Chemical communications (Cambridge, England), Topology-selective photo-crosslinking of G-quadruplexes via dual G-quartet and groove recognition., Ryo Ishikawa; Kazuki Yanagita; Sayuri Shimada; Shogo Sasaki; Takatsugu Hirokawa; Yue Ma; Kazuo Nagasawa; Masayuki Tera, The novel photo-crosslinking ligand 6OTD-Bp, bearing an alkylamine benzophenone (Bp) with macrocyclic hexaoxazole (6OTD), was shown to preferentially ligate with hybrid G4s through recognizing both G-quartets and their characteristic wide groove. Higher crosslinking yield was observed for hybrid G4 with wider grooves., 14 Nov. 2024, 60, 92, 13550, 13553, Scientific journal, True, 10.1039/d4cc04804k

Applied Physics Express, High-speed growth of thick high-purity β-Ga2O3 layers by low-pressure hot-wall metalorganic vapor phase epitaxy, Junya Yoshinaga; Haruka Tozato; Takahito Okuyama; Shogo Sasaki; Guanxi Piao; Kazutada Ikenaga; Ken Goto; Yuzaburo Ban; Yoshinao Kumagai, High-speed growth of thick, high-purity β-Ga2O3 homoepitaxial layers on (010) β-Ga2O3 substrates by low-pressure hot-wall metalorganic vapor phase epitaxy was investigated using trimethylgallium (TMGa) as the Ga precursor. When the reactor pressure was 2.4-3.4 kPa, the growth temperature was 1000 °C, and a high input VI/III (O/Ga) ratio was used, the growth rate of β-Ga2O3 could be increased linearly by increasing the TMGa supply rate. A thick layer was grown at a growth rate of 16.2 μm h−1 without twinning. Incorporated impurities were not detected, irrespective of the growth rate, demonstrating the promising nature of β-Ga2O3 growth using TMGa., 01 Sep. 2023, 16, 9, Scientific journal, 10.35848/1882-0786/acf8ae

Chemical communications (Cambridge, England), Regulation of thrombin activity by ligand-induced topological alteration in a thrombin-binding aptamer., Shogo Sasaki; Yue Ma; Takatsugu Hirokawa; Kazunori Ikebukuro; Masayuki Tera; Kazuo Nagasawa, Thrombin-binding aptamer (TBA), which forms a G-quadruplex (G4) structure with anti-parallel topology, interacts with thrombin to inhibit its enzymatic activity. Here we show that the G4-topology-altering ligand L2H2-2M2EA-6LCO (6LCO) changes the anti-parallel topology of TBA G4 to the parallel topology, thereby abrogating the thrombin-inhibitory activity of TBA. This finding suggests that G4 ligands that alter topology may be promising drug candidates for diseases involving G4-binding proteins., 13 Jul. 2023, 59, 57, 8862, 8865, Scientific journal, True, 10.1039/d3cc02308g

Journal of Vacuum Science and Technology A: Vacuum, Surfaces and Films, Comparison of triethylgallium and diethylgallium ethoxide for β-Ga2O3 growth by metalorganic vapor phase epitaxy, Ken Goto; Taro Nishimura; Masato Ishikawa; Takahito Okuyama; Haruka Tozato; Shogo Sasaki; Kazutada Ikenaga; Yoshihiko Takinami; Hideaki Machida; Yoshinao Kumagai, The suitability of diethylgallium ethoxide (Et2GaOEt) containing Ga-O bonds as a Ga precursor for beta-gallium oxide (β-Ga2O3) growth by metalorganic vapor phase epitaxy (MOVPE) was investigated. Because estimating the growth behavior by thermodynamic analysis is difficult as a result of a lack of knowledge about the thermodynamics of Et2GaOEt, the growth behavior was estimated by observing its pyrolysis and combustion processes. Mass spectrometric analysis of gases sampled directly from an MOVPE reactor when only Et2GaOEt was supplied revealed that Et2GaOEt was decomposed to gallane, ethylene, and acetaldehyde by β-hydrogen (β-H) elimination at temperatures greater than 450 °C. However, when Et2GaOEt was supplied together with O2 to the MOVPE reactor maintained at 1000 °C, the combustion of hydrogen and carbon derived from Et2GaOEt was accelerated as the O2 supply was increased. In addition, the amount of O2 required for the complete combustion of Et2GaOEt (i.e., the amount required for the growth of β-Ga2O3) was clarified. On the basis of this pyrolysis/combustion behavior, homoepitaxial growth of β-Ga2O3 layers on β-Ga2O3 substrates was investigated at 1000 °C using Et2GaOEt as a Ga precursor and the growth behavior was compared with that when triethylgallium (Et3Ga) was used as a Ga precursor. Because both Ga precursors ultimately provide Ga gas after β-H elimination, no substantial difference in the growth rate was observed with respect to the amount of Ga atoms injected into the growth reactor. In addition, no substantial difference in crystallinity was observed; homoepitaxial layers grown at 0.7—0.8 μm/h were single crystals without twins, whereas those at 1.5—1.6 μm/h had twins. Et2GaOEt was found to be suitable as a Ga precursor for MOVPE of β-Ga2O3, with performance comparable to that of Et3Ga., 01 Jul. 2023, 41, 4, Scientific journal, 10.1116/6.0002732

