Regulating genetic codes by high pressure

• Project/Area Number: 26620138
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Bio-related chemistry
• Research Institution: Konan University
• Principal Investigator: Sugimoto Naoki 甲南大学, 先端生命工学研究所, 教授 (60206430)
• Co-Investigator(Kenkyū-buntansha): Shuntaro Takahashi 甲南大学, 先端生命工学研究所, 講師 (40456257)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 核酸 / RNA / DNA / 熱力学的安定性 / 高圧力 / 遺伝暗号

Outline of Final Research Achievements

In this study, we used high pressure and investigated to regulate gene expression by changing the stability of non-canonical structure of nucleic acids selectively. As a result, the non-canonical structures such as G-quadruplex was largely destabilized with increasing pressure. By using this property, we found that gene expression from the DNA including non-canonical nucleic acids structure could be regulated by tuning pressure. These results shed light on the development of novel system of gene expression by using pressure changes and the elucidation of the origin of life, which was possibly born under a high pressure condition.

Research Products

• [Int'l Joint Research] スロベニア国立NMRセンター(スロベニア)
• [Journal Article] Real-time monitoring of G‑quadruplex formation during transcription (2016)
  • Author(s): T. Endoh, A. B. Rode, S. Takahashi, Y. Kataoka, M. Kuwahara, and N. Sugimoto
  • Journal Title: Anal. Chem. Volume: 88 Issue: 4 Pages: 1984-1989
  • DOI: 10.1021/acs.analchem.5b04396
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Pressure-dependent formation of i-motif and G-quadruplex DNA structures (2015)
  • Author(s): S. Takahashi, N. Sugimoto
  • Journal Title: Physical Chemistry Chemical Physics Volume: 17 Issue: 46 Pages: 31004-31010
  • DOI: 10.1039/c5cp04727g
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structural foundation for DNA behavior in hydrated ionic liquid: An NMR study (2015)
  • Author(s): M. Marusic, H. Tateishi-Karimata, N. Sugimoto, and J. Plavec
  • Journal Title: Biochimie Volume: 108 Pages: 169-177
  • DOI: 10.1016/j.biochi.2014.11.015
  • Peer Reviewed / Open Access
• [Journal Article] Thermodynamic Properties of Water Molecules in the Presence of Cosolute Depend on DNA Structure: A Study Using Grid Inhomogeneous Solvation Theory (2015)
  • Author(s): M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto
  • Journal Title: Nucl. Acids Res. Volume: 43 Pages: 10114-10125
  • DOI: 10.1093/nar/gkv1133
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] i-Motifs Are More Stable than G-Quadruplexes in a Hydrated Ionic Liquid (2015)
  • Author(s): H. Tateishi-Karimata, M. Nakano, S. Pramanik, S. Tanaka, N. Sugimoto
  • Journal Title: Chem. Commun. Volume: 51 Issue: 32 Pages: 6909-6912
  • DOI: 10.1039/c5cc00666j
  • Peer Reviewed
• [Journal Article] Tuning riboswitch-mediated gene regulation by rational control of aptamer ligand binding properties (2015)
  • Author(s): A. B. Rode, T. Endoh, and N. Sugimoto
  • Journal Title: Angew. Chem. Int. Ed. Volume: 54 Issue: 3 Pages: 905-909
  • DOI: 10.1002/anie.201407385
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] 核酸構造の熱力学的安定性に及ぼす分子環境と高圧力の効果 (2015)
  • Author(s): 高橋俊太郎, 杉本直己
  • Journal Title: 高圧力の科学と技術 Volume: 25
  • NAID: 130005075752
