 2025.10
Authorship：Last author, Corresponding author
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Effects of molecular crowding on the structure, folding, stability, and catalysis of RNA Invited Reviewed International journal
Shu-Ichi Nakano
Subcellular Biochemistry, (Macro)Molecular Crowding (Springer) 109 155 - 185 2025.10
Single Work
Authorship：Lead author, Corresponding author Publisher：Springer
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Effects of acid-mediated deamination of cytidine and 5-methylcytidine on solid-phase synthesis of oligonucleotides Reviewed
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 2025.10
Publisher：Elsevier BV
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Metal-organic framework-injectable hydrogel hybrid scaffolds promote accelerated angiogenesis for in vivo tissue engineering Reviewed
S. S. Islam, T. Dode, S. Kawashima, M. Fukuoka, T. Tsuruoka, K. Nagahama
RSC Adv. 15 32143 - 32154 2025.9
Authorship：Corresponding author
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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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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