学生 | バイオ分子機能研究室

学生メンバー（2023年度）

M1	花畑　伊吹（Ibuki Hanabata）
B4	岡本　大輝（Daiki Okamoto）
B4	岩崎　愛美（Aimi Iwasaki）
B4	土井　明日香（Asuka Doi）
B4	山田　未来（Mirai Yamada）
B3	芦田　昂大（Koudai Ashida）
B3	犬塚　晴彦（Haruhiko Inuzuka）
B3	西山　和樹（Kazuki Nishiyama）
B2	高木　良磨（Ryouma Takagi）

卒業生

北林　歩（Ayumi Kitabayashi, 2022）
卒業論文：ポリアミン添加時のmini i-motif DNAとi-motif DNAの熱安定性比較

植田　尚人　（Naoto Ueda, 2021）
卒業論文：i-モチーフDNAの熱安定性を低下させるポリアミンの作用メカニズムの検討

梅野　光莉　（Hikari Umeno, 2021）
卒業論文：サイズの大きいカチオン性分子によって引き起こされる自己相補的DNAの構造遷移

　公表論文：Basic protein- and peptide-induced stabilization of long-loop DNA G-quadruplexes
　Biochimie, 219, 110-117 (2024)

吉岡　扇里　（Senri Yoshioka, 2020）
卒業論文：一本鎖DNAに対する嵩高いカチオン性分子の結合選択性

秋山　智美　（Tomomi Akiyama, 2020）
卒業論文：脳で発現する脂肪酸結合タンパク質と脂肪酸の結合性評価

武本　満理奈　（Marina Takemoto, 2020）
卒業論文：RNAループ構造の熱安定性に及ぼす塩基性タンパク質の影響

　公表論文：Basic protein- and peptide-induced stabilization of long-loop DNA G-quadruplexes
　Biochimie, 219, 110-117 (2024)

林　花莉　（Karin Hayashi, 2020）
卒業論文：ペプチドによる四重鎖DNAの安定性の変化

宮嵜　光一　（Koichi Miyazaki, 2020）
卒業論文：分子クラウディング環境下での塩基性タンパク質による四重鎖DNAの安定化

　公表論文：Basic protein- and peptide-induced stabilization of long-loop DNA G-quadruplexes
　Biochimie, 219, 110-117 (2024)

梶谷　絵梨　（Eri Kajitani, 2019）
卒業論文：脂肪酸結合タンパク質による核内受容体リガンドの認識

橋本　留奈　（Runa Hashimoto, 2019）
卒業論文：カチオンによって誘起されるDNA四重鎖構造のコンフォメーション変化

田辺　和也　（Kazuya Tanabe, 2016-2018）
修士論文：DNA四重鎖の非塩基対部位が嵩高いカチオン性分子から受ける影響

　公表論文：Bulky cations greatly increase the turnover of a native hammerhead ribozyme.
　RSC Advances, 9, 35820-35824 (2019)

　公表論文：Basic protein- and peptide-induced stabilization of long-loop DNA G-quadruplexes
　Biochimie, 219, 110-117 (2024)

堀田　政夫　（Masao Horita, 2017-2018)
卒業論文：生体内模倣環境が促進させる塩基性タンパク質とDNA二重鎖構造の相互作用

　公表論文：Evaluation of weak interactions of proteins and organic cations with DNA duplex structures.
　Biophys. J., 121, 2873-2881 (2022)

鹿籠六　真弘　（Sadahiro Kagoroku, 2018）
卒業論文：カチオンを用いたDNA構造遷移の誘導

森田　紗奈（Suzuna Morita, 2018）
卒業論文：ﾎﾟﾘｱﾐﾝ存在下におけるDNA四重鎖構造の熱安定性評価

森本　隆太（Ryuta Morimoto, 2016）
卒業論文：タンパク質を含む分子クラウディング環境が及ぼすDNA熱安定性への影響

　公表論文：Evaluation of weak interactions of proteins and organic cations with DNA duplex structures.
　Biophys. J., 121, 2873-2881 (2022)

