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Professor |
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Research Field |
thermodynamic stability, reaction rate, molecular interaction, DNA, RNA, protein, peptide, nucleic acid structure,nucleic acid interaction, molecular crowding |
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Graduating School 【 display / non-display 】
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Konan University Faculty of Science Graduated
- 1994.3
Graduate School 【 display / non-display 】
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Konan University Graduate School, Division of National Science and Technology Doctor's Course Completed
- 1999.3
Studying abroad experiences 【 display / non-display 】
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1999.4-2001.3
Penn State University, USA Postdoctoral fellow
Campus Career 【 display / non-display 】
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フロンティアサイエンス学部 生命化学科 教授
2013.4
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フロンティアサイエンス学部 生命化学科 准教授
2009.4 - 2013.3
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KONAN UNIVERSITY Frontier Institute for Biomolecular Engineering Research Lecturer
2004.4 - 2009.3
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ハイテク・リサーチ・センター 博士研究員
2001.4 - 2004.3
External Career 【 display / non-display 】
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米国ペンシルバニア州立大学
1999.4 - 2001.3
Country：United States
Research Career 【 display / non-display 】
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Mechanisms for functionalization of RNA ribozymes
(not selected)
Project Year： 2006.4 -
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Thermodynamic and kinetic analysis of DNA and RNA interactions under molecular crowding conditions
(not selected)
Project Year： 2004.4 -
Papers 【 display / non-display 】
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Inhibition of RNA phosphodiester backbone cleavage in the presence of organic cations of different sizes Invited Reviewed International journal
S. Yoshioka, A. Doi, and S. Nakano
ChemBioChem 25 ( 13 ) e202400276 2024.5
Joint Work
Authorship：Last author, Corresponding author Publisher：Wiley
Living cells contain various types of organic cations that may interact with nucleic acids. In order to understand the nucleic acid–binding properties of organic cations of different sizes, we investigated the ability of simple organic cations to inhibit the RNA phosphodiester bond cleavage promoted by Mg2+, Pb2+, and RNA-cleaving serum proteins. Kinetic analysis using chimeric DNA–RNA oligonucleotides showed that the cleavage at ribonucleotide sites was inhibited in the presence of monovalent cations comprising alkyl chains or benzene rings. The comparison of the cleavage rates in the presence of quaternary ammonium and phosphonium ions indicated that the steric hindrance effect of organic cations on their binding to the RNA backbone is significant when the cation size is larger than the phosphate–phosphate distance of a single-stranded nucleic acid. The cleavage inhibition was also observed for ribonucleotides located in long loops but not in short loops of oligonucleotide structures, indicating less efficient binding of bulky cations to structurally constrained regions. These results reveal the unique nucleic acid–binding properties of bulky cations distinct from those of metal ions.
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Basic protein- and peptide-induced stabilization of long-loop DNA G-quadruplexes Reviewed International journal
K. Tanabe, K. Miyazaki, H. Umeno, M. Takemoto, and S. Nakano
Biochimie 219 110 - 117 2024.4
Joint Work
Authorship：Last author, Corresponding author Publisher：Elsevier
The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.
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Evaluation of thermal stability of DNA oligonucleotide structures embedded in hydrogels Invited Reviewed International journal
D. Yamaguchi, M. Yoshida, S. Nakano
DNA 2 ( 4 ) 302 - 313 2022.12
Joint Work
Authorship：Last author, Corresponding author Publisher：MDPI
Understanding the self-assembly and hybridization properties of DNA oligonucleotides in confined spaces can help to improve their applications in biotechnology and nanotechnology. This study investigates the effects of spatial confinement in the pores of hydrogels on the thermal stability of DNA oligonucleotide structures. The preparation of oligonucleotides embedded in agarose gels was simple, whereas the preparation of oligonucleotides embedded in polyacrylamide gels was required to remove unpolymerized monomers. In the latter case, a method for rehydrating a washed dry gel with a buffer solution containing oligonucleotides was developed. Fluorescence measurements of oligonucleotides bearing fluorescent probes revealed no significant influence of the internal environment of the gel pores on the stability of DNA duplex, hairpin, and G-quadruplex structures. Moreover, the effects of poly(ethylene glycol) on the stability of DNA structures in the gels were similar to those in solutions. It is likely that the oligonucleotides are not strongly constrained in the gels and may be preferentially located in a water-rich environment in the gel matrix. The gel preparation was also applied to the assessment of the stability of DNA structures under the conditions of a reduced number of water molecules. The studies using hydrogels provide insights into the ability of self-assembly and hybridization of oligonucleotides in confined environments and under low-water-content conditions.