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] New insights into transcription fidelity : thermal stability of non-cononical structures in template DNA regulates transcriptional arrest, pause, and slippage (2014)
  • Author(s): H. Tateishi-Karimata, N. Isono, and N. Sugimoto
  • Journal Title: PLoS ONE Volume: 9 Issue: 3 Pages: e90580-e90580
  • DOI: 10.1371/journal.pone.0090580
  • Peer Reviewed / Open Access
• [Journal Article] The affinity of molecular ions for DNA structures is determined by solvent accessible surface area (2014)
  • Author(s): M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
  • Journal Title: J. Phys. Chem. B Volume: 118 Issue: 32 Pages: 9583-9594
  • DOI: 10.1021/jp505107g
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription (2014)
  • Author(s): S. Pramanik, H. Tateishi-Karimata, and N. Sugimoto
  • Journal Title: Nucleic Acids Res. Volume: 42 Issue: 20 Pages: 12949-12959
  • DOI: 10.1093/nar/gku998
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (16): Replication reaction of DNA regulated by the formation of i-motif structure (2016)
  • Author(s): S. Takahashi, J. Brazier A., N. Sugimoto
  • Organizer: 日本化学会第96春季年会（2016）
  • Place of Presentation: 同志社大学京田辺キャンパス（京都府・京田辺市）
  • Year and Date: 2016-03-24
• [Presentation] Regulation of Gene Expression under Molecular Crowding Conditions (2016)
  • Author(s): 杉本直己
  • Organizer: バイオマイクロセンシング技術研究センター成果報告会 －生命を工学で解明し、医 療分野に挑む
  • Place of Presentation: 北九州国際会議場（福岡県・北九州市）
  • Year and Date: 2016-01-23
  • Invited
• [Presentation] New Targets of Pharmaceutical Products; G-quadruplexes of DNA and RNA (2016)
  • Author(s): N. Sugimoto
  • Organizer: 第8回武田科学振興財団薬化学シンポジウム
  • Place of Presentation: 武田薬品工業研修所（大阪府・吹田）
  • Year and Date: 2016-01-21
  • Invited
• [Presentation] G-quadruplexes Regulate Transcription and Translation (2015)
  • Author(s): H. Tateishi-Karimata, T. Endoh, S. Takahashi, N. Sugimoto
  • Organizer: 2015環太平洋国際化学会議（Pacifichem 2015）
  • Place of Presentation: Honolulu, (USA)
  • Year and Date: 2015-12-15
  • Int'l Joint Research
• [Presentation] G-quadruplexes Control Gene Expression under Molecular Crowding Condition (2015)
  • Author(s): N. Sugimoto
  • Organizer: Biochemistry and Molecular Biology (BMB2015)
  • Place of Presentation: 神戸国際会議場（兵庫県・神戸市）
  • Year and Date: 2015-12-01
  • Invited
• [Presentation] トリプレット病関連遺伝子の複製反応における圧力効果 (2015)
  • Author(s): 高橋俊太郎、杉本直己
  • Organizer: 第56回高圧討論会
  • Place of Presentation: JMSアステールプラザ（広島県・広島市）
  • Year and Date: 2015-11-10
• [Presentation] 分子クラウディングと高圧力が与える核酸の非標準型構造への影響 (2015)
  • Author(s): 高橋 俊太郎、杉本直己
  • Organizer: 第38回溶液化学シンポジウム
  • Place of Presentation: 高知市文化プラザカルポート（高知県・高知市）
  • Year and Date: 2015-10-20
  • Invited
• [Presentation] Role of poly(ethylene glycol) during the formation of G-quadruplex under high pressure (2015)
  • Author(s): S. Takahashi, N. Sugimoto
  • Organizer: 第42回国際核酸化学シンポジウム (ISNAC2015)
  • Place of Presentation: イーグレひめじ あいめっせホール（兵庫県・姫路市）
  • Year and Date: 2015-09-23
  • Int'l Joint Research
• [Presentation] Analysis of the formation of G-quadruplex DNA with hemin under high pressure (2015)
  • Author(s): S. Takahashi, N. Sugimoto
  • Organizer: 第65回錯体化学会討論会
  • Place of Presentation: 奈良女子大学（奈良県・奈良市）
  • Year and Date: 2015-09-22
• [Presentation] 高圧力が拓く核酸の新たな可能性 (2015)
