Papers - MIYOSHI Daisuke
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Identification of Ligand-Responsive RNA G-Quadruplexes in the 3′ UTRs of Dengue Virus Serotypes Reviewed
Mohammad Jafar Sheikhi, Ayuka Onuma, Yutaro Imachi, Akira Shiraishi, Shoko Mori, Kohtaro Sugahara, Daisuke Miyoshi, Yue Ma, Takayuki Hishiki, Kazuo Nagasawa and Masayuki Tera
Biomolecules 2026.6
DOI： 10.3390/biom16070946
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Exclusion of RNA-binding domains from G-quadruplex condensates by G-quadruplex ligands Invited Reviewed International coauthorship
Yoshiki Hashimoto, Ryosuke Suzuki, Mizuho Aya, Nagisa Takamiya, Mitsuki Tsuruta,Takeru Torii, Toshiyuki Goto, Keiko Kawauchi and Daisuke Miyoshi
RSC Chemical Biology 2026.6
Authorship：Last author, Corresponding author
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Loss of p53 Provokes NF-κB-Dependent Disruption of Nucleolar Cap and Nucleoplasmic Redistribution of Fibrillarin During Nucleolar Stress
Takeru Torii, Mako Sumida, Atsushi Kobayashi, Toshiyuki Goto, Ryosuke Suzuki, Shin Kuwamoto, Wataru Nakajima, Wataru Sugimoto, Kohei Takeuchi, Yuma Tanaya, Masayuki Tera, Nobuyuki Tanaka, Hiroaki Hirata, Hisae Tateishi-Karimata, Takahito Nishikata, Miwako Kato Homma, Daisuke Miyoshi, Keiko Kawauchi
BIOMOLECULES 16 ( 2 ) 2026.2
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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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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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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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Three- and four-stranded nucleic acid structures and their ligands Invited Reviewed International journal
Yoshiki Hashimoto, Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi, and Daisuke Miyoshi
RSC Chemical Biology 6 ( 4 ) 466 - 491 2025.3
Authorship：Corresponding author
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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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
Minori Nakata, Naoki Kosaka, Keiko Kawauchi, Daisuke Miyoshi
Biochemistry 64 609 - 619 2025.1
Authorship：Corresponding author
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Heterogeneity of Molecular Crowding and Liquid-Liquid Phase Separation. International journal
Mitsuki Tsuruta, Sumit Shil, Keiko Kawauchi, Daisuke Miyoshi
Sub-cellular biochemistry 109 327 - 345 2025
The inside of a living cell is highly crowded with extremely diverse biomacromolecules, small metabolites and osmolytes. The molecular conditions in cells change dynamically and rapidly depending on the cell cycle and state, organelle, and compartment. Much remains unknown regarding how biomolecular interactions and reactions can proceed in a spatiotemporally specific manner in such crowded, heterogeneous, and dynamic molecular environments. Selective condensation/droplet formation of biomolecules via liquid-liquid phase separation may be critical for interactions and reactions inside cells. In this chapter, we briefly describe the heterogeneity of molecular environments inside cells and the biological roles of liquid-liquid phase separation that allows biomolecular interactions and reactions in such heterogenous molecular environments. Finally, we discuss the mutual relationship between molecular crowding and liquid-liquid phase separation.
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NRAS DNA G-quadruplex-targeting molecules for sequence-selective enzyme inhibition Invited Reviewed
Yoshiki Hashimoto, Hiroki Kubo, Keiko Kawauchi and Daisuke Miyoshi
Chem. Commun. 60 13179 - 13182 2024.10
Authorship：Corresponding author
DOI： 10.1039/D4CC03753G
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The role of cytosine methylation in regulating the topology and liquid-liquid phase separation of DNA G-quadruplexes Reviewed International journal
Mitsuki Tsuruta, Sumit Shil, Shinya Taniguchi, Keiko Kawauchi and Daisuke Miyoshi
Chem. Sci. 16 ( 10 ) 4213 - 4225 2024.10
Authorship：Corresponding author
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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Factors Affecting Liquid-Liquid Phase Separation of RGG Peptides with DNA G-Quadruplex Invited Reviewed
Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi, Daisuke Miyoshi
ChemMedChem 2024.9
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Bioinformatic Analysis of Actin-Binding Proteins in the Nucleolus During Heat Shock Invited Reviewed International journal
Shinya Taniguchi, Takeru Torii ,Toshiyuki Goto, Kohei Takeuchi, Rine Katsumi, Mako Sumida, Sunmin Lee, Wataru Sugimoto, Masaya Gessho, Katsuhiko Itoh, Hiroaki Hirata, Junji Kawakami, Daisuke Miyoshi and Keiko Kawauchi
Genes 15 ( 12 ) 1580 2024.9
BACKGROUND/OBJECTIVES: Actin plays a crucial role not only in the cytoplasm, but also in the nucleus, influencing various cellular behaviors, including cell migration and gene expression. Recent studies reveal that nuclear actin dynamics is altered by cellular stresses, such as DNA damage; however, the effect of heat shock on nuclear actin dynamics, particularly in the nucleolus, remains unclear. This study aims to elucidate the contribution of nucleolar actin to cellular responses under heat shock conditions. METHODS: Nuclear actin dynamics in response to heat shock were investigated using nAC-GFP, a GFP-tagged actin chromobody, to visualize nuclear actin in HeLa cells. Bioinformatic analyses were also performed. RESULTS: Heat shock induced the reversible assembly of nAC-GFP in the nucleolus, with disassembly occurring upon recovery in a heat shock protein (Hsp) 70-dependent manner. Because the nucleolus, formed via liquid-liquid phase separation (LLPS), sequesters misfolded proteins under heat shock to prevent irreversible aggregation, we hypothesized that nucleolar actin-binding proteins might also be sequestered in a similar manner. Using several databases, we identified 47 actin-binding proteins localized in the nucleolus and determined the proportion of intrinsically disordered regions (IDRs) known to promote LLPS. Our analysis revealed that many of these 47 proteins exhibited high levels of IDRs. CONCLUSIONS: The findings from our bioinformatics analysis and further cellular studies may help elucidate new roles for actin in the heat shock response.
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Quantitative Effects of the Loop Region on Topology, Thermodynamics, and Cation Binding of DNA G-quadruplexes Reviewed International journal
Minori Nakata, Naoki Kosaka, Keiko Kawauchi, Daisuke Miyoshi
ACS Omega 9 ( 32 ) 35028 - 35036 2024.7
Authorship：Last author, Corresponding author
The thermal stability of G-quadruplexes is important for their biological roles. G-quadruplexes are stable in the presence of cations such as K+ and Na+ because these cations coordinate in the G-quartet of four guanine bases. It is well known that the number of G-quartets and the configuration of the guanine bases affect the binding affinity of the cation. Recently, structures formed in the loop regions connecting the guanine stretches have attracted significant attention, because the loop region affects G-quadruplex properties, such as topology, thermal stability, and interactions with proteins and small molecules. Considering these effects, the loop region can also affect the binding affinity of the cations. Here, we designed a series of G-quadruplex-forming DNA sequences that contain a hairpin in a loop region and investigated the effects of the sequence and structure of the loop region on the cation binding affinity as well as the thermal stability of the G-quadruplex as a whole. First, structural analysis of the DNA sequences showed that the hairpin at the loop plays a key role in determining G4 topology (strand orientation). Second, in the case of the G-quadruplexes with the hairpin-forming loop region, it was found that a longer loop length led to a higher thermodynamic stability of the G-quadruplex as well as higher cation binding affinity. In contrast, an unstructured loop region did not lead to such effects. Interestingly, the cation binding affinity was correlated to the thermodynamic stability of the hairpin structure at the loop region. It was quantitatively demonstrated that the stable loop region stabilized the whole G-quadruplex structure, which induced higher cation binding affinity. These systematic and quantitative results showed that the loop region is one of the determinants of cation binding and expanded the possibilities of drug development targeting G4s by stabilizing the loop region.