DOI： 10.3390/dna2040021
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Evaluation of weak interactions of proteins and organic cations with DNA duplex structures Reviewed International journal
R. Morimoto, M. Horita, D. Yamaguchi, H. Nakai, and S. Nakano
Biophys. J. 121 ( 15 ) 2873 - 2881 2022.8
Joint Work
Authorship：Last author, Corresponding author Publisher：Cell Press
Molecular interactions and reactions in living cells occur with high background concentrations of organic compounds including proteins. Uncharged water-soluble polymers are commonly used cosolutes in studies on molecular crowding, and most studies argue about the effects of intracellular crowding based on results obtained using polymer cosolutes. Further investigations using protein crowders and organic cations are important in understanding the effects of cellular environments on nucleic acids with negatively charged surfaces. We assessed the effects of using model globular proteins, serum proteins, histone proteins, structurally flexible polypeptides, di- and polyamines, and uncharged polymers. Thermal stability analysis of DNA oligonucleotide structures revealed that unlike conventional polymer cosolutes, basic globular proteins (lysozyme and cytochrome c) at high concentrations stabilized long internal and bulge loop structures but not fully matched duplexes. The selective stabilization of long loop structures suggests preferential binding to unpaired nucleotides in loops through weak electrostatic interactions. Furthermore, the ability of the proteins to stabilize the loop structures was enhanced under macromolecular crowding conditions. Remarkably, the effects of basic proteins on the stability of fully matched duplexes were dissimilar to those of basic amino-acid-rich polypeptides and polyamines. This study provides new insights into the interaction of nucleic acid structures with organic cations.
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Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations. Reviewed International journal
Shu-Ichi Nakano, Hirofumi Yamashita, Naoki Sugimoto
ChemBioChem 22 ( 17 ) 2721 - 2728 2021.7
Joint Work
Authorship：Lead author, Corresponding author
Catalytic turnover is important for the application of ribozymes to biotechnology. However, the turnover is often impaired because of the intrinsic high stability of base pairs with cleaved RNA products. Here, organic cations were used as additives to improve the catalytic performance of hammerhead ribozyme constructs that exhibit different kinetic behaviors. Kinetic analysis of substrate cleavage demonstrated that bulky cations, specifically tetra-substituted ammonium ions containing pentyl groups or a benzyl group, have the ability to greatly increase the turnover rate of the ribozymes. Thermal stability analysis of RNA structures revealed that the bulky cations promote the dissociation of cleaved products and refolding of incorrectly folded structures with small disruption of the catalytic structure. The use of bulky cations is a convenient method for enhancing the catalytic activity of hammerhead ribozymes, and the approach may be useful for advancing ribozyme technologies.
