2019年度

卒業生

田辺　和也　（Kazuya Tanabe, 2016-2018）

卒業論文：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

S. Nakano, H. Yamashita, K. Tanabe, and N. Sugimoto
Bulky cations greatly increase the turnover of a native hammerhead ribozyme.
RSC Advances, 9, 35820-35824 (2019)

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

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

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

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

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

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

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

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

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

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

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

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

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

共同研究者

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)