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Dive into the research topics where Tsukasa Mashima is active.

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Featured researches published by Tsukasa Mashima.


Nucleic Acids Research | 2009

Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein

Tsukasa Mashima; Akimasa Matsugami; Fumiko Nishikawa; Satoshi Nishikawa; Masato Katahira

RNA aptamers against bovine prion protein (bPrP) were obtained, most of the obtained aptamers being found to contain the r(GGAGGAGGAGGA) (R12) sequence. Then, it was revealed that R12 binds to both bPrP and its β-isoform with high affinity. Here, we present the structure of R12. This is the first report on the structure of an RNA aptamer against prion protein. R12 forms an intramolecular parallel quadruplex. The quadruplex contains G:G:G:G tetrad and G(:A):G:G(:A):G hexad planes. Two quadruplexes form a dimer through intermolecular hexad–hexad stacking. Two lysine clusters of bPrP have been identified as binding sites for R12. The electrostatic interaction between the uniquely arranged phosphate groups of R12 and the lysine clusters is suggested to be responsible for the affinity of R12 to bPrP. The stacking interaction between the G:G:G:G tetrad planes and tryptophan residues may also contribute to the affinity. One R12 dimer molecule is supposed to simultaneously bind the two lysine clusters of one bPrP molecule, resulting in even higher affinity. The atomic coordinates of R12 would be useful for the development of R12 as a therapeutic agent against prion diseases and Alzheimers disease.


Nucleic Acids Research | 2013

Anti-prion activity of an RNA aptamer and its structural basis

Tsukasa Mashima; Fumiko Nishikawa; Yuji O. Kamatari; Hiromichi Fujiwara; Masayuki Saimura; Takashi Nagata; Tsutomu Kodaki; Satoshi Nishikawa; Kazuo Kuwata; Masato Katahira

Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrPC) of PrP into an abnormal form (PrPSc) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrPC is expected to block this conversion and to thereby prevent prion diseases. Here, we show that an RNA aptamer comprising only 12 residues, r(GGAGGAGGAGGA) (R12), reduces the PrPSc level in mouse neuronal cells persistently infected with the transmissible spongiform encephalopathy agent. Nuclear magnetic resonance analysis revealed that R12, folded into a unique quadruplex structure, forms a dimer and that each monomer simultaneously binds to two portions of the N-terminal half of PrPC, resulting in tight binding. Electrostatic and stacking interactions contribute to the affinity of each portion. Our results demonstrate the therapeutic potential of an RNA aptamer as to prion diseases.


International Journal of Biological Macromolecules | 2010

Solubilization and structural determination of a glycoconjugate which is assembled into the sheath of Leptothrix cholodnii

Minoru Takeda; Keiko Kondo; Mina Yamada; Jun-ichi Koizumi; Tsukasa Mashima; Akimasa Matsugami; Masato Katahira

The sheath of Leptothrix cholodnii is constructed from a structural glycoconjugate, a straight-chained amphoteric heteropolysaccharide modified with glycine and cysteine. Though the structure of the glycan core is already determined, its modifications with amino acids and other molecules are not fully resolved. In this study, we aimed to determine the chemical structure of the glycoconjugate as a whole. Enantiomeric determination of cysteine in the sheath was performed and as a result, L-cysteine was detected. NMR spectroscopy was endeavored to determine overall structure of the glycoconjugate. Prior to NMR analysis, solubilization of the glycoconjugate was attempted by adding denaturing reagents or by derivatization. As far as tested, sulfonation by performic acid oxidation was suitable for solubilization, but further improvement was achieved by N-acetylation. The approximate molecular weight of the derivative was estimated to be 4.5 x 10(4) by size-exclusion chromatography. The NMR studies for the sulfonated glycoconjugate and its N-acetylated derivative revealed that the sheath glycoconjugate is a glycosaminoglycan consisting of a pentasaccharide repeating unit which is substoichiometrically esterified with 3-hydroxypropionic acid and stoichiometrically amidated with acetic acid and glycyl-L-cysteine.


Nucleic acids symposium series (2004) | 2008

Structural analysis of r(GGA)4 found in RNA aptamer for bovine prion protein

Akimasa Matsugami; Tsukasa Mashima; Fumiko Nishikawa; Kazuyoshi Murakami; Satoshi Nishikawa; Ken Noda; Takashi Yokoyama; Masato Katahira

RNA aptamers for bovine prion protein (bPrP) were obtained by in vitro selection. It was found that the r(GGA) triplet repeat was frequently present in these aptamers. We already reported that both DNA and RNA containing the GGA repeat form unique quadruplex structures. The unique structures may be utilized for the recognition of bPrP by these aptamers. One of these aptamers contains four continuous repeat of r(GGA), r(GGA)(4). Here, we analyzed the structure of r(GGA)(4) under physiological ionic conditions by NMR. It was revealed on the basis of characteristic NOEs that an r(GGA)(4) strand forms the quadruplex composed of one G:G:G:G tetrad plane and one G(:A):G:G(:A):G hexad plane. Furthermore, two monomers form a dimeric structure in a tail-to-tail manner. The dimeric quadruplex structure of r(GGA)(4) is similar to that of d(GGA)(4), but the difference between two structures was also noticed.


Nucleic acids symposium series (2004) | 2008

Interactions between antitumor drugs and vault RNA

Tsukasa Mashima; Michiko Kudo; Yusuke Takada; Akimasa Matsugami; Subash C. B. Gopinath; Penmetcha K. R. Kumar; Masato Katahira

It is supposed that ribonucleoprotein particle vault is involved in detoxification processes and thus is related to multidrug resistance. The vault is composed of three proteins and three vault RNAs, hvg-1, -2 and -3. The direct interactions between vault components and drugs were not reported. Recently, we revealed the interactions between vault RNAs and mitoxantrone. Here, we examined the interactions between hvg-2 and six antitumor drugs by a chemical shift perturbation method of NMR. It was found that in addition to mitoxantrone, hvg-2 can interact with two drugs basically in the same way using the same site. The difference in the affinity was also noticed among three drugs. Hvg-2 did not bind to the other three drugs. It is suggested that the common or closely related chemical structure of the positive three drugs is recognized by vault RNA.