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細胞内環境で安定化する核酸構造を標的にした低分子薬の開発 Invited
橋本 佳樹, 川内 敬子, 三好 大輔
MEDCHEM NEWS (日本薬学会） 34 ( 1 ) 36 - 42 2024.4
Authorship：Corresponding author
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RNA 高次構造を標的とした光線力学療法の展望 Invited
取井猛流・木下菜月・橋本佳樹・杉本渉・川内敬子・三 好大輔
38 ( 13 ) 1154 - 1156 2023.11
Authorship：Last author, Corresponding author
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Loss of p53 function promotes DNA damage-induced formation of nuclear actin filaments Reviewed International journal
Takeru Torii, Wataru Sugimoto, Katsuhiko Itoh, Natsuki Kinoshita, Masaya Gessho, Toshiyuki Goto, Ikuno Uehara, Wataru Nakajima, Yemima Budirahardja, Daisuke Miyoshi, Takahito Nishikata, Nobuyuki Tanaka, Hiroaki Hirata, Keiko Kawauchi
Cell Death & Disease 14 ( 11 ) 766766 - 766 2023.8
Tumor suppressor p53 plays a central role in response to DNA damage. DNA-damaging agents modulate nuclear actin dynamics, influencing cell behaviors; however, whether p53 affects the formation of nuclear actin filaments remains unclear. In this study, we found that p53 depletion promoted the formation of nuclear actin filaments in response to DNA-damaging agents, such as doxorubicin (DOXO) and etoposide (VP16). Even though the genetic probes used for the detection of nuclear actin filaments exerted a promotive effect on actin polymerization, the detected formation of nuclear actin filaments was highly dependent on both p53 depletion and DNA damage. Whilst active p53 is known to promote caspase-1 expression, the overexpression of caspase-1 reduced DNA damage-induced formation of nuclear actin filaments in p53-depleted cells. In contrast, co-treatment with DOXO and the pan-caspase inhibitor Q-VD-OPh or the caspase-1 inhibitor Z-YVAD-FMK induced the formation of nuclear actin filament formation even in cells bearing wild-type p53. These results suggest that the p53-caspase-1 axis suppresses DNA damage-induced formation of nuclear actin filaments. In addition, we found that the expression of nLifeact-GFP, the filamentous-actin-binding peptide Lifeact fused with the nuclear localization signal (NLS) and GFP, modulated the structure of nuclear actin filaments to be phalloidin-stainable in p53-depleted cells treated with the DNA-damaging agent, altering the chromatin structure and reducing the transcriptional activity. The level of phosphorylated H2AX (γH2AX), a marker of DNA damage, in these cells also reduced upon nLifeact-GFP expression, whilst details of the functional relationship between the formation of nLifeact-GFP-decorated nuclear actin filaments and DNA repair remained to be elucidated. Considering that the loss of p53 is associated with cancer progression, the results of this study raise a possibility that the artificial reinforcement of nuclear actin filaments by nLifeact-GFP may enhance the cytotoxic effect of DNA-damaging agents in aggressive cancer cells through a reduction in gene transcription.
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The iron chelator deferriferrichrysin induces paraptosis via extracellular signal-related kinase activation in cancer cells Invited Reviewed International journal
Natsuki Kinoshita, Masaya Gessho, Takeru Torii, Yukako Ashida, Minori Akamatsu, Alvin Kunyao Guo, Sunmin Lee, Tatsuya Katsuno 3, Wataru Nakajima Yemima Budirahardja, Daisuke Miyoshi, Takehiko Todokoro, Hiroki Ishida, Takahito Nishikata, Keiko Kawauchi
Genes Cells 28 ( 9 ) 653 - 662 2023.6
Cancer cells generally exhibit increased iron uptake, which contributes to their abnormal growth and metastatic ability. Iron chelators have thus recently attracted attention as potential anticancer agents. Here, we show that deferriferrichrysin (Dfcy), a natural product from Aspergillus oryzae acts as an iron chelator to induce paraptosis (a programmed cell death pathway characterized by ER dilation) in MCF-7 human breast cancer cells and H1299 human lung cancer cells. We first examined the anticancer efficacy of Dfcy in cancer cells and found that Dfcy induced ER dilation and reduced the number of viable cells. Extracellular signal-related kinase (ERK) was activated by Dfcy treatment, and the MEK inhibitor U0126, a small molecule commonly used to inhibit ERK activity, prevented the increase in ER dilation in Dfcy-treated cells. Concomitantly, the decrease in the number of viable cells upon treatment with Dfcy was attenuated by U0126. Taken together, these results demonstrate that the iron chelator Dfcy exhibits anticancer effects via induction of ERK-dependent paraptosis.
DOI： 10.1111/gtc.13053
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Quantification of the concentration in a droplet formed by liquid–liquid phase separation of G-quadruplex-forming RNA Reviewed
Kohei Yokosawa, Mitsuki Tsuruta, Shinji Kajimoto, Naoki Sugimoto, Daisuke Miyoshi, Takakazu Nakabayashi
Chem. Phys. Lett. 826 140634 - 140634 2023.6
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Biomolecular Liquid–Liquid Phase Separation for Biotechnology Invited Reviewed
Sumit Shil, Mitsuki Tsuruta, Keiko Kawauchi and Daisuke Miyoshi
BioTech 12 ( 2 ) 26 2023.3
Authorship：Corresponding author
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The role of G-quadruplex in expression of retrotransposon LINE-1 Invited
23 48 - 48 2023.3
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Simple and fast screening for structure-selective G-quadruplex ligands Reviewed International journal
Yoshiki Hashimoto, Yoshiki Imagawa, Kaho Nagano, Ryuichi Maeda, Naho Nagahama, Takeru Torii, Natsuki Kinoshita, Nagisa Takamiya, Keiko Kawauchi, Hisae Tatesishi-Karimata, Naoki Sugimoto and Daisuke Miyoshi
Chem. Commun. 59 ( 33 ) 4891 - 4894 2023.2
Authorship：Corresponding author
Structural selectivity of G-quadruplex ligands is essential for cellular applications since there is an excess of nucleic acids forming duplex structures compared to G-quadruplex structures in living cells. In this study, we developed new structure-selective G-quadruplex ligands utilizing a simple and fast screening system. The affinity, selectivity, enzymatic inhibitory activity and cytotoxicity of the structure-selective G-quadruplex ligands were demonstrated along with a structural selectivity-cytotoxicity relationship of G-quadruplex ligands.
