Review Papers (Misc) - KOUMOTO Kazuya
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水和を介して酵素の活性化、安定化を引き起こす低分子双性イオン性分子の開発 Invited
甲元一也
野口研究所時報 ( 66 ) 3 - 9 2023.10
Authorship：Lead author, Corresponding author Publishing type：Article, review, commentary, editorial, etc. (other)
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「受動的な学び」から「能動的な学び」へ 〜高大連携活動の展開と可能性〜 Invited
甲元一也
月刊「兵庫教育」 74 ( 3 ) 4 - 7 2022.6
Authorship：Lead author, Corresponding author Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)
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Formation of beta-(1,3-1,6)-D-glucan-complexed [70]fullerene and its photodynamic activity towards macrophages (vol 15, pg 1990, 2017) International journal
Atsushi Ikeda, Motofusa Akiyama, Kouta Sugikawa, Kazuya Koumoto, Yuta Kagoshima, Jiawei Li, Toshio Suzuki, Takeshi Nagasaki
ORGANIC & BIOMOLECULAR CHEMISTRY 15 ( 45 ) 9734 - 9734 2017.12
Publisher：ROYAL SOC CHEMISTRY
Correction for 'Formation of β-(1,3-1,6)-d-glucan-complexed [70]fullerene and its photodynamic activity towards macrophages' by Atsushi Ikeda et al., Org. Biomol. Chem., 2017, 15, 1990-1997.
DOI： 10.1039/c7ob90179h
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化学修飾技術を利用した乳酸菌模倣粒子による免疫賦活 Invited
甲元一也、長濱宏治、松井淳
バイオインダストリー 32 ( 9 ) 42 - 47 2015.9
Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)
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代謝産物アナログによる酵素活性化・安定化
高木琴味、甲元一也
月刊バイオインダストリー 30 ( 8 ) 43 - 50 2013.8
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media) Publisher：CMC出版
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Cellular zwitterionic metabolite analogs simultaneously enhance reaction rate, thermostability, salt tolerance, and substrate specificity of alpha-glucosidase International journal
Eisuke Deguchi, Kazuya Koumoto
BIOORGANIC & MEDICINAL CHEMISTRY 19 ( 10 ) 3128 - 3134 2011.5
Publisher：PERGAMON-ELSEVIER SCIENCE LTD
We investigated the structural effects of metabolite analogs derived from a naturally-occurring zwitterionic metabolite, glycine betaine, on the activity of several hydrolases. The initial velocities of the hydrolases were enhanced by the addition of the solutes into the buffer solution. Based on a detailed study using alpha-glucosidases, the acceleration efficiency of the enzymatic activity was strongly induced by solutes possessing bulky and aliphatic ammonium cations, indicating that enhancement of activity by the solutes depended on their chemical structures. Kinetic analysis revealed that the acceleration of the hydrolysis reaction was related to both the decrement of K-m and increment of V-max values. Furthermore, the addition of the metabolite analogs enhanced not only the rate constant but also the thermostability, salt tolerance, and substrate specificity of alpha-glucosidase simultaneously through the reduction of conformational perturbation of the enzyme. (C) 2011 Elsevier Ltd. All rights reserved.
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糖分子を認識する人工レセプター：ボロン酸
甲元一也、新海征治
月刊バイオインダストリー 27 ( 2 ) 18 - 23 2010.2
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media) Publisher：CMC出版
水中で糖のもつ水酸基と可逆的なエステル結合を形成するボロン酸基を有する糖レセプターの設計、合成に関する動向を纏めた。
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Reversible stability switching of a hairpin DNA via a photo-responsive linker unit International journal
Li Wu, Kazuya Koumoto, Naoki Sugimoto
CHEMICAL COMMUNICATIONS ( 14 ) 1915 - 1917 2009
Publisher：ROYAL SOC CHEMISTRY
We have designed and synthesized a novel photo-responsive linker unit, 4,4'-bis(hydroxymethyl)-azobenzene, which was introduced to the loop oligonucleotide in a DNA hairpin and was able to reversibly control the stability of the whole hairpin structure via UV or visible light irradiation.