Nucleic acids symposium series (2004) | 2008

Structural analysis of Musashi-RNA complex on the basis of long-range structural information.

Takako Ohyama; Ayako Furukawa; Tsukasa Mashima; Takashi Sugiyama; Shouta Ohgara; Toshio Yamazaki; Takao Imai; Hideyuki Okano; Takashi Nagata; Masato Katahira

Musashi protein is supposed to be involved in the regulation of differentiation of neural stem cells. Musashi binds to 3 untranslated region of target mRNA and represses the translation of mRNA. Musashi has two tandem RNA-binding domains (RBDs), RBD1 and RBD2. Both RBDs cooperatively bind to the target mRNA. Here, we determined the structure of RBD1-RBD2 in complex with target RNA. First, the structures of two RBDs in the complex were determined on the basis of short-range distance restrains derived from NOEs. However, the relative position of two RBDs was not determined due to the lack of long-range distance restraints across two RBDs. In order to overcome the situation, we introduced the paramagnetic center into Musashi by attaching MTSL carrying the NO radical. The long-range distance restraints (ca. 20-40 A) between two RBDs were derived from paramagnetic relaxation enhancement (PRE) caused by the paramagnetic center. The relative position of two RBDs was successfully determined on the basis of these long-range distance restraints. The change in the relative position of two RBDs on binding to the target RNA was also detected by PRE. The determined structure of RBD1-RBD2 in the complex has suggested how Musashi recognizes its target mRNA.


Nucleic acids symposium series (2004) | 2009

Structural analysis of ribonucleopeptide aptamer against ATP

Tsukasa Mashima; Akimasa Matsugami; Shun Nakano; Masafumi Inoue; Masatora Fukuda; Takashi Morii; Masato Katahira

A ribonucleopeptide aptamer against ATP was obtained by the in vitro selection method. This ribonucleopeptide aptamer comprises a randomized and selected RNA linked to the Rev-responsive element (RRE) in complex with a peptide derived from an HIV Rev protein. The ribonucleopeptide aptamer selectively binds ATP in the presence of the Rev-derived peptide, exclusively. Here, we present the structural analysis of the ribonucleopeptide aptamer with NMR. The secondary structure of the RNA part of the aptamer, the selected RNA region linked to RRE, in the presence of the Rev-derived peptide was determined in an Ado-bound form. G:A and G:G base pairs, together with canonical base pairs, are formed in a duplex of RRE. The selected RNA region plays a crucial role in target binding. It has been found that the two U residues located in the selected RNA region trap Ado through the formation of the U:A:U base triple. This was directly confirmed by the HNN-COSY experiment through the detection of spin-spin couplings across the hydrogen bonds for Watson-Crick and Hoogsteen A:U base pairs in the U:A:U base triple.


Nucleic acids symposium series (2004) | 2009

Structural aspects for the function of ATP-binding ribonucleopeptide receptors

Shun Nakano; Masatora Fukuda; Tsukasa Mashima; Masato Katahira; Takashi Morii

We describe here analyses of the secondary structure of ATP-binding ribonucleopeptide (RNP) receptors. Mapping of the RNA structure of ATP-binding RNP receptors by using hydrolytic enzymes, chemical probing with dimethyl sulfate (DMS), and in-line probing indicated that ATP-binding RNP receptors take the loop structure at the nucleotide position of the variable region. In addition, it was evident that a part of the consensus region located next to the variable region directly participated in the binding to ATP. The completely preserved three U nucleotides were essential for the binding of RNP to ATP as revealed by the affinity evaluation and the secondary structure analyses of the U nucleotides mutants of the ATP-binding RNP receptor. Interestingly, two mutants with an adenosine introduced to either of the two U nucleotides showed similar secondary structures to the original ATP-binding RNP. These results imply the possibility that the adenine base introduced at the U position acts just like the substrate ATP, and suggest that the U nucleotides in these positions interact directly to ATP.


Biomedical Sciences | 2018

Multiplicity in Long Noncoding RNA in Living Cells

Riki Kurokawa; Reina Komiya; Takanori Oyoshi; Yoko Matsuno; Hidenori Tani; Masato Katahira; Keisuke Hitachi; Yuji Iwashita; Takefumi Yamashita; Keiko Kondo; Ryoma Yoneda; Yudai Yamaoki; Naomi Ueda; Tsukasa Mashima; Naohiro Kobayashi; Takashi Nagata; Ayaka Kiyoishi; Masayuki Miyake; Fumi Kano; Masayuki Murata; Nesreen Hamad; Kohei Sasaki; Naoyuki Shoji


生物物理 | 2014

1P121 新規プリオンアプタマーの探索とその構造研究(05A. 核酸 : 構造・物性,ポスター,第52回日本生物物理学会年会(2014年度))

Tsukasa Mashima; Fumiko Nishikawa; Yuji O. Kamatari; Takashi Nagata; Satoshi Nishikawa; Kazuo Kuwata; Masato Katahira

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Fumiko Nishikawa

National Institute of Advanced Industrial Science and Technology

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Masayuki Saimura

National Institute of Advanced Industrial Science and Technology

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Satoshi Nishikawa

Japanese Ministry of International Trade and Industry

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Ayako Furukawa

Tokyo University of Science

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