DOI： 10.1039/D3CC00556A
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Controlling liquid–liquid phase separation of G-quadruplex-forming RNAs in a sequence-specific manner Reviewed International journal
Mitsuki Tsuruta, Takeru Torii, Kazuki Kohata, Keiko Kawauchi, Hisae Tateishi-Karimata, Naoki Sugimoto and Daisuke Miyoshi
Chem. Commun. 58 ( 93 ) 12931 - 12934 2022.11
We constructed a minimum liquid-liquid phase separation model system to form liquid droplets using only G-quadruplex-forming oligonucleotides and R- and G-rich oligopeptides. We found that the G-quadruplex structure is an essential component for RNA to form droplets with the peptide. Based on this model system and our findings, droplet redissolution via structure transition from a G-quadruplex to a duplex was achieved in a sequence-specific manner.
DOI： 10.1039/D2CC04366A
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rDNAおよびrRNAが形成する四重らせん構造による核小体機能の制御 Invited
川内敬子、取井猛流、月生雅也、木下菜月、三好大輔
月刊細胞 54 ( 12 ) 36 - 39 2022.11
Authorship：Corresponding author
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細胞内環境で安定化される核酸非構造を狙った分子標的薬の開発 Invited
川内敬子・橋本佳樹・杉本 渉・三好大輔
バイオマテリアル = Journal of Japanese Society for Biomaterials : 生体材料 40 ( 3 ) 206 - 211 2022.7
Authorship：Corresponding author
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核酸の化学修飾と構造や相分離能の相関 Invited
鶴田 充生・取井 猛流・杉本 渉・川内 敬子・三好 大輔
月刊「細胞」（ニューサイエンス社） 53 ( 14 ) 910 - 913 2022.6
Authorship：Last author, Corresponding author
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Significant structural change in human c-Myc promoter G-quadruplex upon peptide binding in potassium Reviewed International coauthorship
Nikita Kundu, Taniya Sharma, Sarvpreet Kaur, Mamta Singh, Vinit Kumar, Uttam Sharma, Aklank Jain, Jadala Shankaraswamy, Daisuke Miyoshi, Sarika Saxena
RSC Adv. 12 7594 - 7604 2022.4
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核酸の四重らせん構造を狙った治療薬の展望 Invited
37 ( 4 ) 52 - 55 2022.3
Authorship：Corresponding author
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Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gene Reviewed
Chem. Commun. 58 48 - 51 2022.1
Authorship：Corresponding author
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Detection of Intracellular Reactive Oxidative Species Using the Fluorescent Probe Hydroxyphenyl Fluorescein Invited Reviewed
Wataru Sugimoto, Daisuke Miyoshi, Keiko Kawauchi
Methods in Molecular Biology 2274 207 - 215 2021.5
Publisher：Humana Press Inc.
Various fluorescent probes for the detection of intracellular reactive oxidative species (ROS) have been developed because ROS levels are closely associated with cellular states. Here, we describe a method for detection of intracellular ROS in living cells using the fluorescent probe, hydroxyphenyl fluorescein (HPF), which detects hydroxyl radicals and peroxynitrite. NIH3T3 cells and p53 knockout (p53−/−) mouse embryonic fibroblasts (MEFs) were transformed by expressing oncogenic RAS using a retrovirus system. The cells were treated with HPF at 37 °C for 30 min, and subsequently, images were acquired using a confocal fluorescence microscope at an excitation wavelength of 488 nm after washing with PBS.
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Molecularly targeted photodynamic therapy for cancer mRNAs Invited Reviewed
杉本渉, 橋本佳樹, 川内敬子, 三好大輔
Bio Clinica 36 ( 5 ) 65 - 67 2021.5
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核小体ストレスにより形成するrDNA G-quadruplex集合体とその機能
杉本 渉, 桑本 慎, 建石 寿枝, 岩根 敦子, 高橋 宏隆, 三好 大輔, 川内 敬子
日本薬学会年会要旨集 141年会 29V05 - am10S 2021.3
Publisher：(公社)日本薬学会
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Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes Invited Reviewed
Combined Effects of Methylated Cytosine, Molecular Crowding, on, the Thermodynamic Stability of, DNA Duplexes
Int. J. Mol. Sci. 22 ( 2 ) 947 2021.1
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Photosensitizers Based on G-Quadruplex Ligand for Cancer Photodynamic Therapy Invited International journal
Keiko Kawauchi, Ryoto Urano, Natsuki Kinoshita, Shin Kuwamoto, Takeru Torii, Yoshiki Hashimoto, Shinya Taniguchi, Mitsuki Tsuruta, Daisuke Miyoshi
Genes 11 ( 11 ) 1340 2020.11
Joint Work
G-quadruplex (G4) is the non-canonical secondary structure of DNA and RNA formed by guanine-rich sequences. G4-forming sequences are abundantly located in telomeric regions and in the promoter and untranslated regions (UTR) of cancer-related genes, such as RAS and MYC. Extensive research has suggested that G4 is a potential molecular target for cancer therapy. Here, we reviewed G4 ligands as photosensitizers for cancer photodynamic therapy (PDT), which is a minimally invasive therapeutic approach. The photosensitizers, such as porphyrins, were found to be highly toxic against cancer cells via the generation of reactive oxidative species (ROS) upon photo-irradiation. Several porphyrin derivatives and analogs, such as phthalocyanines, which can generate ROS upon photo-irradiation, have been reported to act as G4 ligands. Therefore, they have been implicated as promising photosensitizers that can selectively break down cancer-related DNA and RNA forming G4. In this review, we majorly focused on the potential application of G4 ligands as photosensitizers, which would provide a novel strategy for PDT, especially molecularly targeted PDT (mtPDT).
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TakahiroYamauchi, Takafumi Kubodera, Daisuke Miyoshi, Naoki Sugimoto, Shuji Hirohata
Journal of Bioscience and Bioengineering 2020.10
Joint Work
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Photodynamic therapy targeting RAS mRNA
Wataru Sugimoto, Keiko Kawauchi, Daisuke Miyoshi
Medical Science Digest 46 ( 9 ) 26 - 27 2020.7
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Novel Strategy of Photodynamic Therapy Targeting RAS mRNA with G-Quadruplex Ligands for Cancer Treatment Invited Reviewed
Takeru Torii, Wataru Sugimoto, Keiko Kawauchi, Daisuke Miyoshi
Journal of Data Mining in Genomics & Proteomics 2020.6
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RNA Phase Separation-Mediated Direction of Molecular Trafficking Under Conditions of Molecular Crowding Invited Reviewed
Kazuki Kohata, Daisuke Miyoshi
Biophys. Rev. 12 669 - 676 2020.5
Joint Work
Living cells are highly crowded with large and small biomolecules. The total concentration of biomolecules can reach 400 mg/ml, and 40% of the cell volume is occupied by biomolecules. Droplet formation in cells via liquid-liquid phase separation may play a role in controlling biochemical reactions in this complex molecular environment. Liquid-liquid phase separation generally involves nucleic acids and proteins as anionic and cationic components, respectively. Significant characteristics of droplets, which make them different from protein aggregation or fibril formation, are reversibility of formation and responsiveness to the molecular environment. In this review, we quantitatively describe the molecular environment inside cells and droplets that participate in controlling central dogma reactions. Finally, we discuss the importance of droplets under conditions of molecular crowding within living cells.