  • Author(s): 高橋俊太郎、杉本直己
  • Organizer: 第64回高分子討論会
  • Place of Presentation: 東北大学川内キャンパス（宮城県・仙台市）
  • Year and Date: 2015-09-15
• [Presentation] 二次構造を形成するDNAの複製反応を圧力で制御する (2015)
  • Author(s): 高橋 俊太郎、杉本 直己
  • Organizer: 第9回バイオ関連化学シンポジウム
  • Place of Presentation: 熊本大学工学部（熊本県・熊本市）
  • Year and Date: 2015-09-10
• [Presentation] G-quadruplex and i-motif of Nucleic Acids under Molecular Crowding and High Pressure (2015)
  • Author(s): S. Takahashi, N. Sugimoto
  • Organizer: International Conference on High Pressure Science and Technology (AIRAPT)
  • Place of Presentation: Complutense University of Madrid, Madrid (Spain)
  • Year and Date: 2015-08-30
  • Int'l Joint Research
• [Presentation] G-quadruplexes control Gene expression (2015)
  • Author(s): H. Tateishi-Karimata, T. Endoh, N. Sugimoto
  • Organizer: Gordon Research Conference -Nucleosides, Nucleotides & Oligonucleoside-
  • Place of Presentation: Salve Regina Univerisity, New Port (USA)
  • Year and Date: 2015-06-28
  • Int'l Joint Research
• [Presentation] Thermodynamic Behaviors of Nucleic Acids in a Hydrated Ionic Liquid (2015)
  • Author(s): H. Tateishi-Karimata, N. Sugimoto
  • Organizer: 28th European Symposium on Applied Thermodynamics (ESAT 2015)
  • Place of Presentation: Royal Olympic Hotel , Athens (Greece)
  • Year and Date: 2015-06-11
  • Int'l Joint Research
• [Presentation] 非二重らせん構造のDNA・RNAの重要な役割 (2015)
  • Author(s): 杉本直己
  • Organizer: 第55回澱粉研究懇親会
  • Place of Presentation: ホテルラヴィエ川良（静岡県・伊東市）
  • Year and Date: 2015-06-04
  • Invited
• [Presentation] Translation suppression by G-quadruples (2015)
  • Author(s): T. Endoh, N. Sugimoto
  • Organizer: 5th International Meeting on Quadruplex Nucleic Acids G4thering in Bordeaux
  • Place of Presentation: IECB University of Bordeaux, Bordeaux (France)
  • Year and Date: 2015-05-26
  • Int'l Joint Research
• [Presentation] Stability and Function of Quadruplexes of Nucleic Acids (2015)
  • Author(s): N. Sugimoto
  • Organizer: Institute of Atomic and Molecular Sciences, Academia Sinica
  • Place of Presentation: National Taiwan University, Taipei (Taiwan)
  • Year and Date: 2015-05-12
  • Int'l Joint Research / Invited
• [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (6): Binding Mechanism of G-quadruplex and Its Ligands Elucidated by Pressure Effect (2015)
  • Author(s): S. Takahashi, S. Bhowmik, N. Sugimoto
  • Organizer: 日本化学会第95春季年会（2015）
  • Place of Presentation: 日本大学（船橋キャンパス）
  • Year and Date: 2015-03-26 – 2015-03-29
• [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (7): Molecular Crowding Effect on Ribozyme- or Protein-based Polymerase Reactions (2015)
  • Author(s): H. Okura, S. Takahashi, N. Sugimoto
  • Organizer: 日本化学会第95春季年会（2015）
  • Place of Presentation: 日本大学（船橋キャンパス）
  • Year and Date: 2015-03-26 – 2015-03-29
• [Presentation] Structures, Interactions, and Functions of Nucleic Acids under Molecular Crowding Conditions (2014)
  • Author(s): N.Sugimoto
  • Organizer: Asian Chemical Biology Conference (ACBC 2014)
  • Place of Presentation: National University of Singapore, Singapore
  • Year and Date: 2014-12-15 – 2014-12-17
  • Invited
• [Presentation] DNAとRNAに潜むもうひとつの遺伝暗号 (2014)
  • Author(s): 杉本 直己
  • Organizer: 近畿大学産業理工学研究科セミナー
  • Place of Presentation: 近畿大学（飯塚キャンパス）
