IKEBUKURO LABORATORY NEWS

2018

  1. Riboregulator elements as tools to engineer gene expression in cyanobacteria.
    Kinuko Ueno, Kaori Tsukakoshi and Kazunori Ikebukuro
    Applied Microbiology and Biotechnology (2018). [Epub ahead of print]



  2. CpG Methylation Changes G-Quadruplex Structures Derived from Gene Promoters and Interaction with VEGF and SP1
    Kaori Tsukakoshi†, Shiori Saito†, Wataru Yoshida†, Shinichi Goto and Kazunori Ikebukuro
    Molecules (2018). 23 (4), 944

    3. †: These authors contributed equally to this work.



  3. Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand
    Wataru Yoshida, Hiroki Saikyo, Kazuhiko Nakabayashi, Hitomi Yoshioka, Daniyah Habiballah Bay, Keisuke Iida, Tomoko Kawai, Kenichiro Hata, Kazunori Ikebukuro, Kazuo Nagasawa and Isao Karube
    Scientific Reports (2018). 8, 3116



  4. Improving the induction fold of riboregulators for cyanobacteria
    Ippei Sakamoto†, Koichi Abe†, Sumiya Kawai†, Kaori Tsukakoshi†, Yuta Sakai, Koji Sode and Kazunori Ikebukuro
    RNA Biology (2018). 15 (2), 353-358

    5. †: 筆頭著者




2017

  1. Applying a riboregulator as a new chromosomal gene regulation tool for higher glycogen production in Synechocystis sp. PCC 6803
    Kinuko Ueno, Yuta Sakai, Chika Shono, Ippei Sakamoto, Kaori Tsukakoshi, Yukako Hihara, Koji Sode and Kazunori Ikebukuro
    Applied Microbiology and Biotechnology (2017). 101 (23-24), 8465–8474



  2. Development of aptamers against unpurified proteins.
    Shinichi Goto, Kaori Tsukakoshi and Kazunori Ikebukuro
    Biotechnology and Bioengineering (2017). [Epub ahead of print]



  3. Development of HGF-binding aptamers with the combination of G4 promoter-derived aptamer selection and in silico maturation.
    Tomomi Yokoyama†, Kaori Tsukakoshi†, Wataru Yoshida, Taiki Saito, Kentaro Teramoto, Nasa Savory, Koichi Abe and Kazunori Ikebukuro
    Biotechnology and Bioengineering (2017). [Epub ahead of print]

    4. †: These authors contributed equally to this work.



  4. DNA aptamers against FokI nuclease domain for genome editing applications
    Maui Nishio, Daisuke Matsumoto, Yoshio Kato, Koichi Abe, Jinhee Lee, Kaori Tsukakoshi, Ayana Yamagishi, Chikashi Nakamura and Kazunori Ikebukuro
    Biosensors and Bioelectronics (2017). 93 (15), 26-31



  5. Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands
    Daniyah H. Bay†, Annika Busch†, Fred Lisdat, Keisuke Iida, Kazunori Ikebukuro, Kazuo Nagasawa, Isao Karube and Wataru Yoshida
    BMC Molecular Biology (2017).18 (1), 17

    6. †: These authors contributed equally to this work.



  6. Pipette tip biosensors for bacterial double-stranded DNA using bioluminescence induced by zinc finger luciferase
    Eri Takano, Nobuaki Shimura, Takeshi Akiba, Yukiya Kitayama, Hirobumi Sunayama, Koichi Abe, Kazunori Ikebukuro and Toshifumi Takeuchi
    Microchimica Acta (2017). 184 (6), 1595–1601



  7. Development of an electrochemical detection system for measuring DNA methylation levels using methyl CpG-binding protein and glucose dehydrogenase-fused zinc finger protein
    Jinhee Lee, Wataru Yoshida, Koichi Abe, Kazuhiko Nakabayashi, Hironobu Wakeda, Kenichiro Hata, Christophe A. Marquette, Loïc J. Blum, Koji Sode and Kazunori Ikebukuro
    Biosensors and Bioelectronics (2017). 93, 118-123




2016

  1. Detection of DNA Methylation of G-Quadruplex and i-Motif-Forming Sequences by Measuring the Initial Elongation Efficiency of Polymerase Chain Reaction.
    Wataru Yoshida, Hitomi Yoshioka, Daniyah Habiballah Bay, Keisuke Iida, Kazunori Ikebukuro, Kazuo Nagasawa and Isao Karube
    Analytical Chemistry (2016). 88 (14), 7101-7107