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Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA Reviewed
H. Tateishi-Karimata, D. Banerjee, T. Ohyama, S. Matsumoto, D. Miyoshi, S. Nakano, and N. Sugimoto
Biochemical and Biophysical Research Communications 525 ( 1 ) 177 - 183 2020.4
Joint Work
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Hydroxyl groups in cosolutes regulate the G-quadruplex topology of telomeric DNA. Reviewed International journal
Hisae Tateishi-Karimata, Dipanwita Banerjee, Tatsuya Ohyama, Saki Matsumoto, Daisuke Miyoshi, Shu-Ich Nakano, Naoki Sugimoto
Biochemical and biophysical research communications 2020.2
Telomeric G-quadruplex topology has the ability to regulate telomerase activity, which counteracts the shortening of telomere with successive cell divisions, thereby causing genomic longevity. However, the detailed mechanism of G-quadruplexes topologies formed by telomeric sequences requires further investigation. In this study, we quantitatively investigated the effect of cosolutes, particularly the varying number of hydroxyl groups, on the structural transition between hybrid type and parallel G-quadruplexes formed by telomeric DNA sequences. Cosolutes with one or no hydroxyl groups in the vicinal position more efficiently induced the transition to parallel G-quadruplex from hybrid G-quadruplex than those with more hydroxyl groups. We also examined the effect of cosolute structures on the hydration of G-quadruplex formation; the results indicated that cosolutes with fewer hydroxyl groups lead to the release of greater amount of water during G-quadruplex formation. Molecular dynamics results showed that the parallel G-quadruplex was more dehydrated than the hybrid type G-quadruplex. Generally, a dehydrated structure is favored under crowding condition. Thus, depending on the surrounding cosolutes, the G-quadruplex topology can be controlled by the G-quadruplex hydration state.
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Shikhar Tyagi, Sarika Saxena, Nikita Kundu, Taniya Sharma, Amlan Chakraborty, Sarvpreet Kaur, Daisuke Miyoshi, Jadala Shankaraswamy
RSC Advances 9 40255 - 40262 2019.12
Joint Work
We described a novel synthetic peptide in which a glutamine residue binds through hydrogen bonding to a guanine-base and a trytophan residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over its complementary c-rich strand and a double-stranded DNA and its complementary C-rich strand. This peptide offers great potential for cancer treatment by inhibiting the telomere extension by telomerase.
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The RAS mRNA G-quadruplex: making undruggable cancer targets druggable
Keiko Kawauchi, Wataru Sugimoto, Daisuke Miyoshi
The Atlas of Science 2019.10
Joint Work
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細胞の分子夾雑環境における核酸構造と核酸構造リガンドの挙動 ～細胞内でも望みの機能を発現する分子の合理設計に向けて～
三好大輔
生命化学研究レター 58 ( 1 ) 17 - 21 2019.4
Single Work
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Osmolyte-Enhanced Protein Synthesis Activity of a Reconstituted Translation System Reviewed
Yoshiki Moriizumi, Kazuhito V. Tabata, Daisuke Miyoshi, Hiroyuki Noji
ACS Synth Biol. 8 ( 3 ) 557 - 567 2019.2
Joint Work
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Metal sensitive and DNA concentration dependent structural rearrangement of short oligonucleotide into large suprastructures Reviewed
J. Shankaraswamy, Shikhar Tyagi, Anju Singh, Daisuke Miyoshi, Sarika Saxena
Journal of Biomolecular Structure and Dynamics 37 ( 9 ) 2211 - 2218 2018.12
Joint Work
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An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex Reviewed
Keiko Kawauchi, Wataru Sugimoto, Takatoshi Yasui, Kohei Murata, Katsuhiko Itoh, Kazuki Takagi, Takaaki Tsuruoka, Kensuke Akamatsu, Hisae Tateishi-Karimata, Naoki Sugimoto, and Daisuke Miyoshi
Nature Communicationsvolume 9 2271 2018.6
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DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity Reviewed
Kenji Usu, Arisa Okada, Shungo Sakashita, Masayuki Shimooka, Takaaki Tsuruoka, Shu-ichi Nakano, Daisuke Miyoshi, Tsukasa Mashima, Masato Katahira and Yoshio Hamada
Molecules 22 1991 2017.11
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Highly Sensitive Telomerase Assay Insusceptible to Telomerase and Polymerase Chain Reaction Inhibitors for Cervical Cancer Screening Using Scraped Cells. Reviewed
Hidenobu Yaku , Yoshio Yoshida, Hidehiko Okazawa, Yasushi Kiyono, Yuko Fujita, Daisuke Miyoshi
Anal. Chem. 89 ( 13 ) 6948 - 6953 2017.5
Joint Work
-
Cell and Molecular Mechanics in Health and Disease Invited Reviewed
BioMed Research International Article ID 2860241 2017.2
Joint Work
DOI： 10.1155/2017/2860241
-
Unexpected Position-Dependent Effects of Ribose G‑Quartets in G‑Quadruplexes Reviewed
J. Zhou, S. Amrane, F. Rosu, G.F. Salgado, Y. Bian, H. Tateishi-Karimata, E. Largy, D. N. Korkut, A. Bourdoncle, D. Miyoshi, J. Zhang, H. Ju, W. Wang, N. Sugimoto, V. Gabelica, and J. Mergny
J. Am. Chem. Soc. 139 7768 - 7779 2017
Joint Work
-
Selective and Robust Stabilization of Triplex DNA Structures Using Cationic Comb-type Copolymers. Reviewed
Yamayoshi A, Miyoshi D, Zouzumi YK, Matsuyama Y, Ariyoshi J, Shimada N, Murakami A, Wada T, Maruyama A
J Phys Chem B 121 ( 16 ) 4015 - 4022 2017
Joint Work
Authorship：Lead author
-
Reevaluation of the stability of G-quadruplex structures under crowding conditions Reviewed
Jun Zhou, Hisae Tateishi-Karimata, Jean-Louis Mergny, Mingpan Cheng, Zhaochi Feng, Daisuke Miyoshi, Naoki Sugimoto, Can Li