Japanese Journal of Applied Physics, Mass spectrometric study of β-Ga2O3growth process by metalorganic vapor phase epitaxy, Kazutada Ikenaga; Takahito Okuyama; Haruka Tozato; Taro Nishimura; Shogo Sasaki; Ken Goto; Masato Ishikawa; Yoshihiko Takinami; Hideaki Machida; Yoshinao Kumagai, In metalorganic vapor phase epitaxy of β-Ga2O3 using triethylgallium (TEGa) and O2 as precursors and Ar as the carrier gas, the gases directly above the substrate were sampled and analyzed by time-of-flight mass spectrometry. TEGa was found to decompose at 400 °C-600 °C via β-hydrogen elimination reaction to generate gaseous Ga, hydrocarbons (C2H4, C2H2, C2H6), and H2. When β-Ga2O3 was grown at temperatures greater than 1000 °C and with input VI/III ratios greater than 100, the hydrocarbons and H2 were combusted and CO2 and H2O were generated. The C and H impurity concentrations measured by secondary-ion mass spectrometry in the β-Ga2O3(010) homoepitaxial layer grown under these conditions were less than their respective background levels. Thus, to grow β-Ga2O3 without C and H contamination, conditions that favor the complete combustion of hydrocarbons and H2 generated by the decomposition of TEGa should be used., 01 Jun. 2023, 62, SF, Scientific journal, 10.35848/1347-4065/acc53c

Not Refereed, Analytical biochemistry, Single-molecule displacement assay reveals strong binding of polyvalent dendrimer ligands to telomeric G-quadruplex., Pravin Pokhrel; Shogo Sasaki; Changpeng Hu; Deepak Karna; Shankar Pandey; Yue Ma; Kazuo Nagasawa; Hanbin Mao, Binding between a ligand and a receptor is a fundamental step in many natural or synthetic processes. In biosensing, a tight binding with a small dissociation constant (Kd) between the probe and analyte can lead to superior specificity and sensitivity. Owing to their capability of evaluating competitors, displacement assays have been used to estimate Kd at the ensemble average level. At the more sensitive single-molecule level, displacement assays are yet to be established. Here, we developed a single-molecule displacement assay (smDA) in an optical tweezers instrument and used this innovation to evaluate the binding of the L2H2-6OTD ligands to human telomeric DNA G-quadruplexes. After measuring Kd of linear and dendrimer L2H2-6OTD ligands, we found that dendrimer ligands have enhanced binding affinity to the G-quadruplexes due to their polyvalent geometry. This increased binding affinity enhanced inhibition of telomerase elongation on a telomere template in a Telomerase Repeated Amplification Protocol (TRAP). Our experiments demonstrate that the smDA approach can efficiently evaluate binding processes in chemical and biological processes., Jul. 2022, 649, 114693, 114693, Scientific journal, True, 10.1016/j.ab.2022.114693

Not Refereed, Organic & biomolecular chemistry, Selective alkylation of parallel G-quadruplex structure., Kazumitsu Onizuka; Erchissaran Ganbold; Yue Ma; Shogo Sasaki; Madoka E Hazemi; Yutong Chen; Norihiro Sato; Mamiko Ozawa; Kazuo Nagasawa; Fumi Nagatsugi, The selective alkylation of nucleic acids is important for a medicinal approach and biological study. We now report a novel selective alkylation of the parallel G-quadruplex structure using the conjugate of the macrocyclic hexaoxazole L2G2-6OTD-1M1PA and vinyl-quinazolinone-S(O)Me (6OTD-VQ-S(O)Me)., 2021, 19, 13, 2891, 2894, Scientific journal, True, 10.1039/d0ob02365e

