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Position |
Associate Professor |
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Research Field |
Nanotechnology/Materials / Bio chemistry |
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External Link |
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Graduating School 【 display / non-display 】
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Tokyo Institute of Technology Faculty of Life Science and Engineering Graduated
- 2002.3
Graduate School 【 display / non-display 】
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Tokyo Institute of Technology Graduate School, Division of Life Science and Engineering Doctor's Course Completed
- 2007.3
Studying abroad experiences 【 display / non-display 】
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2005.1-2005.4
メルボルン大学 客員研究員
Campus Career 【 display / non-display 】
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KONAN UNIVERSITY Frontier of Institute for Biomolecular Engineering Research in Science and Technology Department of Nanobiochemistry Associate Professor
2020.4
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KONAN UNIVERSITY Frontier of Institute for Biomolecular Engineering Research in Science and Technology Department of Nanobiochemistry Lecturer
2012.6 - 2020.3
External Career 【 display / non-display 】
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東京工業大学 大学院生命理工学研究科
2012.4 - 2012.5
Country：Japan
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東京工業大学 大学院生命理工学研究科
2007.10 - 2012.3
Country：Japan
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東京工業大学
2007.4 - 2007.9
Country：Japan
Papers 【 display / non-display 】
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Development of a pseudocellular system to quantify specific interactions determining the g-quadruplex function in cells
Hisae Tateishi-Karimata, Keiko Kawauchi, Shuntaro Takahashi, Naoki Sugimoto
Journal of the american chemical society 2024.3
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In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics. International journal
Dipanwita Banerjee, Hisae Tateishi-Karimata, Maria Toplishek, Tatsuya Ohyama, Saptarshi Ghosh, Shuntaro Takahashi, Marko Trajkovski, Janez Plavec, Naoki Sugimoto
Journal of the American Chemical Society 145 ( 43 ) 23503 - 23518 2023.11
In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear. Therefore, the mechanistic details of the effect of such molecular crowding were investigated at the molecular level by using thermodynamic and nuclear magnetic resonance analyses, revealing structure-dependent destabilization of the duplexes under crowded conditions. The transition from B- to A-like hybrid duplexes due to a change in conformation of the DNA strand guided by purine-pyrimidine asymmetry significantly increased the hydration number, which resulted in greater destabilization by the addition of cosolutes. By quantifying the individual contributions of environmental factors and the bulk structure of the duplex, we developed a set of parameters that predict the stability of hybrid duplexes with conformational dissimilarities under diverse crowding conditions. A comparison of the effects of environmental conditions in living cells and in vitro crowded solutions on hybrid duplex formation using the Förster resonance energy transfer technique established the applicability of our parameters to living cells. Moreover, our derived parameters can be used to estimate the efficiency of transcriptional inhibition, genome editing, and silencing techniques in cells. This supports the usefulness of our parameters for the visualization of cellular mechanisms of gene expression and the development of nucleic acid-based therapeutics targeting different cells.
DOI： 10.1021/jacs.3c06706
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Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet. Reviewed International journal
Sinjan Das, Shuntaro Takahashi, Tatsuya Ohyama, Sudipta Bhowmik, Naoki Sugimoto
Scientific reports 13 ( 1 ) 14338 - 14338 2023.9
Ligands that recognise specific i-motif DNAs are helpful in cancer diagnostics and therapeutics, as i-motif formation can cause cancer. Although the loop regions of i-motifs are promising targets for ligands, the interaction between a ligand and the loop regions based on sequence information remains unexplored. Herein, we investigated the loop regions of various i-motif DNAs to determine whether these regions specifically interact with fluorescent ligands. Crystal violet (CV), a triphenylmethane dye, exhibited strong fluorescence with the i-motif derived from the promoter region of the human BCL2 gene in a sequence- and structure-specific manner. Our systematic sequence analysis indicated that CV was bound to the site formed by the first and third loops through inter-loop interactions between the guanine bases present in these loops. As the structural stability of the BCL2 i-motif was unaffected by CV, the local stabilisation of the loops by CV could inhibit the interaction of transcription factors with these loops, repressing the BCL2 expression of MCF-7 cells. Our finding suggests that the loops of the i-motif can act as a novel platform for the specific binding of small molecules; thus, they could be utilised for the theranostics of diseases associated with i-motif DNAs.
