Screening of quadruplex-forming anti-prion nucleic acids and molecular design on the basis of its mechanism

• Project/Area Number: 26840020
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Kyoto University
• Principal Investigator: Mashima Tsukasa 京都大学, エネルギー理工学研究所, 助教 (20707426)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2014: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: アプタマー / 四重鎖核酸 / プリオン病 / 立体構造 / NMR

Outline of Final Research Achievements

Prion diseases typified by the spongiform encephalopathy (BSE) are thought to be caused by the accumulation of abnormal form of prion protein (PrPSc). In this study, we have performed screening of the quadruplex-forming nucleic acids that reduce PrPSc levels in prion-infected cells. We have succeeded in obtaining an RNA molecule whose IC50 value is around 100 nM. Unfortunately, NMR spectra of this RNA were too complex to analyze on account of the poor dispersion of signals. Therefore, we carried out the modification of sequence of RNA and the investigation of optimal buffer condition for NMR measurement. As a result, we found a mutated RNA molecule showing good dispersion of NMR signals and also established the suitable buffer condition for NMR measurement.

Research Products

• [Journal Article] Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA (2016)
  • Author(s): Masuda, K., Ripley, B., Nyati, K., Dubey, P., Zaman, M., Hanieh, H., Hoga, M., Yamashita, K., Standley, D., Mashima, T., Katahira, M., Okamoto, T., Matsuura, Y., Takeuchi, O. and Kishimoto, T.
  • Journal Title: Journal of Experimental Medicine Volume: 213 Issue: 4 Pages: 605-619
  • DOI: 10.1084/jem.20151289
  • Peer Reviewed / Open Access
• [Journal Article] The binding specificity of translocated in liposarcoma/fused in sarcoma with lncRNA transcribed from the promoter region of cyclin D1 (2016)
  • Author(s): Yoneda, R., Suzuki, S., Mashima, T., Kondo, K., Nagata, T., Katahira, M. and Kurokawa, R.
  • Journal Title: Cell Biosci. Volume: 6(4) Issue: 1 Pages: 1-12
  • DOI: 10.1186/s13578-016-0068-8
  • NAID: 120005763383
  • Peer Reviewed / Open Access
• [Journal Article] K+-responsive off-to-on switching of hammerhead ribozyme through dual G-quadruplex formation requiring no heating and cooling treatment (2015)
  • Author(s): Yamaoki Y, Nagata T, Mashima T, Katahira M
  • Journal Title: Biochemical and biophysical research communications Volume: 468(1-2) Issue: 1-2 Pages: 27-31
  • DOI: 10.1016/j.bbrc.2015.10.173
  • NAID: 120005712951
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases Both through Hydrogen Bonding and Metal Coordination (2015)
  • Author(s): Takezawa, Y., Nishiyama K., Mashima T., Katahira, M. and Shionoya, M.
  • Journal Title: Chemistry Volume: 21 Issue: 42 Pages: 14713-14716
  • DOI: 10.1002/chem.201502772
  • Peer Reviewed / Open Access
• [Journal Article] Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts (2015)
  • Author(s): S.Kusano, S. Ishiyama,Sik Lok Lam, T. Mashima, M. Katahira, K. Miyamoto, M. Aida, F. Nagatsugi
  • Journal Title: Nucl.Acids Res Volume: 43 Issue: 16 Pages: 7717-7730
  • DOI: 10.1093/nar/gkv797
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Boosting of activity enhancement of K+-responsive quadruplex hammerhead ribozyme (2015)
  • Author(s): Yudai Yamaoki, Tsukasa Mashima, Takashi Nagata and Masato Katahira
  • Journal Title: Chemical Communications Volume: 51 Issue: 27 Pages: 5898-5901
  • DOI: 10.1039/c5cc00961h
  • Peer Reviewed / Open Access
• [Journal Article] Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition (2014)
  • Author(s): T. Hayashi, H. Oshima, T. Mashima, T. Nagata, M. Katahira, M. Kinoshita