Not Refereed, Translational and Regulatory Sciences, Catalyst Unit, Identification of G-quadruplex sequences in severe acute respiratory syndrome coronavirus 2, SASAKI Shogo; KITAMURA Junya; ENDO Hiroyuki; SHIRAISHI Akira; IKEBUKURO Kazunori; MIZUTANI Tetsuya; TERA Masayuki, 2021, 3, 3, 89, 92, 10.33611/trs.2021-019

Not Refereed, Chemical communications (Cambridge, England), Stabilization of telomeric G-quadruplex by ligand binding increases susceptibility to S1 nuclease., Ryo Ishikawa; Mizuho Yasuda; Shogo Sasaki; Yue Ma; Kazuo Nagasawa; Masayuki Tera, The extent of thermodynamic stabilization of telomeric G-quadruplex (G4) by isomers of G4 ligand L2H2-6OTD, a telomestatin analog, is inversely correlated with susceptibility to S1 nuclease. L2H2-6OTD facilitated the S1 nuclease activities through the base flipping in G4, unlike the conventional role of G4 ligands which inhibit the protein binding to DNA/RNA upon ligand interactions., 2021, 57, 59, 7236, 7239, Scientific journal, True, 10.1039/d1cc03294a

Not Refereed, RSC advances, Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex., Shogo Sasaki; Yue Ma; Takumi Ishizuka; Hong-Liang Bao; Takatsugu Hirokawa; Yan Xu; Masayuki Tera; Kazuo Nagasawa, G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA., 2020, 10, 71, 43319, 43323, Scientific journal, True, 10.1039/d0ra09413g

Not Refereed, Molecules, Synthesis and Telomeric G-Quadruplex-Stabilizing Ability of Macrocyclic Hexaoxazoles Bearing Three Side Chains, ヒロカワ, タカツグ; Ma, Yue; Iida, Keisuke; Sasaki, Shogo; Heddi, Brahim; Phan, Anh; Nagasawa, Kazuo, G-quadruplexes (G4s), which are structures formed in guanine-rich regions of DNA, are involved in a variety of significant biological functions, and therefore "sequence-dependent" selective G4-stabilizing agents are required as tools to investigate and modulate these functions. Here, we describe the synthesis of a new series of macrocyclic hexaoxazole-type G4 ligand (6OTD) bearing three side chains. One of these ligands, 5b, stabilizes telomeric G4 preferentially over the G4-forming DNA sequences of c-kit and K-ras, due to the interaction of its piperazinylalkyl side chain with the groove of telomeric G4., Jan. 2019, 24, 2, 263, Scientific journal, True, 10.3390/molecules24020263

Not Refereed, Angewandte Chemie (International ed. in English), Binding of a Telomestatin Derivative Changes the Mechanical Anisotropy of a Human Telomeric G-Quadruplex., Sagun Jonchhe; Chiran Ghimire; Yunxi Cui; Shogo Sasaki; Mason McCool; Soyoung Park; Keisuke Iida; Kazuo Nagasawa; Hiroshi Sugiyama; Hanbin Mao, Mechanical anisotropy is an essential property for biomolecules to assume structural and functional roles in mechanobiology. However, there is insufficient information on the mechanical anisotropy of ligand-biomolecule complexes. Herein, we investigated the mechanical property of individual human telomeric G-quadruplexes bound to telomestatin, using optical tweezers. Stacking of the ligand to the G-tetrad planes changes the conformation of the G-quadruplex, which resembles a balloon squeezed in certain directions. Such a squeezed balloon effect strengthens the G-tetrad planes, but dislocates and weakens the loops in the G-quadruplex upon ligand binding. These dynamic interactions indicate that the binding between the ligand and G-quadruplex follows the induced-fit model. We anticipate that the altered mechanical anisotropy of the ligand-G-quadruplex complex can add additional level of regulations on the motor enzymes that process DNA or RNA molecules., 12 Dec. 2018, 58, 3, 877, 881, Scientific journal, True, 10.1002/anie.201811046