  2. ATP-mediated Release of a DNA-binding Protein from a Silicon Nanoneedle Array
    Daisuke Matsumoto, Maui Nishio, Yoshio Kato, Wataru Yoshida, Koichi Abe, Kyoko Fukazawa, Kazuhiko Ishihara, Futoshi Iwata, Kazunori Ikebukuro and Chikashi Nakamura
    Electrochemistry (2016). 84 (5), 305-307



  3. Methods for Improving Aptamer Binding Affinity.
    Hijiri Hasegawa, Nasa Savory, Koichi Abe and Kazunori Ikebukuro
    Molecules (2016). 21 (4), 421



  4. Sensitive and Homogeneous Detection System with Aptamer-Based Biosensor
    Kaori Tsukakoshi and Kazunori Ikebukuro
    Sensors and Materials (2016). 28 (3), 1083-1089



  5. Structural regulation by a G-quadruplex ligand increases binding abilities of G-quadruplex-forming aptamers.
    Kaori Tsukakoshi, Yuri Ikuta, Koichi Abe, Wataru Yoshida, Keisuke Iida, Yue Ma, Kazuo Nagasawa, Koji Sodea and Kazunori Ikebukuro
    Chemical Communications (2016). 52 (85), 12646-12649




2015

  1. Inhibition of an Allergen-Antibody Reaction Related to Japanese Cedar Pollinosis Using DNA Aptamers Against the Cry j 2 Allergen.
    Kazumasa Ogihara, Nasa Savory, Koichi Abe, Wataru Yoshida, Mitsuru Arakawa, Masahiko Asahi, Seika Kamohara and Kazunori Ikebukuro
    Nucleic Acid Therapeutics (2015), 25 (6), 311-316



  2. アプタマーを用いた機能性電極
    Jinhee Lee and Kazunori Ikebukuro
    Electrochemistry (2015), 83-12, 1085-1090



  3. Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA
    Taiki Saito†, Wataru Yoshida†, Tomomi Yokoyama, Koichi Abe and Kazunori Ikebukuro
    Molecules (2015). 20 (11), 20832–20840

    4. †: These authors contributed equally to this work.



  4. DNA Detection Technology Using Zinc Finger Protein
    Takenori Kumagai, Koichi Abe, Wataru Yoshida and Kuzunori Ikebukuro
    Journal of Microbial & Biochemical Technology (2015). 7:5, 278-281



  5. Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy
    Takahiro Fukaya†, Koichi Abe†, Nasa Savory, Kaori Tsukakoshi, Wataru Yoshida, Stefano Ferri, Koji Sode, and Kazunori Ikebukuro
    Journal of Biotechnology (2015). 212, 99–105

    6. †: These authors contributed equally to this work.



  6. Enzyme linking to DNA aptamers via a zinc finger as a bridge
    Koichi Abe, Yoshiyuki Murakami, Atsuro Tatsumi, Koichi Sumida, Aki Kezuka, Takahiro Fukaya, Takenori Kumagai, Yuko Osawa, Koji Sode and Kazunori Ikebukuro
    Chemical Communications (2015). 51 (57 ), 11467-11469



  7. Development of an automated direct blotting electrophoresis system for bioanalytical applications
    Shinichi Goto, Nasa Savory, Koichi Abe, Hideki Kinoshita and Kazunori Ikebukuro
    Analytical Methods (2015). 7, 4881-4884



  8. Scaffold-fused riboregulators for enhanced gene activation in Synechocystis sp. PCC 6803
    Yuta Sakai, Koichi Abe, Saki Nakashima, James J. Ellinger, Stefano Ferri, Koji Sode and Kazunori Ikebukuro
    MicrobiologyOpen (2015). 4(4), 533-540




2014

  1. Chapter 11: In silico Maturation: Processing Sequences to Improve Biopolymer Functions Based on Genetic Algorithms
    Nasa Savory, Koichi Abe, Wataru Yoshida, Kazunori Ikebukuro
    Applications of Metaheuristics in Process Engineering Springer International Publishing, Switzerland (2014) pp 271-288



  2. DNA aptamers against the Cry j 2 allergen of Japanese cedar pollen for biosensing applications
    Kazumasa Ogihara, Nasa Savory, Koichi Abe, Wataru Yoshida, Masahiko Asahi, Seika Kamohara, and Kazunori Ikebukuro
    Biosensors and Bioelectronics (2015). 63, 159-165