  • Year and Date: 2014-12-11
  • Invited
• [Presentation] 核酸の挙動に及ぼす分子クラウディングと圧力の影響 (2014)
  • Author(s): 杉本 直己, 高橋 俊太郎
  • Organizer: 第55回高圧討論会
  • Place of Presentation: 徳島大学（常三島キャンパス）
  • Year and Date: 2014-11-22 – 2014-11-24
  • Invited
• [Presentation] テロメアDNA配列のP-T依存的構造変化 (2014)
  • Author(s): 高橋 俊太郎, 杉本 直己
  • Organizer: 第55回高圧討論会
  • Place of Presentation: 徳島大学（常三島キャンパス）
  • Year and Date: 2014-11-22 – 2014-11-24
• [Presentation] New insights into the binding nucleolin to nucleic acids from physicochemical analysis (2014)
  • Author(s): S. Pramanik, H. Tateishi-Karimata, S. Takahashi, and N. Sugimoto
  • Organizer: 第41回国際核酸化学シンポジウム (ISNAC2014)
  • Place of Presentation: 北九州国際会議場（小倉）
  • Year and Date: 2014-11-05 – 2014-11-07
• [Presentation] Pressure and temperature stability diagram of human telomeric DNA (2014)
  • Author(s): S. Takahashi, S. Bhowmik, and N. Sugimoto
  • Organizer: 第41回国際核酸化学シンポジウム (ISNAC2014)
  • Place of Presentation: 北九州国際会議場（小倉）
  • Year and Date: 2014-11-05 – 2014-11-07
• [Presentation] 非二重らせん構造に隠された核酸の機能を知る (2014)
  • Author(s): 杉本 直己
  • Organizer: 14-1バイオ・高分子研究会
  • Place of Presentation: にっしょうかん新館（長崎市）
  • Year and Date: 2014-09-26 – 2014-09-28
  • Invited
• [Presentation] 核酸の熱力学的挙動解析と核酸ナノマテリアルの創製 (2014)
  • Author(s): 杉本 直己
  • Organizer: 第64回錯体化学討論会
  • Place of Presentation: 中央大学
  • Year and Date: 2014-09-18 – 2014-09-20
  • Invited
• [Presentation] 高圧力で誘起されるi-motif DNAの構造安定化効果 (2014)
  • Author(s): 高橋 俊太郎、杉本 直己
  • Organizer: 第8回バイオ関連化学シンポジウム
  • Place of Presentation: 岡山大学（津島キャンパス）
  • Year and Date: 2014-09-11 – 2014-09-13
• [Presentation] DNA四重鎖は転写の二次情報を保持しているか？ (2014)
  • Author(s): 建石 寿枝、遠藤 玉樹、高橋 俊太郎、杉本 直己
  • Organizer: 第8回バイオ関連化学シンポジウム
  • Place of Presentation: 岡山大学（津島キャンパス）
  • Year and Date: 2014-09-11 – 2014-09-13
• [Presentation] Effect of pressure and molecular crowding on the stability of G-quadruplex DNA (2014)
  • Author(s): S. Takahashi and N. Sugimoto
  • Organizer: 8th International Conference on High Pressure Bioscience and Biotechnology (HPBB)
  • Place of Presentation: Oniris-Nantes-Atlantic National College of Veterinary Medicine, Food Science and Engineering, France
  • Year and Date: 2014-07-15 – 2014-07-18
• [Presentation] Thermal Stability and Application of Unusual structures of DNA and RNA (2014)
  • Author(s): N. Sugimoto
  • Organizer: The 5th International Conference on the Development of Biomedical Engineering
  • Place of Presentation: International University, Ho Chi Minh City, Vietnam
  • Year and Date: 2014-06-16 – 2014-06-18
• [Presentation] Thermal Stability of Non-cannonical structures in Template DNA and its Effect on Transcription (2014)
  • Author(s): H. Tateishi-Karimata and N. Sugimoto
  • Organizer: Gordon Research Conference – Biopolymers
  • Place of Presentation: Salve Regina University, Newport, USA
  • Year and Date: 2014-06-01 – 2014-06-06
• [Book] 高圧下での核酸の挙動:極限環境の生命化学(CSJカレントレビュー) (2014)
  • Author(s): 高橋俊太郎, 杉本直己
  • Publisher: 化学同人
• [Book] Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowing: beyond the Watson-Crick double helix: International Review of Cell and Molecular Biology (2014)
  • Author(s): N. Sugimoto
  • Publisher: Elsevier
• [Remarks] FIBER 甲南大学 先端生命工学研究所
  • URL: http://www.konan-fiber.jp