Biochimie 121 204 - 208 2016
Joint Work
-
A reversible B-A transition of DNA duplexes induced by synthetic cationic copolymers Reviewed
Nonoka Yamaguchi, Yu-ki Zouzumi, Naohiko Shimada, Shuichi Nakano, Naoki Sugimoto, Atsushi Maruyama, Daisuke Miyoshi
Chem. Commun. 52 7446 - 7449 2016
Joint Work
Authorship：Lead author
-
Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg2+-unsaturated solutions Reviewed
Shu-ichi Nakano, Yuichi Kitagawa, Daisuke Miyoshi, Naoki Sugimoto
J. Biol. Inorg. Chem. 20 1049 - 1058 2015
Joint Work
-
Stabilization of DNA Structures With Poly(ethylene sodium phosphate) Reviewed
R. Moriyama, Y. Iwasaki, D. Miyoshi
J. Phys. Chem. B 119 11969 - 11977 2015
Joint Work
-
Effects of cosolvents on the folding and catalytic activities of the hammerhead ribozyme Reviewed
S. Nakano, Y. Kitagawa, H. Yamashita, D. Miyoshi, N. Sugimoto
ChemBioChem 16 1803 - 1810 2015
Joint Work
-
A mRNA-responsive G-quadruplex-based drug release system Invited Reviewed
Hidenobu Yaku, Takashi Murashima, Daisuke Miyoshi, and Naoki Sugimoto
Sensors 15 ( 4 ) 9388 - 9403 2015
Joint Work
Authorship：Lead author
-
DNA G-quadruplex detection system employing a protein fibril ligand Invited Reviewed
Ryuichi Maeda, Hidenobu Yaku, Takakazu Nakabayashi, Takashi Murashima, Naoki Sugimoto, Daisuke Miyoshi
Telomere and Telomerase 2 e691 2015
Joint Work
Authorship：Lead author
-
DNA structures under molecular crowding conditions with a phosphorylcholine derivative (MPC) Reviewed
Yu-mi Ueda, Tomohiro Konno, Kazuhiko Ishihara, Naoki Sugimoto, Daisuke Miyoshi
Transact. Mat. Res. Soc. Japan 40 99 - 102 2015
Joint Work
Authorship：Lead author
-
DNA structures under molecular crowding conditions with a phosphorylcholine derivative (MPC)
Yu-mi Ueda, Tomohiro Konno, Kazuhiko Ishihara, Naoki Sugimoto, Daisuke Miyoshi
Transact. Mat. Res. Soc. Japan 40 99 - 102 2015
Joint Work
-
Stabilization of DNA Structures With Poly(ethylene sodium phosphate)
R. Moriyama, Y. Iwasaki, D. Miyoshi
J. Phys. Chem. B 119 11969 - 11977 2015
Joint Work
-
A fluorescent probe for detection of an intracellular prognostic indicator in early-stage cancer (10.1039/c4cc08789e Reviewed
Haiwei Ji, Yijia Guan, L Wu, Jinsong Ren, Daisuke Miyoshi, Naoki Sugimoto Xiaogang Qu
Chem. Commun. 51 1479 - 1482 2014
Joint Work
-
Preparation of hydrogels for the study of the effects of spatial confinement on DNA Reviewed
Shu-ichi Nakano, Masatoshi Yoshida, Daisuke Yamaguchi, Naoki Sugimoto
Transact. Mat. Res. Soc. Japan 39 435 - 438 2014
Joint Work
-
Dangling ends perturb the stability of RNA duplex responsive to surrounding condition Invited Reviewed
H. Tateishi-Karimata, S. Pramanik, S. Nakano, D. Miyoshi and N. Sugimoto
ChemMedChem 9 ( 9 ) 2150 - 2155 2014
Joint Work
-
Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds Reviewed
Shu-ichi Nakano, Yuichi Kitagawa, Daisuke Miyoshi, Naoki Sugimoto
FEBS Open Bio 4 643 - 650 2014
Joint Work
-
Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain Reviewed
Daisuke Miyoshi, Yu-mi Ueda, Naohiko Shimada, Shu-ichi Nakano, Naoki Sugimoto, Atsushi Maruyama
ChemMedChem 9 ( 9 ) 2156 - 2163 2014
Joint Work
Authorship：Lead author
-
Biosensors Based on Graphene and Biomolecules Invited Reviewed
Bioscience and Bioindustry 72 ( 2 ) 117 - 120 2014
Joint Work
Authorship：Lead author
-
measure” FRET-based telomeric tandem repeat sequence detection and telomerase assay method Reviewed
Koji Kawamura, Hidenobu Yaku, Daisuke Miyoshi, Takashi Murashima
Org. Biomol. Chem. 12 934 - 941 2014
Joint Work
-
Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids Reviewed
Shu-ichi Nakano, Daisuke Miyoshi, Naoki Sugimoto
Chem. Rev. 114 ( 5 ) 2733 - 2758 2014
Joint Work
Authorship：Lead author
-
In Vitro Assays Predicting of Telomerase Inhibitory Effect of G-Quadruplex Ligands in Cell Nuclei Reviewed
Hidenobu Yaku, Takashi Murashima, Daisuke Miyoshi, Naoki Sugimoto
J. Phys. Chem. B 118 2605 - 2614 2014
Joint Work
Authorship：Lead author
-
Reduced Graphene Oxide Upconversion Nanoparticle Hybrid for Electrochemiluminescent Sensing of a Prognostic Indicator in Early-Stage Cancer Reviewed
Li Wu, Jiasi Wang, Meili Yin, Jinsong Ren, Daisuke Miyoshi, Naoki Sugimoto, Xiaogang Qu
Small 10 330 - 336 2014
Joint Work
-
Preparation of hydrogels for the study of the effects of spatial confinement on DNA
Shu-ichi Nakano, Masatoshi Yoshida, Daisuke Yamaguchi, Naoki Sugimoto
Transact. Mat. Res. Soc. Japan 39 435 - 438 2014
Joint Work
-
Biosensors Based on Graphene and Biomolecules
Bioscience and Bioindustry 72 ( 2 ) 117 - 120 2014
Joint Work
-
Thermodynamics - Hydration Relationships within Loops that Affect G-Quadruplexes under Molecular Crowding Conditions Reviewed
Takeshi Fujimoto, Shu-ichi Nakano, Naoki Sugimoto, Daisuke Miyoshi
J. Phys. Chem. B 117 963 - 972 2013.1
Joint Work
Authorship：Lead author
-
A Highly Sensitive Telomerase Activity Assay that Eliminates False-Negative Results Caused by PCR Inhibitors Reviewed
Hidenobu Yaku, Takashi Murashima, Daisuke Miyoshi, and Naoki Sugimoto
Molecules 18 ( 10 ) 11751 - 11767 2013
Joint Work
Authorship：Lead author
-
Sequence and Solvent Effects on Telomeric DNA Bimolecular G-Quadruplex Folding Kinetics Reviewed
Adrien Marchand, Ruben Ferreira, Hisae Tateishi-Karimata, Daisuke Miyoshi, Naoki Sugimoto, Valerie Gabelica
J. Phys. Chem. B 117 ( 41 ) 12391 - 12401 2013
Joint Work
-
Multiple and cooperative binding of fluorescence light-up probe Thioflavin T with human telomere DNA G-quadruplex Reviewed
Valerie Gabelica, Ryuichi Maeda, Takeshi Fujimoto, Hidenobu Yaku, Takashi Murashima, Naoki Sugimoto, and Daisuke Miyoshi