Books and Other Publications 【 display / non-display 】
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バイオチップ実用化ハンドブック
杉本直己・中野修一（ Role： Joint author , 第一節 DNAチップの基礎 １ ハイブリダイゼーション）
エヌティーエス 2010.4 （ ISBN:978-4-86043-270-6 ）
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Bottom-up Nanofabrication: Supramolecules, Self-Assemblies, and Organized Films
S. Nakano and N. Sugimoto（ Role： Joint author , Energy of nucleic acid self-assemblies: From sequence to function through structure）
American Scientific Publishers 2009.1 （ ISBN:1-58883-079-9 ）
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11. デザイナブル核酸修飾核酸（共著）
中野 修一
先端生物医学研究・医療のため遺伝子導入テクノロジー「ウイルスを用いない遺伝子導入法の材料、技術、方法論の新たな展開」遺伝子医学MOOK5（メディカルドゥ） 2006
Review Papers (Misc) 【 display / non-display 】
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核酸医薬の効果に影響する細胞内物質のin vitro評価 Invited
中野修一
Precision Medicine 5 ( 14 ) 64 - 67 2022.11
Authorship：Lead author, Last author, Corresponding author Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media) Publisher：北隆館
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核酸医薬の配列設計のためのin vitro評価：細胞内物質との弱い相互作用の影響 Invited
中野修一
Bio Clinica 12 ( 36 ) 1426 - 1428 2021.12
Authorship：Lead author, Corresponding author Publishing type：Article, review, commentary, editorial, etc. (scientific journal)
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How does intracellular environment affect oligonucleotides used for nucleic acid pharmaceuticals? Invited
Shu-ichi Nakano
52 ( 5 ) 42 - 44 2020.5
Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)
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分子夾雑環境が制御する核酸分子の機能
中野修一、杉本直己
化学と工業 72 ( 5 ) 401 - 403 2019.5
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (international conference proceedings) Publisher：日本化学会
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化学ツールとしての分子クラウディング
中野修一・杉本直己
化学フロンティア22 生命現象を理解する分子ツール最前線〜イメージングから生体機能解析まで〜 145 - 153 2010.9
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media) Publisher：化学同人
Presentations 【 display / non-display 】
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Structural transition of DNA induced by organic cations
2023.12
Event date： 2023.12
Country：Japan
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DNAの構造遷移を促進する物質の探索
梅野光莉、橋本留奈、中野修一
第45回分子生物学会年会 (幕張メッセ、千葉) 2022.11 分子生物学会
Event date： 2022.11 - 2022.12
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What effects does intracellular environment have on nucleic acid structures? Invited
Shu-ichi Nakano
Pacifichem 2021 (Hawaii (on-line congress)) 2021.12 Pacifichem 2020 Administration
Event date： 2021.12
Country：United States
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細胞内分子環境は不安定なDNA四重鎖の形成に有利に働く
梅野光莉、宮嵜光一、林花莉、中野修一
第44回分子生物学会年会 2021.12 日本分子生物学会
Event date： 2021.12
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塩基性タンパク質を含む分子クラウディング環境におけるDNA四重鎖構造の安定化
宮嵜光一、田辺一也、林花梨、武本満理奈、橋本留奈、梅野光莉、中野修一
第43回分子生物学会年会 2020.12 日本分子生物学会
Event date： 2020.12
Other Research Activities 【 display / non-display 】
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擬塩基対ヌクレオシドを用いてプリンとピリミジン塩基によるスタッキングの違いを解明する
2006.11
第8回生命化学会シンポジウム、16（2006）
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The effect of the structure of cosolutes on the DNA duplex formation
2006.11
第33回核酸化学シンポジウム(2006).
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DNAポリメラーゼによる擬塩基対ヌクレオシドの認識
2006.11
第33回核酸化学シンポジウム(2006).
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ハンマーヘッドリボザイムの切断活性に及ぼす共存溶質の役割
2006.11
第33回核酸化学シンポジウム(2006).