Not Refereed, Biochemistry, Random Formation of G-Quadruplexes in the Full-Length Human Telomere Overhangs Leads to a Kinetic Folding Pattern with Targetable Vacant G-Tracts., Jibin Abraham Punnoose; Yue Ma; Mohammed Enamul Hoque; Yunxi Cui; Shogo Sasaki; Athena Huixin Guo; Kazuo Nagasawa; Hanbin Mao, G-Quadruplexes formed in the 3' telomere overhang (∼200 nucleotides) have been shown to regulate biological functions of human telomeres. The mechanism governing the population pattern of multiple telomeric G-quadruplexes is yet to be elucidated inside the telomeric overhang in a time window shorter than thermodynamic equilibrium. Using a single-molecule force ramping assay, we quantified G-quadruplex populations in telomere overhangs over a full physiological range of 99-291 nucleotides. We found that G-quadruplexes randomly form in these overhangs within seconds, which leads to a population governed by a kinetic, rather than a thermodynamic, folding pattern. The kinetic folding gives rise to vacant G-tracts between G-quadruplexes. By targeting these vacant G-tracts using complementary DNA fragments, we demonstrated that binding to the telomeric G-quadruplexes becomes more efficient and specific for telomestatin derivatives., 27 Nov. 2018, 57, 51, 6946, 6955, Scientific journal, True, 10.1021/acs.biochem.8b00957

Not Refereed, Organic & biomolecular chemistry, Development of G-quadruplex ligands for selective induction of a parallel-type topology., Yue Ma; Yamato Tsushima; Mai Sakuma; Shogo Sasaki; Keisuke Iida; Sachiko Okabe; Hiroyuki Seimiya; Takatsugu Hirokawa; Kazuo Nagasawa, G-Quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. The G4-forming DNAs can form three kinds of topologies, i.e., parallel, anti-parallel, and hybrid. In this paper, we present G4 ligands L2H2-2M2EA-6OTD (3) and L2G2-2M2EG-6OTD (4) bearing tetra-aminoalkyl and -guanidinylalkyl side chains, respectively, in a macrocyclic hexaoxazole structure. These ligands efficiently induce the parallel-type topology of telomeric G4 regardless of the effects of cations. Titration with 4 results in a drastic topology switch to the parallel topology from the anti-parallel structure induced by the structurally related ligand L2H2-6OTD (1)., 2018, 16, 40, 7375, 7382, Scientific journal, True, 10.1039/c8ob01702f

Not Refereed, Scientific reports, Targeting glioma stem cells in vivo by a G-quadruplex-stabilizing synthetic macrocyclic hexaoxazole., Takahiro Nakamura; Sachiko Okabe; Haruka Yoshida; Keisuke Iida; Yue Ma; Shogo Sasaki; Takao Yamori; Kazuo Shin-Ya; Ichiro Nakano; Kazuo Nagasawa; Hiroyuki Seimiya, G-quadruplex (G4) is a higher-order nucleic acid structure that is formed by guanine-rich sequences. G4 stabilization by small-molecule compounds called G4 ligands often causes cytotoxicity, although the potential medicinal impact of this effect has not been fully established. Here we demonstrate that a synthetic G4 ligand, Y2H2-6M(4)-oxazole telomestatin derivative (6OTD), limits the growth of intractable glioblastoma (grade IV glioma) and glioma stem cells (GSCs). Experiments involving a human cancer cell line panel and mouse xenografts revealed that 6OTD exhibits antitumor activity against glioblastoma. 6OTD inhibited the growth of GSCs more potently than it did the growth of differentiated non-stem glioma cells (NSGCs). 6OTD caused DNA damage, G1 cell cycle arrest, and apoptosis in GSCs but not in NSGCs. These DNA damage foci tended to colocalize with telomeres, which contain repetitive G4-forming sequences. Compared with temozolomide, a clinical DNA-alkylating agent against glioma, 6OTD required lower concentrations to exert anti-cancer effects and preferentially affected GSCs and telomeres. 6OTD suppressed the intracranial growth of GSC-derived tumors in a mouse xenograft model. These observations indicate that 6OTD targets GSCs through G4 stabilization and promotion of DNA damage responses. Therefore, G4s are promising therapeutic targets for glioblastoma., 15 Jun. 2017, 7, 1, 3605, 3605, Scientific journal, True, 10.1038/s41598-017-03785-8

Patent right, グアニン四重鎖形成配列予測装置及び機械学習方法、並びに化合物又はその塩、及びグアニン四重鎖結合性リガンド, 寺 正行; 野原 玲奈; 佐々木 捷悟; 白石 慧; 佐竹 炎, 国立大学法人東京農工大学, 特願2023-087449, 29 May 2023, 特開2023-174616, 07 Dec. 2023, j_global