  • Journal Title: Nucleic Acids Research Volume: 42 Issue: 11 Pages: 6861-6875
  • DOI: 10.1093/nar/gku382
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Development of the selective crosslinking reactions to 8-oxoguanine (2015)
  • Author(s): Nagatsugi, F., Kusano, S., Ishiyama, S., Lam, S. L., Mashima, T. and Katahira, M.
  • Organizer: The 42nd International Symposium on Nucleic Acids Chemistry
  • Place of Presentation: Egret Himeji, Himeji-shi, Hyogo
  • Year and Date: 2015-09-23
  • Int'l Joint Research
• [Presentation] NMR study of the recognition of non-coding RNA and DNA by TLS/FUS, a key regulator of cyclin D1 (2015)
  • Author(s): Kondo, K., Mashima, T., Oyoshi, T., Kurokawa, R., Nagata, T. and Katahira, M.
  • Organizer: The 42nd International Symposium on Nucleic Acids Chemistry
  • Place of Presentation: Egret Himeji, Himeji-shi, Hyogo
  • Year and Date: 2015-09-23
  • Int'l Joint Research
• [Presentation] カリウムイオンを認識して活性がスイッチングするTat結合RNAアプタマーおよびハンマーヘッドリボザイムの創製 (2015)
  • Author(s): 山置 佑大、真嶋 司、永田 崇、片平 正人
  • 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] 異常型プリオン蛋白質の産生を抑制する四重鎖核酸の構造解析 (2015)
  • Author(s): 真嶋 司、西川 富美子、鎌足 雄司、永田 崇、西川 諭、桑田 一夫、片平 正人
  • 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] 転写抑制やテロメア短縮を引き起こすTLS/FUSと長鎖非コードRNAおよびDNAとの結合の構造基盤 (2015)
  • Author(s): 近藤 敬子、真嶋 司、大吉 崇文、黒川 理樹、永田 崇、片平 正人
  • Organizer: 第17回RNAミーティング
  • Place of Presentation: ホテルライフォート札幌, 北海道札幌市
  • Year and Date: 2015-07-15
• [Presentation] CCND1転写抑制とテロメア短縮をもたらすTLS/FUSによる非コードRNAとDNA認識機構のNMR法による解明 (2014)
  • Author(s): 近藤 敬子、真嶋 司、大吉 崇文、黒川 理樹、永田 崇、片平 正人
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: 神奈川県横浜市、パシフィコ横浜
  • Year and Date: 2014-11-25 – 2014-11-27
• [Presentation] Creation of novel Tat-binding aptamer and ribozyme whose activities switch on in response to K+ via quadruplex formation (2014)
  • Author(s): Yamaoki, Y., Mashima, T., Nagata, T. and Katahira, M.
  • Organizer: The 41st International Symposium on Nucleic Acids Chemistry
  • Place of Presentation: Kitakyushu International Conference Center, Kitakyushu-shi, Fukuoka
  • Year and Date: 2014-11-05 – 2014-11-07
• [Presentation] Real-time NMR monitoring of enzymatic reaction of anti-HIV protein, structure of anti-prion RNA aptamer and wood biomass analysis (2014)
  • Author(s): Kanba, K., Mashima, T., Okamura, H., Furukawa, A., Sugase, K., Nishimura, H., Watanabe, T., Nagata, T., and Katahira, M.
  • Organizer: The 5th Japan-Taiwan NMR symposium
  • Place of Presentation: Hokkaido University, Hokkaido
  • Year and Date: 2014-09-29 – 2014-09-30
  • Invited
• [Presentation] Screening for novel aptamer against prion protein and its structural study (2014)
  • Author(s): 真嶋 司、西川 富美子、鎌足 雄司、永田 崇、西川 諭、桑田 一夫、片平 正人
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 北海道札幌市、札幌コンベンションセンター
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] Development of Tat-binding aptamer and ribozyme which switch their activities in response to K+ (2014)
  • Author(s): 山置 佑大、真嶋 司、永田 崇、片平 正人
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 北海道札幌市、札幌コンベンションセンター
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] カリウムイオンを感知して自らの活性をスイッチングするTat捕捉アプタマーおよびリボザイムの創製 (2014)
  • Author(s): 山置 佑大、真嶋 司、永田 崇、片平 正人
  • Organizer: 第16回日本RNA学会年会
  • Place of Presentation: 愛知県名古屋市、ウインクあいち
  • Year and Date: 2014-07-23 – 2014-07-25
• [Presentation] CCND1転写抑制とテロメア短縮に関与する天然変性蛋白質TLS/FUSによる非コードRNAとDNAの認識機構のNMR法による解明 (2014)
  • Author(s): 近藤 敬子、真嶋 司、大吉 崇文、黒川 理樹、永田 崇、片平 正人
  • Organizer: 第14回日本蛋白質科学会年会
  • Place of Presentation: 神奈川県横浜市、ワークピア横浜
  • Year and Date: 2014-06-25 – 2014-06-27