小林　未来（Miku Kobayashi, 2015）
卒業論文：クラウディング環境界下におけるリガーゼリボザイムの反応促進

　公表論文：Catalytic activities of ribozymes and DNAzymes in water and mized aqueous media.
　Catalysis, 7, 355-348 (2017)

鮎沢　隼哉（Toshiya Ayusawa, 2015）
卒業論文：カチオンサイズが及ぼす核酸の構造安定性への影響

　公表論文：Stabilization of DNA loop structures by large cations
　J. Phys. Chem. B, 123, 7687-7694 (2019)

岩木　研太（Kenta Iwaki, 2015）
卒業論文：四重鎖DNAの構造形成に対する溶媒の影響

中井　大樹（Hiroki Nakai, 2015）
卒業論文：タンパク質を用いた新規クラウディング実験によるDNAの安定性評価

　公表論文：Evaluation of weak interactions of proteins and organic cations with DNA duplex structures.
　Biophys. J., 121, 2873-2881 (2022)

谷野　裕一（Yuichi Tanino, 2014）
卒業論文：脂肪酸結合タンパク質のリガンド探索のための新規アプローチ

　公表論文：Stabilization of DNA loop structures by large cations
　J. Phys. Chem. B, 123, 7687-7694 (2019)

　公表論文：Thermal stability of RNA structures with bulky cations in mixed aqueous solutions.
　Biophys. J., 111, 1350-1360 (2016)

山下　博史（Hiroshi Yamashita, 2014）
卒業論文：ハンマーヘッドリボザイムのターンオーバー促進法の開発

　公表論文：Enhancement of the catalytic activity of hammerhead ribozymes by organic cations
　ChemBioChem, 22, 2721-2728 (2021)

　公表論文：Bulky cations greatly increase the turnover of a native hammerhead ribozyme
　RSC Advances, 9, 35820-35824 (2019)

　公表論文：Effects of cosolvents on the folding and catalytic activities of the hammerhead ribozyme.
　ChemBioChem, 16, 1803–1810 (2015)

吉田　将敏（Masatoshi Yoshida, 2013）
卒業論文：ゲル繊維の閉じ込め効果によるDNA分子の構造安定性の評価

　公表論文：Evaluation of thermal stability of DNA oligonucleotide structures embedded in hydrogels.
　DNA, 2, 302-313 (2022)

　公表論文：Preparation of hydrogels for the study of the effects of spatial confinement on DNA.
　Trans. Mat. Res. Soc. Japan, 39, 435-438 (2014)

田中　駿平（Shunpei Tanaka, 2013）
卒業論文：リボザイムのターンオーバーの制御

山口　大輔（Daisuke Yamaguchi, 2011-2012）
修士論文：新規モデル実験系を用いた分子クラウディング環境における核酸構造の安定性評価

　公表論文：Evaluation of thermal stability of DNA oligonucleotide structures embedded in hydrogels.
　DNA, 2, 302-313 (2022)

　公表論文：Evaluation of weak interactions of proteins and organic cations with DNA duplex structures.
　Biophys. J., 121, 2873-2881 (2022)

　公表論文：Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels.
　Mol. Biol. Rep., 45, 403-411 (2018)

　公表論文：Preparation of hydrogels for the study of the effects of spatial confinement on DNA.
　Trans. Mat. Res. Soc. Japan, 39, 435-438 (2014)

　公表論文：Hydration changes upon DNA folding studied by osmotic stress experiments.
　Biophys. J., 102, 2808-2817 (2012)

　公表論文：Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative.
　Org. Biomol. Chem., 10, 9664-9670 (2012)

三軒　隼人（Hayato Sangen, 2012）
卒業論文：分子クラウディング環境によるDNA四重鎖とカチオンの結合性変化

共同研究者

渡部　剛明（Watabe Takaaki, 2011）
卒業論文：鉛イオン依存性リボザイムに対する分子環境効果の検討

Modulation of the ribozyme and deoxyribozyme activities using tetraalkylammonium ions.ChemPhysChem, 18, 3614-3619 (2017)

平山　英伸（Hidenobu Hirayama, 2008-2010）
修士論文：ヘアピンRNAの二量化形成反応に及ぼす溶液環境の影響

Thermal stability of RNA structures with bulky cations in mixed aqueous solutions.
Biophys. J., 111, 1350-1360 (2016)