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Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions. Reviewed International journal
Saptarshi Ghosh, Shuntaro Takahashi, Dipanwita Banerjee, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic acids research 51 ( 9 ) 4101 - 4111 2023.5
RNA performs various spatiotemporal functions in living cells. As the solution environments significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in diverse crowded conditions is required to understand and modulate gene expression in heterogeneously crowded intracellular conditions. Herein, we determined the nearest-neighbor (NN) parameters for RNA duplex formation when subjected to crowding conditions with an ionic concentration relevant to that found in cells. Determination of the individual contributions of excluded volume effect and water activity to each of the NN parameters in crowded environments enabled prediction of the thermodynamic parameters and their melting temperatures for plenty of tested RNA duplex formation in vitro and in cell with significant accuracy. The parameters reported herein will help predicting RNA duplex stability in different crowded environments, which will lead to an improved understanding of the stability-function relationship for RNAs in various cellular organelles with different molecular environments.
DOI： 10.1093/nar/gkad020
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Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase. Reviewed International journal
Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Chemical communications (Cambridge, England) 59 ( 7 ) 872 - 875 2023.1
Replication of RNA viruses is catalysed by virus-specific polymerases, which can be targets of therapeutic strategies. In this study, we used a selection strategy to identify endogenous RNAs from a transcriptome library derived from lung cells that interact with the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Some of the selected RNAs weakened the activity of RdRp by forming G-quadruplexes. These results suggest that certain endogenous RNAs, which potentially form G-quadruplexes, can reduce the replication of viral RNAs.
DOI： 10.1039/d2cc05858h
Books and Other Publications 【 display / non-display 】
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Quantitative Analysis of Stall of Replicating DNA Polymerase by G-Quadruplex Formation
Shuntaro Takahashi, Naoki Sugimoto（ Role： Joint author）
Springer 2019.8
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生体分子化学 基礎から応用まで
杉本直己・編著（ Role： Joint editor）
講談社 2017.1 （ ISBN:978-4-06-156806-8 ）
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生体分子化学 : 基礎から応用まで = biomolecular chemistry
杉本, 直己, 内藤, 昌信, 橋詰, 峰雄, 高橋, 俊太郎, 田中, 直毅, 建石, 寿枝, 遠藤, 玉樹, 津本, 浩平, 長門石, 曉, 松原, 輝彦, 上田, 実, 朝山, 章一郎, 講談社サイエンティフィク
講談社 2017.1 （ ISBN:9784061568068 ）
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高圧下での核酸の挙動、CSJカレントレビュー17極限環境の生命化学
高橋俊太郎,杉本直己（ Role： Joint author）
化学同人 2014.11
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バイオセンシングのための水晶発振子マイクロバランス法ー原理から応用例まで
岡畑恵雄,森俊明,古澤宏幸,高橋俊太郎（ Role： Joint editor）
講談社サイエンティフィク 2013.3
Review Papers (Misc) 【 display / non-display 】
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高圧力が生物関連成分に及ぼす影響-1 高圧力がDNAに及ぼす影響 非標準構造と分子クラウディングの視点
高橋俊太郎, 杉本直己, 杉本直己
化学と生物 58 ( 8 ) 2020.8
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平成の化学キーワード 核酸の多様性を生みだすもう一つの塩基対相互作用 フーグスティーン塩基対
高橋俊太郎、杉本直己
化学 74 ( 5 ) 24 - 25 2019.5
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (scientific journal) Publisher：化学同人
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分子夾雑系の生命化学（２）
高橋俊太郎、杉本直己
現代化学 575 34 - 38 2019.2
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (scientific journal) Publisher：東京化学同人
Presentations 【 display / non-display 】
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核酸化学のNew Data Science (2): 最近接塩基対パラメータとAIを用いたリボザイムの機能予測
高橋俊太郎、S. Ghoshi、建石寿枝, 福永津嵩、浜田道昭、杉本直己
日本化学会第104回春季年会
Event date： 2024.3
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New Data Science in Nucleic Acids Chemistry (7): Quantitative study of formation of DNA tetraplexes during cell cycle
S. Das, S. Takahashi, N. Sugimoto
日本化学会第104回春季年会
Event date： 2024.3
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New Data Science in Nucleic Acids Chemistry (6): Complementary effect of hydrogen bonding and base stacking on the stability of double-stranded nucleic acids