DOI： 10.1039/b819643e
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Hydration is an important factor to regulate thermodynamic stability of a DNA duplex under molecular crowding conditions
Kazuya Koumoto, Hirofumi Ochiai, Naoki Sugimoto
CHEMISTRY LETTERS 37 ( 8 ) 864 - 865 2008.8
Publisher：CHEMICAL SOC JAPAN
By using a DNA duplex. (5'-GTTACTATATGA-3'/5'-TCATATAGTAAC-3') under molecular crowding, conditions, it was revealed that hydration plays a significant role in the stability of the duplex, in contrast to viscosity and dielectric constant which have little effect.
DOI： 10.1246/cl.2008.864
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NanoBioNow(10)周辺の分子環境に応答するDNAナノスイッチの構築
狩俣寿枝, 三好大輔, 藤本健史, 甲元一也, WANG Zhong‐Ming, 杉本直己
日本化学会講演予稿集 88th ( 2 ) 823 2008.3
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Structural effect of synthetic zwitterionic cosolutes on the stability of DNA duplexes
Kazuya KouMoto, Hirofumi Ochiai, Naoki Sugimoto
TETRAHEDRON 64 ( 1 ) 168 - 174 2008.1
Publisher：PERGAMON-ELSEVIER SCIENCE LTD
The molecular design of useful cosolutes for polymerase chain reaction (PCR), which is one of the most important techniques in molecular biology, plays a significant role in amplification of highly stable genome sequences because during PCR, strand dissociation sometimes fails due to high melting temperature. Here, we designed and synthesized eight new zwitterionic cosolutes derived from glycine betaine, a destabilizing reagent for GC-rich DNA duplexes, and systematically compared their ability to destabilize DNA duplexes and to amplify genome DNA by PCR. We found that introduction of n-butyl groups rather than methyl groups into the ammonium group reduced the melting temperature of DNA duplexes 11-fold more than what was observed for the scaffold cosolute, glycine betaine, and furthermore, the cosolute can amplify the stable genome sequence by PCR. (c) 2007 Elsevier Ltd. All rights reserved.
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Enhanced amplification of polymerase chain reaction by addition of cosolutes derived from a cellular compatible solute. International journal
Kazuya Koumoto, Hirofumi Ochiai, Naoki Sugimoto
Nucleic acids symposium series (2004) 52 ( 52 ) 257 - 8 2008
We designed and synthesized artificial compatible solutes which can not only decrease the melting temperature of DNA duplexes dependent of their chemical structures but also improve the amplification of highly stable genome DNA sequence.
DOI： 10.1093/nass/nrn130
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分子クラウディング環境下においてDNA二重鎖の安定性に及ぼす水和の影響
甲元一也, 落合洋文, 狩俣寿枝, 中野修一, 杉本直己
高分子学会予稿集(CD-ROM) 56 ( 2 Disk1 ) 2X15 2007.9
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Delivery of antisense oligonucleotides to nuclear telomere RNA by use of a complex between polysaccharide and polynucleotide
Jusaku Minari, Takanori Kubo, Hideki Ohba, Naohiko Shimada, Yoich Takeda, Ryouji Karinaga, Takahisa Anada, Kazuya Koumoto, Takeshi Kawazu, Takeshi Nagasaki, Seiji Shinkai, Kazuo Sakurai
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 80 ( 6 ) 1091 - 1098 2007.6
Publisher：CHEMICAL SOC JAPAN
Telomerase, which is highly activated in neoplastic cells, can be a target for antisense therapy, and for that purpose, antisense oligonucleotides (AS ODNs) have to be effectively delivered into cellular nucleus where the target telomerase is present. The present work shows a new strategy to deliver AS ODNs to nucleus by use of a novel complex made from a natural polysaccharide schizophyllan (SPG) and AS ODNs. Nuclear transport is strictly regulated by the nuclear pore size and the related proteins. If the molecular weight of SPG is decreased, the SPG/AS ODN complex should be easily transported, although the stability of the complex decreases with a decrease in the molecular weight. We optimized the molecular weight of SPG to be 25 K. Furthermore, we attached importin-beta (a nuclear transport protein) to the side chain of SPG by use of a streptavidin-biotin interaction. When this complex was added to Jurkat cells, the telomerase activity was more suppressed than the naked dose, indicating that the importin-P in the complex induced the nuclear transport of the complexed AS ODN and the AS ODN inhibited the telomerase. The present work shows a new methodology for nuclear anti-sense therapy that should be important in future anti-cancer therapies.