Biochemistry 52 5620 - 5628 2013
Joint Work
Authorship：Lead author
-
The beads-on-a-string structure of long telomeric DNAs under molecular crowding conditions Reviewed
Haiqing Yu, Gu Xiaobo Gu, Shu-ichi Nakano, Daisuke Miyoshi, Naoki Sugimoto
J. Am. Chem. Soc. (Higthlighted as the cover and introduced in the Spotslights on Recent JACS Publications) 134 20060 - 20069 2012.12
Joint Work
Authorship：Lead author
-
Aptamer carbon nanodot sandwich used for fluorescent detection of protein Reviewed
Bailu Xu, Chuanqi Zhao, Weili Wei, Jinsong Ren, Daisuke Miyoshi, Naoki Sugimoto, and Xiaogang Qu
Analyst 137 5483 - 5486 2012.12
Joint Work
-
Specific Binding of Anionic Porphyrin and Phthalocyanine to the G-quadruplex Invited Reviewed
Hidenobu Yaku, Takashi Murashima, Daisuke Miyoshi, Naoki
Molecules 17 10586 - 10613 2012.8
Joint Work
-
Detection of a Prognostic Indicator in Early-Stage Cancer Using Functionalized Graphene-Based Peptide Sensors Reviewed
Lingyan Feng, Li Wu, Jiasi Wang, Jinsong Ren, Daisuke Miyoshi, Naoki Sugimoto, Xiaogang Qu
Advanced Materials 24 ( 1 ) 125 - 131 2012.1
Joint Work
-
DNA devises responding to cellular environmental factors Invited
D. Miyoshi
Chemistry and chemical industry (Chemical Society of Japan) 64 ( 12 ) 956 - 956 2011.12
Single Work
Authorship：Lead author
-
Effects of protein binding on DNA G-quadruplex structures Invited
S. Nagatoishi, D. Miyoshi and N. Sugimoto
Int. Rev. Biophys. Chem. 2 129 - 134 2011.12
Joint Work
-
Synthesis and Application of Functional Nucleic Acids Invited
Daisuke Miyoshi, Friedrich C. Simmel, Souvik Maiti, and Luis A. Marky
Journal of Nucleic Acids 2011 547245 2011.12
Joint Work
Authorship：Lead author
-
DNA devises responding to cellular environmental factors
D. Miyoshi
Chemistry and chemical industry (Chemical Society of Japan) 64 ( 12 ) 956 - 956 2011.12
Single Work
-
Rational design of a new IMP aptamer based on a TPP riboswitch and a hypoxanthine aptamer Reviewed
Misato Tokui, Takahiro Yamauchi, Daisuke Miyoshi, Hisaya Kamiya, Akira Nishimura, Naoki Sugimoto
Chemistry Letters 40 ( 11 ) 1313 - 1314 2011.11
Joint Work
Authorship：Lead author
-
Measurements of the binding of a large protein using a substrate density-controlled DNA chip Reviewed
S. Nakano, T. Kanzaki, M. Nakano, D. Miyoshi, N. Sugimoto
Analytical Chemistry 83 6368 - 6372 2011.11
Joint Work
-
Graphene biosensors Invited
D. Miyoshi, N. Sugimoto
Chemistry 66 ( 8 ) 30 - 35 2011.9
Joint Work
Authorship：Lead author
-
The effects of molecular crowding on the structure and stability of G-quadruplexes with an abasic site Reviewed
Takeshi Fujimoto, Shu Ichi Nakano, Daisuke Miyoshi, and Naoki Sugimoto
J. Nucleic Acids 2011 857149 2011.9
Joint Work
Authorship：Lead author
-
Graphene biosensors
D. Miyoshi, N. Sugimoto
Chemistry 66 ( 8 ) 30 - 35 2011.9
Joint Work
-
Label-free colorimetric and quantitative detection of cancer marker protein using noncrosslinking aggregation of Au/Ag nanoparticles induced by target-specific peptide probe Reviewed
Xiaohui Wang, Li Wu, Jinsong Ren, Daisuke Miyoshi, Naoki Sugimoto, and Xiaogang Qu
Biosensors and Bioelectronics 26 4804 - 4809 2011.8
Joint Work
-
Thermodynamic Stability of Hoogsteen and Watson-Crick Base Pairs in the Presence of Histone H3-Mimicking Peptide Reviewed
Smritimoy Pramanik, Kaori Nakamura, Kenji Usui, Shu-ichi Nakano, Sarika Saxena, Jun Matsuia, Daisuke Miyoshi, Naoki Sugimoto
Chem. Commun. 47 2790 - 2792 2011.2
Joint Work
Authorship：Lead author
-
Ultrasensitive and Selective Detection of a Prognostic Indicator in Early-Stage Cancer Using Graphene Oxide and Carbon Nanotubes Reviewed
Xiaohui Wang, Chunyan Wang, Konggang Qu, Yujun Song, Jinsong Ren, Daisuke Miyoshi, Naoki Sugimoto, and Xiaogang Qu
Advanced Functional Materials 20 3967 - 3971 2010.12
Joint Work
-
A rapid and sensitive "add-mix-measure" assay for multiple proteinases based on one goldnanoparticle-peptide-fluorophore conjugate Reviewed
X.Wang, J.Geng, D.Miyoshi, J.Ren, N.Sugimoto, and X.Qu
Biosens. Bioelectron. 26 743 - 747 2010.11
Joint Work
-
Sole and stable RNA duplexes of G-rich sequences located in the 5'-untranslated region of protooncogenes Reviewed
Sarika Saxena, Daisuke Miyoshi, Naoki Sugimoto
Biochemistry 49 7190 - 7201 2010.9
Joint Work
Authorship：Lead author
-
Development of new functional nanostructures consisting of both DNA duplex and quadruplex Reviewed
Kakoli Dutta, Takeshi Fujimoto, Mamiko Inoue, Daisuke Miyoshi, and Naoki Sugimoto
Chem. Commun 46 7772 - 7774 2010.9
Joint Work
Authorship：Lead author
-
Anionic Phthalocyanines Targeting G-quadruplexes and Inhibiting Telomerase Activity in the Presence of Excessive DNA Duplexes Reviewed
Hidenobu Yaku, Takashi Murashima, Daisuke Miyoshi, Naoki Sugimoto
Chem. Commun 46 5740 - 5742 2010.8
Joint Work
Authorship：Lead author
-
Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors Reviewed
Dong-Hao Zhang, Takeshi Fujimoto, Sarika Saxena, Hai-Qing Yu, Daisuke Miyoshi, and Naoki Sugimoto
Biochemisry 49 4554 - 4563 2010.7
Joint Work
Authorship：Lead author
-
Utilization of salmon milt DNA against UV damage Reviewed
Yoshiharu Sasaki, Daisuke Miyoshi, and Naoki Sugimoto
Applied Biochem. Biotech. 160 2458 - 2466 2010.2
Joint Work
-
Stabilization of Three-Way Junctions of DNA under Molecular Crowding Conditions Reviewed
Sanjukta Muhuri, Kenta Mimura, Daisuke Miyoshi, and Naoki Sugimoto
J. Am. Chem. Soc. 131 9268 - 9280 2009.12
Joint Work
-
Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions
三好大輔
J. Am. Chem. Soc. ( 131 ) 3522 - 3531 2009.11
Single Work
-
