Papers 【 display / non-display 】
-
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
-
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
-
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.
-
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 2025.11
-
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 2025.11
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
Sobuj Shahidul Islam,Tatsuya Dode,Soma Kawashima,Myu Fukuoka,Takaaki Tsuruoka andKoji Nagahama
Gels 11 ( 7 ) 514 2025.7
Authorship：Last author, Corresponding author
-
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
-
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
-
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
-
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
-
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
-
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
-
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