DOI： 10.1246/bcsj.80.1091
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Artificial G-wire switch with 2,2 '-bipyridine units responsive to divalent metal ions International journal
Daisuke Miyoshi, Hisae Karimata, Zhong-Ming Wang, Kazuya Koumoto, Naoki Sugimoto
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 129 ( 18 ) 5919 - 5925 2007.5
Publisher：AMER CHEMICAL SOC
Development of a guanine nanowire (G-wire) that is controllable and can be switched by external signals is important for the creation of molecular electronic technologies. Here, we constructed a G-wire in which the thymines of the main chain of d(G(4)T(4)G(4)) were replaced with 2,2'-bipyridine units, which have two aromatic rings that rotate arbitrarily upon coordination with metal ions. Circular dichroism of the DNA oligonucleotides with or without the 2,2'-bipyridine unit showed that divalent metal ions induce the bipyridine-containing oligonucleotide to switch from an antiparallel to a parallel G-quadruplex. Native polyacrylamide gel electrophoresis showed that the parallel-stranded G-quadruplex DNA had a high-order structure. Circular dichroism and native gel electrophoresis analyses suggested that adding Na(2)EDTA causes a reverse structural transition from a parallel-stranded high-order structure to an antiparallel G-quadruplex. Moreover, atomic force microscopy showed a long nanowire (similar to 200 nm) in the presence of Ni2+ but no significant image in the absence of Ni2+ or in the presence of both Ni2+ and Na(2)EDTA. These observations revealed that the parallel-stranded high-order structure is a G-wire containing numerous DNA oligonucleotide strands bound together via divalent metal ion-2,2'-bipyridine complexes. Finally, we found that alternating addition of Ni2+ and Na(2)EDTA can cycle the G-wire between the high-order and disorganized structures, with an average cycling efficiency of 0.95 (i.e., 5% loss per cycle). These results demonstrate that a DNA oligonucleotide incorporating the 2,2'-bipyridine unit acts as a G-wire switch that can be controlled by chemical input signals, namely, divalent metal ions.
DOI： 10.1021/ja068707u
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Conformational switch of a functional nanowire based on the DNA G-quadruplex. International journal
Hisae Karimata, Daisuke Miyoshi, Takeshi Fujimoto, Kazuya Koumoto, Zhong-Ming Wang, Naoki Sugimoto
Nucleic acids symposium series (2004) 51 ( 51 ) 251 - 2 2007
A G-wire composing of multiple G-rich sequences in parallel orientations via G-quartet formations is promising as a structurally well-defined nanowire. Here, in order to control the G-wire by the metal ion, we incorporated 2,2'-bipyridine unit, which has two aromatic rings rotating arbitrarily by coordination with metal ions, into the main chain of d(G4T4G4) instead of thymine (G1). Circular dichroism (CD) spectra showed that G1 formed an antiparallel G-quadruplex. Interestingly, Ni(2+) induces G1 to switch from an antiparallel G-quadruplex to a parallel. On the other hand, the parallel G-quadruplex reversed the structural transition to an antiparallel G-quadruplex by the addition of Na2EDTA. Moreover, the study of the atomic force microscopy (AFM) showed that G1 formed a long nanowire ( approximately 200 nm) in the presence of Ni(2+), whereas no significant image was observed in the absence of Ni(2+) or in the presence of both Ni(2+) and Na2EDTA. From these results, it can be concluded that Ni(2+) induces a structural transition of G1 from an antiparallel G-quadruplex to a G-wire and that metal ion chelator induces the reverse structural transition from the G-wire to the antiparallel G-quadruplex. The G-wire responsive to metal ions would be useful for development of functional nanomaterials.