  3. Selection of DNA aptamers against uropathogenic Escherichia coli NSM59 by quantitative PCR controlled Cell-SELEX
    Nasa Savory, Jonathan Nzakizwanayo, Koichi Abe, Wataru Yoshida, Stefano Ferri, Cinzia Dedi, Brian V. Jones, and Kazunori Ikebukuro
    Journal of Microbiological Methods (2014) 104, 94-100



  4. Electrochemical detection of pathogenic bacteria by using a glucose dehydrogenase fused zinc finger protein
    Jinhee Lee, Atsuro Tatsumi, Koichi Abe, Wataru Yoshida, Koji Sode and Kazunori Ikebukuro
    Analytical Methods (2014) 6, 4991-4994



  5. Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans
    by in silico maturation for biosensor development
    Nasa Savory†, Yayoi Takahashi†, Kaori Tsukakoshi, Hijiri Hasegawa, Madoka Takase, Koichi Abe, Wataru Yoshida, Stefano Ferri, Shizuko Kumazawa, Koji Sode and Kazunori Ikebukuro
    Biotechnology and Bioengineering. (2014). 111 (3), 454-461

    6. †: These authors contributed equally to this work.

  6. Vascular Endothelial Growth Factor (VEGF) Detection Using an Aptamer and PNA-Based Bound/Free Separation System
    Chifuku Mita†, Koichi Abe†, Takahiro Fukaya and Kazunori Ikebukuro
    Materials. (2014). 7 (2), 1046-1054

    7. †: These authors contributed equally to this work.


  7. Improving the Gene-Regulation Ability of Small RNAs by Scaffold Engineering in Escherichia coli
    Yuta Sakai, Koichi Abe, Saki Nakashima,Wataru Yoshida, Stefano Ferri,Koji Sode and Kazunori Ikebukuro
    ACS Synth. Biol. 3 (3) 152-162 (2014)



  8. Design of riboregulators for control of cyanobacterial (Synechocystis) protein expression
    Koichi Abe, Yuta Sakai, Saki Nakashima, Masataka Araki, Wataru Yoshida, Koji Sode and Kazunori Ikebukuro
    Biotechnology Letters. (2014). 36 (2), 287-294



  9. The development of an autonomous self-powered bio-sensing actuator
    Takuya Hanashi, Tomohiko Yamazaki, Hiroshi Tanaka, Kazunori Ikebukuro, Wakako Tsugawa and Koji Sode
    Sensors and Actuators B: Chemical (2014). 196 (2), 429-433



  10. Emerging techniques employed in aptamer-based diagnostic tests
    Wataru Yoshida, Koichi Abe and Kazunori Ikebukuro
    Expert Review of Molecular Diagnostics (2014). 14 (2), 143-151



  11. Electrochemical Biosensors Using Aptamers for Theranostics
    Koichi Abe, Wataru Yoshida and Kazunori Ikebukuro
    Biosensors Based on Aptamers and Enzymes (2014). 140, 183-202



  12. A green-light inducible lytic system for cyanobacterial cells
    Kotone Miyake, Koichi Abe, Stefano Ferri, Mitsuharu Nakajima, Mayumi Nakamura, Wataru Yoshida, Katsuhiro Kojima, Kazunori Ikebukuro and Koji Sode
    Biotechnology For Biofuels (2014). 7, 56



  13. Engineering of a green-light inducible gene expression system in Synechocystis sp PCC6803
    Koichi Abe, Kotone Miyake, Mayumi Nakamura, Katsuhiro Kojima, Stefano Ferri, Kazunori Ikebukuro and Koji Sode
    Microbial Biotechnology (2014). 7 (2), 177-183




2013

  1. Two-Dimensional Electrophoresis-Based Selection of Aptamers Against an Unidentified Protein in a Tissue Sample
    Nasa Savory, Shinichi Goto, Wataru Yoshida, Yutaka Unuma, Makoto Nakamura, Koichi Abe, Stefano Ferri, Kazunori Ikebukuro
    Analytical Letters. (2013). 46 (18), 2954-2963



  2. Screening of Peptide Ligands for Pyrroloquinoline Quinone Glucose Dehydrogenase Using Antagonistic Template-Based Biopanning
    Koichi Abe, Wataru Yoshida, Kotaro Terada, Yukiko Yagi-Ishii, Stefano Ferri, Kazunori Ikebukuro, Koji Sode
    International journal of molecular sciences. (2013). 14 (12), 23244-23256



  3. Fluorescent-Ligand-Mediated Screening of G-Quadruplex Structures Using a DNA Microarray.
    Keisuke Iida†, Takahiro Nakamura†, Wataru Yoshida†, Masayuki Tera, Kazuhiko Nakabayashi, Kenichiro Hata, Kazunori Ikebukuro, Dr. Kazuo Nagasawa
    Angew Chem Int Ed Engl. (2013) Epub ahead of print. doi: 10.1002/anie.201305366

    4. †: These authors contributed equally to this work.