Thermal stability and hydration state of DNA G-quadruplex regulated by loop regions
T. Fujimoto, D. Miyoshi, H. Tateishi-Karimata, and N. Sugimoto
Nucleic Acids Symp Ser (Oxf) 53 237 - 238 2009.9
Joint Work
Authorship：Lead author
-
DNA junction structure stabilized by molecular crowding conditions
D. Miyoshi, S. Muhuri, K. Mimura, and N. Sugimoto
Nucleic Acids Symp Ser (Oxf) 53 59 - 60 2009.9
Joint Work
Authorship：Lead author
-
DNA junction structure stabilized by molecular crowding conditions
D. Miyoshi, S. Muhuri, K. Mimura, N. Sugimoto
Nucleic Acids Symp Ser (Oxf) 53 59 - 60 2009.9
Joint Work
-
DNAは細胞内で三重らせん・四重らせん構造を形成しているのか？ Invited
三好大輔、杉本直己
化学と生物 7 449 - 451 2009.1
Joint Work
-
Cu(II) ion inhibits early stages of amyloid β fibril formation in vitro
T. Fujimoto, D. Miyoshi, H. Tateishi-Karimata, and N. Sugimoto
J. Biol. Inorg. Chem., Suppl. 1 S118 2009.1
Joint Work
-
An Approach to Peptide-based ATP Receptors by a Combination of Random Selection, Rational Design, and Molecular Imprinting Reviewed
J. Matsui, J. Nagano, D. Miyoshi, K. Tamaki, N. Sugimoto
Biosens. Bioelectron. 25 563 - 567 2009.1
Joint Work
-
Cu(II) ion inhibits early stages of amyloid β fibril formation in vitro
T. Fujimoto, D. Miyoshi, H. Tateishi-Karimata, N. Sugimoto
J. Biol. Inorg. Chem., Suppl. 1 S118 2009.1
Joint Work
-
Telomerase activity regulated by thermodynamic stability of DNA・RNA hybrid
三好大輔
Angew. Chem. Int. Ed., ( 47 ) 9034 - 9038 2008.11
Single Work
-
Small-molecule-directed assembly of DNA: a gold-nanoparticle-based strategy for screening of a DNA duplex binders
三好大輔
Adv. Mat ( 20 ) 706 - 710 2008.11
Single Work
-
Riboswitches for enhancing target gene expression in eukaryotes Reviewed
T. Yamauchi, D. Miyoshi, T. Kubodera, M. Ban, A. Nishimura, and N. Sugimoto
ChemBioChem 9 1040 - 1043 2008.1
Joint Work
-
外部刺激に応答する機能性核酸 －核酸ならではの機能を活用したナノバイオマテリアルの設計－ Invited
三好大輔、杉本直己
化学工業 （化学工業社） 59 ( 11 ) 21 - 27 2008.1
Joint Work
-
Thermodynamics of DNA structures under molecular crowding conditions with neutral and positive charged cosolutes
D. Miyoshi, K. Nakamura, S. Muhuri, H. T. Karimata, N. Sugimoto
Nucleic Acids Symp. Ser. 52 413 - 414 2008.1
Joint Work
-
Cationic porphyrin induced a telomeric DNA to g-quadruplex form in water Reviewed
T. Murashima, D. Sakiyama, D. Miyoshi, M. Kuriyama, T. Yamada, T. Miyazawa, N. Sugimoto
Bioinorg Chem Appl. 294756 2008.1
Joint Work
-
Molecular crowding effects on structure and stability of DNA Invited Reviewed
D. Miyoshi and N. Sugimoto
Biochimie 90 1040 - 1051 2008.1
Joint Work
-
外部刺激に応答する機能性核酸 －核酸ならではの機能を活用したナノバイオマテリアルの設計－
三好大輔, 杉本直己
化学工業 （化学工業社） 59 ( 11 ) 21 - 27 2008.1
Joint Work
-
DNA四重らせん構造を細胞内環境因子で制御する
三好大輔
生体機能関連化学部会 News Letter, 22 ( 3 ) 14 - 17 2007.11
Single Work
-
Synthesis, structure and thermal stability of fully hydrophobic porphyrin-DNA conjugates
三好大輔
Tetrahedron Lett ( 48 ) 8514 - 8517 2007.11
Single Work
-
Effects of cosolutes on the thermodynamic stability of parallel DNA duplex and triplex
三好大輔
Nucleic Acids Symp. Ser. (Oxf), ( 51 ) 167 - 168 2007.11
Single Work
-
Conformational switch of a functional nanowire based on the DNA G-quadruplex
三好大輔
Nucleic Acids Symp. Ser. (Oxf), ( 51 ) 167 - 168 2007.11
Single Work
-
DNAデザイン －機能性分子開発への道しるべ－
三好大輔
化学 62 ( 9 ) 28 - 32 2007.11
Single Work
-
DNAを用いたバイオ計測 －センシング核酸の開発と新展開－
三好大輔
未来材料, 7 ( 6 ) 10 - 18 2007.11
Single Work
-
Regulation of DNA nucleases by molecular crowding
三好大輔
Nucleic Acids Res ( 35 ) 4086 - 4093 2007.11
Single Work
-
Artificial G-wire Switch with 2,2’-Bipyridine Units Responsive to Divalent Metal Ions
三好大輔
J. Am. Chem. Soc ( 129 ) 5919 - 5925 2007.11
Single Work
-
Molecular Imprinting Under Molecular Crowding Conditions: an Aid to the synthesis of a High-capacity Polymeric Sorbent for Triazine Herbicides
三好大輔
Anal. Chem ( 79 ) 1749 - 1757 2007.11
Single Work
-
DNA四重らせん構造を細胞内環境因子で制御する
三好大輔
生体機能関連化学部会 News Letter, 22 ( 3 ) 14 - 17 2007.11
Single Work
-
Hydration regulates thermodynamic stability of DNA structures under molecular crowding conditions Reviewed
D. Miyoshi, H. Karimata, and N. Sugimoto
Nucleosides, Nucleotides and Nucleic Acids 26 589 - 595 2007.1
Joint Work
-
Development of molecular logic gates using the structural switch of telomere DNAs
三好大輔
Nucleic Acids Symp. Ser. ( 50 ) 315 - 316 2006.11
Single Work
-
Molecularly Imprinting within a Single Peptide Molecule for Synthesizing a Water-soluble ATP Receptor
三好大輔
Proceedings of the International Conference of 43rd Japanese Peptide Symposium and 4th Peptide Engineering Meeting 396 - 397 2006.11
Single Work
-
Properties of long telomeric DNAs under cell-mimicking conditions
三好大輔
Nucleic Acids Symp. Ser. ( 50 ) 207 - 208 2006.11
Single Work
-
Factors regulating thermodynamic stability of DNA structures under molecular crowding conditions
三好大輔
Nucleic Acids Symp. Ser ( 50 ) 203 - 204 2006.11
Single Work
-
Characterization of Structure and Stability of Long Telomeric DNA G-Quadruplexes
三好大輔
J. Am. Chem. Soc., ( 128 ) 15461 - 15468 2006.11
Single Work
-
DNA Logic Gates Based on Structural Polymorphism of Telomere DNA Molecules Responding to Chemical Input Signals
三好大輔
Angew. Chem. Int. Ed., ( 45 ) 7716 - 7719 2006.11
Single Work
-
Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions
三好大輔
J. Am. Chem. Soc ( 128 ) 7957 - 7963 2006.11
Single Work
-
生命を制御するのは遺伝子か環境か－細胞内環境に左右される遺伝子の構造と機能－
三好大輔
高分子 55 ( 5 ) 322 - 325 2006.11
Single Work
-
Effect of molecular crowding on DNA polymerase activity
三好大輔
Biotech. J., ( 1 ) 440 - 446 2006.11
Single Work
-
A DNA duplex with Extremely Enhanced Thermal Stability Based on Controlled Immobilization on Gold Nanoparticles.