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CpG DNA/zymosan complex to enhance cytokine secretion owing to the cocktail effect
T Anada, N Okada, J Minari, R Karinaga, M Mizu, K Koumoto, S Shinkai, K Sakurai
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 16 ( 5 ) 1301 - 1304 2006.3
Publisher：PERGAMON-ELSEVIER SCIENCE LTD
Zymosan, classified among beta-(1-->3)-D-glucans, is produced from the cell wall of yeast and well known to induce proinflammatory cytokines when ingested by immune cells. We found that zymosan forms a complex with immunostimulatory CpG DNA, where both zymosan and CpG DNA can induce cytokine secretion according to the different mechanisms (i.e., recognized by different receptors). The complex activated macrophages and induced cytokine secretion, more efficiently than separate administration of zymosan or CpG DNA. Microscopic observation showed that this increment of the cytokine secretion can be explained by the fact that zymosan and zymosan/CpG DNA complex are up-taken more than naked CpG DNA. Additionally, existence of two different immunostimulants in the same cells may enhance the immunoresponse. This report presents a new strategy to construct a delivering vehicle for CpG DNA and to enhance its activity with the 'cocktail effect' of the two immunostimulants. (C) 2005 Elsevier Ltd. All rights reserved.
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Galactose-PEG dual conjugation of beta-(1 -> 3)-D-glucan schizophyllan for antisense oligonucleotides delivery to enhance the cellular uptake
R Karinaga, T Anada, J Minari, M Mizu, K Koumoto, J Fukuda, K Nakazawa, T Hasegawa, M Numata, S Shinkai, K Sakurai
BIOMATERIALS 27 ( 8 ) 1626 - 1635 2006.3
Publisher：ELSEVIER SCI LTD
Antisense oligonucleotides (AS ODNs) are applied to silence a particular gene, and this approach is one of the potential gene therapies. However, naked oligonucleotides are easy to be degraded or absorbed in biological condition. Therefore, we need a carrier to deliver AS ODNs. This paper presents galactose moieties that were conjugated to the side chain of SPG to enhance cellular ingestion through endocytosis mediated by asialoglycoprotein receptor specifically located on parenchymal liver cells. We introduced galactose with two types of chemical bonds; amide and amine, and the amine connection showed lower ingestion and more toxicity than the amide one. Since PEG was known to induce endocytosis escape, we combined PEG and galactose aiming to provide both cellular up-take and subsequent endocytosis escape. We designed lactose or galactose moieties to attach to the end of the PEG chain that connects to the SPG side chain. When the PEG had the molecular weight of 5000-6000, the antisense effect reached the maximum. We believe that this new type of galactose and PEG dual conjugation broaden the horizon in antisense delivery. (c) 2005 Elsevier Ltd. All rights reserved.
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Linear double-stranded DNA that mimics an infective tail of virus genome to enhance transfection
T Anada, R Karinaga, K Koumoto, M Mizu, T Nagasaki, Y Kato, K Taira, S Shinkai, K Sakurai
JOURNAL OF CONTROLLED RELEASE 108 ( 2-3 ) 529 - 539 2005.11
Publisher：ELSEVIER SCIENCE BV
Our previous work showed that a natural beta-(1 -> 3)-D-glucan schizophyllan (SPG) can form a stable complex with single-stranded oligonucleotides (ssODNs). When protein transduction peptides were attached to SPG and this modified SPG was complexed with ssODNs, the resultant complex could induce cellular transfection of the bound ODNs, without producing serious cytotoxicity. However, no technique was available to transfect double-stranded DNAs (dsDNA) or plasmid DNA using SPG. This paper presents a new approach to transfect dsDNA, showing preparation and transfection efficiency for a minimal-size gene having a loop-shaped poly(dA)(80) on both ends. This poly(dA) loops of dsDNA can form a complex with SPG. An siRNA-coding dsDNA with the poly(dA) loop was complexed with Tat-attached SPG to silence luciferase expression. When LTR-Luc-HeLa cells that can express luciferase under the control of the LTR promoter were exposed to this complex, the expression of luciferase was suppressed (i.e., RNAi effect was enhanced). Cytotoxicity studies showed that the Tat-SPG complex induced much less cell death compared to polyethylenimine, indicating that the proposed method caused less harm than the conventional method. The Tat-SPG/poly(dA) looped dsDNA complex had a structure similar to the viral genome in that the dsDNA ends were able to induce transfection and protection. The present work identifies the SPG and poly(dA) looped minimum-sized gene combination as a candidate for a non-toxic gene delivery system. (c) 2005 Elsevier B.V. All rights reserved.