  4. Aptamer selection based on g4-forming promoter region.
    Wataru Yoshida, Taiki Saito, Tomomi Yokoyama, Stefano Ferri, Kazunori Ikebukuro
    PLoS One. 2013;8(6):e65497.



  5. Automatic polymerase chain reaction product detection system for food safety monitoring using zinc finger protein fused to luciferase.
    Wataru Yoshida, Aki Kezuka, Yoshiyuki Murakami, Jinhee Lee, Koichi Abe, Hiroaki Motoki, Takafumi Matsuo, Nobuaki Shimura, Mamoru Noda, Shizunobu Igimi, Kazunori Ikebukuro
    Analytica Chimica Acta (2013) 801, 78-83



  6. In silico maturation of binding‐specificity of DNA aptamers against Proteus mirabilis
    Nasa Savory, Danielle Lednor, Kaori Tsukakoshi, Koichi Abe, Wataru Yoshida, Stefano Ferri, Brian V Jones, Kazunori Ikebukuro
    Biotechnology and Bioengineering. (2013). 110 (10), 2573-2580



  7. Detection of histone modification by chromatin immunoprecipitation combined zinc finger luciferase-based bioluminescence resonance energy transfer assay
    Wataru Yoshida, Aki Kezuka, Koich Abe, Hironobu Wakeda, Kazuhiko Nakabayashi, Kenichiro Hata, Kazunori Ikebukuro
    Analytical Chemistry 85 (13), 6485-6490



  8. Affinity improvement of a VEGF aptamer by in silico maturation for a sensitive VEGF-detection system.
    Yoshihiko Nonaka, Wataru Yoshida, Koichi Abe, Stefano Ferri, Holger Schulze, Till T. Bachmann, Kazunori Ikebukuro
    Analytical Chemistry. (2013). 85(2):1132-7



  9. An Optical Biosensing System Based on Interference-Enhanced Reflection with Aptameric Enzyme Subunits of Thrombin
    Wataru Yoshida and Kazunori Ikebukuro
    Analytical Letters. (2013). 46(2), 242-249



  10. Rapid cytotoxicity screening platform for amyloid inhibitors using a membrane-potential sensitive fluorescent probe
    Jihoon Kim, Yasuhiko Sasak, Wataru Yoshida, Natsuki Kobayashi, Anthony J. Veloso, Kagan Kerman, Kazunori Ikebukuro and Koji Sode
    Analytical Chemistry (2013). 85(1), 185-192




2012

  1. Development of a method to measure DNA methylation levels by using methyl CpG-binding protein and luciferase-fused zinc finger protein
    D Hiraoka, W Yoshida, K Abe, H Wakeda, K Hata, K Ikebukuro
    Analytical Chemistry (2012). 84(19):8259-64

      We have reported DNA methylation detecting system using zinc finger luciferase. This system can easily detect DNA methylation level, which would be biomarker for early　diagnostics of cancer.


  2. Detection of pathogenic bacteria by using zinc finger protein fused with firefly luciferase.
    Abe K, Kumagai T, Takahashi C, Kezuka A, Murakami Y, Osawa Y, Motoki H, Matsuo T, Horiuchi M, Sode K, Igimi S, Ikebukuro K.
    Analytical Chemistry. (2012). 84(18):8028-32.

      We have reported zinc finger luciferase for highly sensitive bacteria detection system. This system achieved detection of less than 10 copies of bacterial genome rapidly.


  3. Selection of DNA aptamers that recognize α-synuclein oligomers using a competitive screening method
    K Tsukakoshi, K Abe, K Sode, K Ikebukuro
    Analytical Chemistry. (2012). 84 (13), 5542-5547

      We have reported aptamers binding to amyloid soluble oligomer with high cell toxicity, which would be pathogen for neurodegenerative diseases. It would be a tool for diagnostics system for Alzheimer’s diseases and Parkinson’s diseases.

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