L. Liu, S. Takahashi, N. Sugimoto
日本化学会第104回春季年会
Event date： 2024.3
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New Data Science in Nucleic Acids Chemistry (5): Effect of local environments on the stability of nucleic acids in mitochondria
S. Ghosh, L. Liu, S. Takahashi, T. Endoh, N. Yoshinaga, K. Numata, N. Sugimoto
日本化学会第104回春季年会
Event date： 2024.3
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人工核酸塩基を用いたDNA二重らせん構造の水和解析
高橋俊太郎, GHOSH Saptarshi, 大山達也, 岡村秀紀, 永次史, 杉本直己
第23回東北大学多元物質科学研究所研究発表会
Event date： 2023.12
Industrial property rights 【 display / non-display 】
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核酸合成法
杉本 直己, 高橋 俊太郎, 大倉 裕道
Academic Awards Received 【 display / non-display 】
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第29回山下太郎学術研究奨励賞
2018.6 財団法人 山下太郎顕彰育英会
高橋俊太郎
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第5回バイオ関連シンポジウム講演賞
2011.9 日本化学会生体機能関連部会
高橋俊太郎
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The 16th Annual Meeting of the RNA Society Nature Reviews Molecular Cell Biology Poster Prizes（2011）
2011.6 The RNA Society
高橋俊太郎
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2010年度 財団法人手島工業教育資金団 手島精一記念研究賞
2011.2 東京工業大学
高橋俊太郎,古澤宏幸,岡畑恵雄
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第89回日本化学会年会春期年会 (2009) 優秀講演賞
2009.3 日本化学会
高橋俊太郎
Grant-in-Aid for Scientific Research 【 display / non-display 】
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Quantitative prediction of nucleic acid structures and functions affected by spaciotemporal environmental factors in cells
2022.4 - 2027.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(S)
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Quantitative analysis and chemical regulation of DNA replication stall depending on mitchondrial environments
2021.4 - 2024.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(C)
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Analysis and regulation of non-canonical nucleic acids under intracellular conditions
2018.10 - 2021.3
JSPS Grants-in-Aid for Scientific Research Fund for the Promotion of Joint International Research ( Fostering Joint International Research (B))
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核酸四重鎖のトポロジーで支配される細胞内機能の解明と制御
2017.4 - 2021.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(C)
本研究の目的は、様々なトポロジーを有する核酸四重鎖の熱力学的安定性とDNA複製速度を多角的に定量解析する手法を開発し、核酸四重鎖のトポロジーが持つ生物学的意義を解明することである。開発した解析法を活用することで、四重鎖のトポロジーの違いをターゲットとするという新しいコンセプトに基づく薬剤分子の探索・開発を行い、細胞内機能の人為的制御を目指す。
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Analysis of Dimensional Code in Central Dogma based on Polymorphic Nucleic Acid Structures
2016.4 - 2019.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(A)
Sugimoto Naoki
In this study, physicochemical analyses of non-canonical nucleic acid structures were performed in consideration of the effect of chemical environment in cells. The functions of the non-canonical nucleic acid structures, which are assumed as Dimensional Code of central dogma in this research, have been clarified at the molecular level. This study also tried artificial regulation of the Dimensional Code by rationally designing molecules that induce and stabilize the non-canonical nucleic acid structures. Throughout the study, various physicochemical parameters in different chemical environments were obtained. Based on the obtained findings, we designed and synthesized artificial small molecules and nucleic acids that specifically interact with the target non-canonical nucleic acid structure. Furthermore, the molecules were applied for controlling fundamental reactions in central dogma, such as replication, transcription, and translation, both inside and outside cells.
Committee Memberships 【 display / non-display 】
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2019 日本高圧力学会 高圧力学会誌編集委員
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2010.4 - 2012.3 日本化学会 生体機能関連化学部会若手の会代表幹事
Social Activities 【 display / non-display 】
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ひらめき☆ときめきサイエンス 「遺伝子暗号を解く」〜光で操る 遺伝子からタンパク質ができるまで〜
2013.7
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ひょうご神戸サイエンスクラスター研究交流会企画委員
2012.9
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ひらめき☆ときめきサイエンス 人工DNAによる次世代バイオセンサー –遺伝子の情報を探れ！−
2012.7