Creation of RNA aptamers for identification of microorganisms

2012 Fiscal Year Final Research Report

• Project/Area Number: 22658034
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Single-year Grants
• Research Field: Applied biochemistry
• Research Institution: Toyohashi University of Technology
• Principal Investigator: KIKUCHI Yo 豊橋技術科学大学, 大学院・工学研究科, 教授 (40273320)
• Research Collaborator: UMEKAGE So 豊橋技術科学大学, 大学院・工学研究科, 専任講師 (30419436)
• Project Period (FY): 2010 – 2012
• Keywords: 生物工学 / 核酸 / RNA / 細菌 / 芽胞 / プローブ

Research Abstract

We have newly developed two methods for RNA aptamer selection: one is a kinetically designed RNA aptamer selection method. The second is a rapid fluorescent labeling method for RNA. Using these methods, we have selected RNA aptamers to bacterial spores from random RNApopulation. The RNA aptamers were isolated from selected RNA population by cloning and characterized. All RNA aptamers bind to bacterial spores specifically, but do not bind to vegetative bacterial cellsat all. The aptamers bind to bacterial spores from any species tested. It has been concluded that the RNA aptamers recognize some structures commonly present in bacterial spores.

Research Products

• [Journal Article] Inhibition of hirame rhabdovirus (HIRRV) growth by RNA aptamers (2012)
  • Author(s): Hwang, S. D., Midorikawa, N., Punnarak, P., Kikuchi, Y., Kondo, H., Hirono, I., Aoki, T.
  • Journal Title: J. Fish Diseases 35(12) Pages: 927-934
  • Peer Reviewed
• [Journal Article] RNA aptamer(s) inhibit the growth of the fish pathogen viral hemorrhagic septicemia virus (VSHV) (2012)
  • Author(s): Punnarak, P.,Santos, M. D., Hwang, S. D., Kondo, H., Hirono, I., Kikuchi, Y., and Aoki, T.
  • Journal Title: Marine Biotechnology14(6) Pages: 752-761
  • Peer Reviewed
• [Journal Article] High-affinity RNA aptamers to C-reactive protein (CRP): newly developed pre-elution methods for aptamer selection (2012)
  • Author(s): Orito, N., Umekage, S., Sato, K., Kawauchi, H., Tanaka, H., Sakai, E., Tanaka, T., and Kikuchi, Y.
  • Journal Title: J. Physics Conf. Ser. Pages: 352
  • DOI: DOI:10.1088/1742-6596/352/1/012042
  • Peer Reviewed
• [Journal Article] Artificial RNA aptamer production by the marine bacterium Rhodovulum sulfidophilum: Improvement of the aptamer yield using a mutated transcriptional promoter (2011)
  • Author(s): Suzuki, H., Umekage, S., Tanaka, T., and Kikuchi, Y.
  • Journal Title: Journal of Bioscience and Bioengineering112(5) Pages: 458-461
  • Peer Reviewed
• [Journal Article] Kinetically designed RNA aptamer selection (2010)
  • Author(s): Umekage, S., Enami, Y., and Kikuchi, Y.
  • Journal Title: ISNAC 2010 Pages: 104-105
  • Peer Reviewed
• [Journal Article] Extracellular production of an RNA aptamer by ribonuclease-free marine bacteria harboring engineered plasmids: a proposal for industrial RNA drug production (2010)
  • Author(s): Suzuki, H., Ando, T., Umekage, S., Tanaka, T., and Kikuchi, Y.
  • Journal Title: Appl. Environ. Microbiol.76(3) Pages: 786-793
  • Peer Reviewed
• [Presentation] 海洋性光合成細菌による人工short hairpin RNAの生産(口頭発表) (2013)
  • Author(s): ○長尾信義、鈴木宏道、沼野利佳、梅影創、菊池洋
  • Organizer: 日本農芸化学会2013年度大会
  • Place of Presentation: 仙台
  • Year and Date: 2013-03-25
• [Presentation] Artificial RNA production using an engineered bacterium(口頭発表) (2011)
  • Author(s): Hiromichi Suzuki, So Umekage, Terumichi Tanaka, and ○Yo Kikuchi
  • Organizer: Annual Meeting of the RNA Society (in conjunction with 13 th Annual Meeting of the RNA Society of Japan)
  • Place of Presentation: 京都
  • Year and Date: 2011-06-18
• [Book] In vivocircular RNA expression by the permuted intron-exon (PIE) method, in Innovations in Biotechnology (Ed. E. C. Agbo, ISBN 978-953-51-0096-6, Intech Open) Chapter 4 (2012)
  • Author(s): Umekage, S., Uehara, T., Fujita, Y., Suzuki, H., and Kikuchi, Y.
  • Total Pages: 75-90
  • Publisher: Intech Open
• [Book] 生体エネルギーと代謝、「理工系学生のための生命科学・環境科学」榊佳之・平石明編 (2011)
  • Author(s): 菊池洋
  • Total Pages: 19-33
  • Publisher: 東京化学同人
• [Book] 「理工系学生のための生命科学・環境科学」榊佳之・平石明編 (2011)
  • Author(s): 菊池洋
  • Total Pages: 5-18
  • Publisher: 東京化学同人
• [Book] Extracellular nucleic acids of the marine phototrophic bacterium Rhodovulum sulfidophilumand related bacteria: Physiology and biotechnology. In "Extracellular nucleic acids"., eds. Kikuchi, Y.and Rykova, E. A series of "Nucleic Acids and Molecular Biology", ed. Gross,H. J., Vol. 25 (2010)
  • Author(s): Kikuchi, Y
  • Total Pages: 55-67
  • Publisher: Springer-Verlag, Heidelberg
• [Book] "Extracellular nucleic acids". A series of "Nucleic Acids and Molecular Biology", ed. Gross, H. J., Vol. 25 (2010)
  • Author(s): Kikuchi, Y.and Rykova, E. eds.
  • Total Pages: 232
  • Publisher: Springer-Verlag, Heidelberg
• [Book] Produktion definierter RNAs im Kulturuberstand von Bakterien (in German) (2010)
  • Author(s): Kikuchi, Y., Suzuki, H., und Umekage, S
  • Total Pages: 6-7
  • Publisher: LABORWELT
• [Remarks]
  • URL: http://www.tut.ac.jp/teach/main.php?mode=detail&article=362
• [Patent(Industrial Property Rights)] 改良されたオリゴヌクレオチドおよびそのオリゴヌクレオチドを含む医薬組成物 (2013)
  • Inventor(s): 梅影創、越智明徳、菊池洋
  • Industrial Property Rights Holder: 国立大学法人豊橋技術科学大学
  • Industrial Property Number: 特許出願2011-120806
  • Filing Date: 2013-05-30
  • Overseas