Dimerization of nucleic acid hairpins in the conditions caused by neutral cosolutes.
J. Phys. Chem. B, 116, 7406-7415 (2012)

北川　雄一（Yuuichi Kitagawa, 2007-2009）
修士論文：機能性核酸の酵素活性に及ぼす溶液環境の影響

Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg2+-unsaturated solutions.
J. Biol. Inorg. Chem.,　20，1049-1058 (2015)

Effects of cosolvents on the folding and catalytic activities of the hammerhead ribozyme.
ChemBioChem, 16, 1803–1810 (2015)

Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds, FEBS Open Bio, 4, 643 – 650 (2014)
Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes.
J. Am. Chem. Soc., 131, 16881–16888 (2009)

岡　裕人（Hirohito Oka, 2005-2007)
修士論文：擬塩基対ヌクレオシドのスタッキング相互作用と塩基対形成能力

Use of a ureido-substituted deoxycytidine module for DNA assemblies.
Nucleosides, Nucleotides and Nucleic Acids, 35, 370-378 (2016)

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules.
Nucleic Acids Res., 41, 8581–8590 (2013)

Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative, Org. Biomol. Chem., 10, 9664-9670 (2012)
Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides.
Mol. BioSyst., 6, 2023-2029 (2010)

Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides.
Biochemistry, 48, 11304-11311 (2009)

Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media.
Mol. BioSyst., 4, 579-588 (2008)

桐畑　俊正（Toshimasa Kirihata, 2003-2005）
修士論文：カチオン性分子に応答して構造を変化させる核酸スイッチの創製

Capture of cationic ligands bound diffusely to base pairs during the DNA refolding.
Chem. Commun., 700-702 (2008)

Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media.
Mol. BioSyst., 4, 579-588 (2008)

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides.
Nucleic Acids Res., 35, 486-494 (2007)

魚谷　有希（Yuuki Uotani, 2002-2004)
修士論文：擬塩基対を含むDNAの構造と熱力学的安定性

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules.
Nucleic Acids Res., 41, 8581–8590 (2013)

Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides.
Mol. BioSyst., 6, 2023-2029 (2010)

Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides.
Biochemistry, 48, 11304-11311 (2009)

DNA base flipping by a base pair-mimic nucleoside.
Nucleic Acids Res., 33, 7111-7119 (2005)

Site-selective RNA cleavage by DNA bearing a base pair-mimic nucleoside.
J. Am. Chem. Soc., 127, 518-519 (2005)

Large stabilization of a DNA duplex by the deoxyadenosine derivatives tethering an aromatic hydrocarbon group.
J. Am. Chem. Soc., 125, 8086-8087 (2003)

狩俣　寿枝（Hisae Karimata, 2004-2009)
Quantitative analyses of nucleic acid stability under the molecular crowding condition induced by cosolute.
Curr. Protoc. Nucleic Acid Chem., Chap. 53, Unit 7.19 (2013)
Hydration changes upon DNA folding studied by osmotic stress experiments, Biophys. J., 102, 2808-2817 (2012)

Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes.
J. Am. Chem. Soc., 131, 16881–16888 (2009)

Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media.
Mol. BioSyst., 4, 579-588 (2008)

Effects of polyethylene glycol on a DNA duplex stability differed by the NaCl concentration.
Bull. Chem. Soc. Jpn., 80, 1987-1994 (2007)

Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides.
Nucleic Acids Res., 35, 486-494 (2007)

The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability.
J. Am. Chem. Soc., 126, 14330-14331 (2004)

神崎　貴之（Takayuki Kanzaki, 2001-2003)
修士論文：Mut Sタンパク質を標的とした新規DNAチップの開発

Measurement of the binding of a large protein usitg a substrate density-controlled DNA chip.
Anal. Chem., 83, 6368-6372 (2011)

Influences of ribonucleotide on a duplex conformation and its thermal stability: Study with the chimeric RNA-DNA strands.
J. Am. Chem. Soc., 126, 1088-1095 (2004)