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金基材に固定化したDNA二重鎖の安定性制御とセンシング特性
2006.11
バイオ関連化学合同シンポジウム（第21回生体機能関連化学シンポジウム、第9回バイオテクノロジー部会、第9回生命化学研究会）（2006）
Grant-in-Aid for Scientific Research 【 display / non-display 】
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細胞内のクラウディング環境で核酸の非標準構造形成を可能にする物理化学的要因の解明
2023.4 - 2026.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(C)
Authorship：Principal investigator
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Studies on the functional role of unpaired regions of nucleic acid structures and their effects of molecular crowding
2018.4 - 2023.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(C)
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イオン液体化合物を利用する核酸テクノロジーの創製
2015.10 - 2019.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(C)
ある種のイオン液体は核酸に選択的に結合するという、従来の水溶媒や有機溶媒では見られない希有な性質をもつ。この性質をうまく利用できれば機能性核酸の開発が進み、その用途が大きく広がることが期待される。本研究は、イオン液体の結合特性を積極的に利用する新規核酸テクノロジーを創製することを目的としている。具体的には、核酸構造安定性の制御に効果的なイオン液体化合物を探索し、DNA 鎖の組換え反応の促進とRNA 酵素（リボザイム）の触媒活性の向上を試みる。この取り組みにより、イオン液体を用いる核酸テクノロジーの有用性を明らかにし、基礎科学から産業応用まで幅広い分野で使うことができる簡便な手法を開発する
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細胞で行われる核酸反応を解明するための新規モデル実験システムの構築と利用
2012.4 - 2015.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(C)
細胞内部の分子を取り巻く環境は、通常のインビトロ実験で用いられる水溶液中とは大きく異なっている。本研究は、化学的立場からの研究アプローチとして、細胞内部の特殊な分子環境が核酸の構造と機能に与える影響を解明するための新規評価システムを構築する。具体的には、大量のタンパク質が共存する環境と、細胞骨格フィラメントがつくり出す繊維状構造体の影響を定量的に評価するためのモデル実験系を構築する。そして、核酸構造の形成に不可欠なカチオンとの結合が、分子環境によってどのような影響を受けるのかを明らかにする。新規評価システムを構築することで、インビトロ実験と細胞実験の橋渡しになるデータと新しい実験系を提供し、従来の分子クラウディング研究を大きく飛躍させることを目指す。
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細胞内分子環境で機能する新規核酸マテリアル創製
2010.4
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(A)
分担研究
細胞内部で使用できる機能性核酸や、様々な環境ではたらく核酸バイオセンサーを開発するには、分子環境の違いが及ぼす核酸機能への影響を分子レベルで解明し、分子環境効果を化学的に解明しておく必要がある。本研究は、核酸の相互作用に対する分子クラウディング効果をナノバイオテクノロジー開発に利用するために、機能性DNAおよびRNAに対する分子クラウディングの化学的側面を明らかにする。分子クラウディング実験系を用いて、分子環境の違いがもたらす核酸構造と相互作用エネルギーへの影響を定量的に解明することで、均一希薄水溶液を使って得られるin vitroデータと、細胞内反応やバイオセンサー表面で行われる相互作用や化学反応の橋渡しとなる実験データを得る。さらに、この定量的な実験データに基づいて、分子クラウディングのような特殊な分子環境を利用した機能性核酸の開発とその機能解析を行い、新規ナノバイオテクノロジーの開発を試みる。
Other External funds procured 【 display / non-display 】
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脂肪酸結合タンパク質FABPのリガンド選択性の解明
2015.4 - 2016.3
自治体 ひょうご科学技術協会学術研究助成金
Joint and Contract research activities (Public) 【 display / non-display 】
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脂肪酸結合タンパク質を使った分子クラウディング研究
Joint Research on Campus
2010.4 - 2019.12
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効率的なPCR診断のためのプライマーDNAの設計
Domestic Joint Research
2007.4 - 2009.3
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人工核酸を使った核酸構造の解明
Joint Research on Campus
2006.4 - 2008.3
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ペプチドを使った神経幹細胞の機能制御
Joint Research on Campus
2005.4 - 2010.3
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人工核酸の物性評価とその利用
Domestic Joint Research
2004.4 - 2016.12
Preferred joint research theme 【 display / non-display 】
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生体分子の相互作用解析 産学連携、民間を含む他機関等との共同研究等を希望する。（受託研究）
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生命分子(核酸・タンパク質等)の物性解析 産学連携、民間を含む他機関等との共同研究等を希望する。（技術相談）
Committee Memberships 【 display / non-display 】
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2016.9 日本核酸化学会 世話人
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2009.10 生命機能研究会 世話役
Social Activities 【 display / non-display 】
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模擬講義
2009.4
依頼があった高校に出向いて、模擬講義を行っている。
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一般公開
2004.4
神戸医療産業都市の一般公開における実験講座の開催。
Qualification acquired 【 display / non-display 】
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Hazardous Material Handler (first kind)