三好大輔
Nano Lett., ( 6 ) 491 - 495 2006.11
Single Work
-
Properties of long telomeric DNAs under cell-mimicking conditions
三好大輔
Nucleic Acids Symp. Ser. ( 50 ) 207 - 208 2006.11
Single Work
-
Use of the polymorphic nature of high-order DNA structures for the design of dynamic and functional nanodevices Invited Reviewed
D. Miyoshi, N. Sugimoto
Recent Devel. Nucleic Acids Res. 2 49 - 70 2006.1
Joint Work
-
Use of the polymorphic nature of high-order DNA structures for the design of dynamic and functional nanodevices
D. Miyoshi, N. Sugimoto
Recent Devel. Nucleic Acids Res. 2 49 - 70 2006.1
Joint Work
-
Thermodynamic and Kinetic Analysis of Nucleic Acid Structures toward Pharmacogenomics.
三好大輔
Current Pharmacogenomics, ( 3 ) 217 - 236 2005.11
Single Work
-
Structural switch of telomere DNA by pH and monovalent cation.
三好大輔
Nucleic Acids Symp. Ser ( 49 ) 243 - 244 2005.11
Single Work
-
Structure and stability of DNA quadruplexes under molecular crowding conditions.
三好大輔
Nucleic Acids Symp. Ser ( 49 ) 239 - 240 2005.11
Single Work
-
DNA nanowire sensitive to the surrounding condition.
三好大輔
Nucleic Acids Symp. Ser. ( 49 ) 43 - 44 2005.11
Single Work
-
DNA-Based Biosensor for Monitoring pH in Vitro and in Living Cells.
三好大輔
Biochemistry ( 44 ) 7125 - 7130 2005.11
Single Work
-
Roles of Mg2+ in TPP-dependent riboswitch.
三好大輔
FEBS Lett. ( 579 ) 2583 - 2588 2005.11
Single Work
-
Drastic Effect of a Single Base Difference between Human and Tetrahymena Telomere Sequences on Their Structures under Molecular Crowding Conditions.
三好大輔
Angew. Chem. Int. Ed. Engl ( 44 ) 3740 - 3744 2005.11
Single Work
-
SPR sensor chip for detection of small molecules using molecularly imprinted polymer with embedded gold nanoparticles.
三好大輔
Anal Chem ( 77 ) 4282 - 4285 2005.11
Single Work
-
Roles of Mg2+ in TPP-dependent riboswitch.
三好大輔
FEBS Lett ( 579 ) 2583 - 2588 2005.11
Single Work
-
Thermodynamic and Kinetic Analysis of Nucleic Acid Structures toward Pharmacogenomics
三好大輔
Current Pharmacogenomics ( 3 ) 217 - 236 2005.11
Single Work
-
Drastic effect of a single base difference between human and tetrahymena telomere sequences on their structures under molecular crowding conditions.
三好大輔
Angew Chem Int Ed Engl. ( 44 ) 3740 - 3744 2005.11
Single Work
-
Duplex Dissociation of Telomere DNA Induced by Molecular Crowding.
三好大輔
J. Am. Chem. Soc. ( 126 ) 165 - 169 2004.11
Single Work
-
生命分子を用いたサブナノデバイスの創製
三好大輔
未来材料(NTS) ( 4 ) 26 - 33 2004.11
Single Work
-
Composite of Au Nanoparticles and molecularly imprinted polymer as a sensing material
三好大輔
Anal. Chem ( 76 ) 1310 - 1315 2004.11
Single Work
-
Structural Competition Involving G-Quadruplex DNA and Its Complement.
三好大輔
Biochemistry ( 42 ) 11736 - 11744 2003.11
Single Work
-
Structural Polymorphism of Telomeric DNA Regulated by pH and Divalent Cation.
三好大輔
Nucleosides, Nucleotides, and Nucleic Acids ( 22 ) 203 - 221 2003.11
Single Work
-
Structural Ttransition from Antiparallel to Parallel G-Quadruplex of d(G4T4G4) Induced by Ca2+.
三好大輔
Nucleic Acids Res ( 31 ) 1156 - 1163 2003.11
Single Work
-
Effect of Putrescine and PEG on a Structural Transition of DNA G-Quadruplex.
三好大輔
Nucleosides, Nucleotides, and Nucleic Acids ( 22 ) 1591 - 1594 2003.11
Single Work
-
バイオインフォマティクスを活用した未来型生体内・外センシングシステム
三好大輔
科学と工業, ( 77 ) 413 - 419 2003.11
Single Work
-
Novel biomaterials derived from deoxyribozyme and NAPzyme
三好大輔
Macromol. Chem. Phys. Macromol. Symp. ( 201 ) 245 - 252 2003.11
Single Work
-
核酸の長鎖ダングリングエンドと四重鎖の構造形成に関する熱力学的研究
三好大輔
2003.3
Single Work
-
Long RNA Dangling End Has Large Energetic Contribution to Duplex Stability.
三好大輔
J. Am. Chem. Soc. ( 124 ) 10367 - 10372 2002.11
Single Work
-
シリーズ「生命を化学する」—モレキュラークラウディングとin cell Chemistry—
三好大輔
化学（化学同人） 57 ( 12 ) 50 - 56 2002.11
Single Work
-
超タンパク質材料—タンパク質活用最前線—
三好大輔
未来材料（NTS） ( 5 ) 29 - 35 2002.11
Single Work
-
Molecular Crowding Regulates the Structural Switch of the DNA G-quadruplex.
三好大輔
Biochemistry, ( 41 ) 15017 - 15024 2002.11
Single Work
-
A Stable DNA tetraloop and Its Structural Tolerance for Modification.
三好大輔
Chem. Lett 258 - 259 2001.11
Single Work
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Structural transition of d(G4T4G4) from antiparallel to parallel G-quartet induced by divalent cations
三好大輔
Nucleic Acids Res. Supple ( 1 ) 259 - 260 2001.11
Single Work
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Effect of Divalent Cations on Antiparallel G-Quartet Structure of d(G4T4G4).
三好大輔
FEBS Lett ( 496 ) 128 - 133 2001.11
Single Work
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Development of Small Peptides Recognizing a Monosaccharide by Combinatorial Chemistry.
三好大輔
Chem. Commun 2295 - 2296 2000.11
Single Work
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ゲノム化学は今3 SNPs解析と次世代の生命化学 —「ニューセントラルドグマ」の構築に向けて.
三好大輔
化学（化学同人） ( 55 ) 20 - 25 2000.11
Single Work
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ゲノム化学は今2 DNAチップとバイオインフォマティクス —遺伝子の定量的解析に向けて.
三好大輔
化学（化学同人） ( 55 ) 14 - 18 2000.11
Single Work
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A Novel Screening Method for Combinatorial Chemistry for Low Affinity Interactions.
三好大輔
Chem. Commun. 677 - 678 1999.11
Single Work
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Selection of peptides that recognize tryptophan by combinatorial chemistry
三好大輔
Peptide Science 281 - 284 1999.11
Single Work
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a-b Structural Transition of Short Oligopeptides by Water/Organic Solvent Titration.
三好大輔
Chem. Lett 637 - 638 1999.11
Single Work