Publication

Articles


    * corresponding author, † equal contribution

    2016
  1. ■Reversible Morphological Control of Tubulin-Encapsulating Giant Liposomes by Hydrostatic Pressure
    Masahito Hayashi, Masayoshi Nishiyama, Yuki Kazayama, Taro Toyota, Yoshie Harada, and Kingo Takiguchi*
    Langmuir 2016, 32 (15), pp 3794–3802, doi:10.1021/acs.langmuir.6b00799 (link).

  2. ■The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein–DNA complex formation
    Yong-Woon Han*, Hiroshi Sugiyama* and Yoshie Harada*
    Biomater. Sci 2016, Advance Article, doi:10.1039/C5BM00214A(link).

    2015
  3. ■Synergistic effect of ATP for RuvA-RuvB-Holiday junction DNA complex formation.
    Takuma Iwasa†, Yong-Woon Han†, Ryo Hiramatsu, Hiroaki Yokota, Kimiko Nakao, Ryuji Yokokawa, Teruo Ono and Yoshie Harad*
    Scientific Reports 5, Article number: 18177 (2015) doi:10.1038/srep18177(link).

  4. ■Suppression of Nonspecific Protein–Nanodiamond Adsorption Enabling Specific Targeting of Nanodiamonds to Biomolecules of Interest
    Shingo Sotoma, Ryuji Igarashi*, Jun Iimura, Yuta Kumiya, Hidehito Tochio, Yoshie Harada and Masahiro Shirakawa*
    Chemistry Letters 44(3), 354-356 (2015) doi:org/10.1246/cl.141036 (link).

  5. ■ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues Nucl.
    Ikumi Oomoto, Asuka Suzuki-Hirano, Hiroki Umeshima, Yong-Woon Han, Hiroyuki Yanagisawa, Peter Carlton, Yoshie Harada, Mineko Kengaku, Akimitsu Okamoto, Tomomi Shimogori and Dan Ohtan Wang*
    Acids Res. gkv614 first published online June 22, 2015, doi: 10.1093/nar/gkv614(link).

  6. ■Comprehensive and quantitative analysis for controlling the physical/chemical states and particle properties of nanodiamonds for biological applications.
    Shingo Sotoma, Kenichi Akagi, Saburo Hosokawa, Ryuji Igarashi, Hideto Tochio, Yoshie Harada and Masahiro Shirakawa*
    RSC Adv.5, 13818-13827 (2015), doi: 10.1039/C4RA16482B(link).

  7. ■Optically Detected Magnetic Resonance of Nanodiamonds In Vivo; Implementation of Selective Imaging and Fast Sampling.
    Yosuke Yoshinari*, Shigeyuki Mori, Ryuji Igarashi, Takuma Sugi, Hiroaki Yokota, Kazuhiro Ikeda, Hitoshi Sumiya, Ikue Mori, Hidehito Tochio,
    Yoshie Harada* and Masahiro Shirakawa
    Journal of Nanoscience and Nanotechnology 15,1014-1021(2015), doi: 10.1166/jnn.2015.9739(link).

    2014
  8. ■Quantitative In Vivo Fluorescence Cross-Correlation Analyses Highlight the Importance of Competitive Effects in the Regulation of Protein-Protein Interactions.
    Wakako Sadaie, Yoshie Harada, Michiyuki Matsuda and Kazuhiro Aoki*
    Molecular and Cellular Biology Sep 2014, 34, 17, 3272-3290, doi: 10.1128/MCB.00087-14(link).

  9. ■Effective Production of Fluorescent Nanodiamond Containing Negatively-Charged Nitro-gen-Vacancy Center by Ion Irradiation.
    Shingo Sotoma, Yosuke Yoshinari, Ryuji Igarashi, Akiyoshi Yamazaki, Shige H. Yoshimura, Hidesato Tochio, Masahiro Shirakawa
    and Yoshie Harada*
    Diamond and Related Materials 2014, 49, 33-38 doi:10.1016/j.diamond.2014.07.011(link).

  10. ■Real-time single-cell imaging of protein secretion.
    Yoshitaka Shirasaki, Mai Yamagishi, Nobutake Suzuki, Kazushi Izawa, Asahi Nakahara, Jun Mizuno, Shuichi Shoji, Toshio Heike, Yoshie Harada, Ryuta Nishikomori and Osamu Ohara*
    Scientific Reports2014 Apr 22, 4, 4736 doi: 10.1038/srep04736(link).

  11. ■Hard X-ray-induced optical luminescence via biomolecule-directed metal clusters.
    Yasuko Osakada*, Guillem Pratx, Conroy Sun, Masanori Sakamoto, Moiz Ahmad, Olga Volotskova, Qunxiang Ong, Toshiharu Teranishi,
    Yoshie Harada and Lei Xing* and Bianxiao Cui*
    Chemical Communications(Camb)2014, 50, 3549-3551 doi: 10.1039/c3cc48661c(link).

  12. ■Construction and Characterization of Cy3- or Cy5-Conjugated Hairpin Pyrrole/Imidazole Polyamides binding to DNA in the Nucleosome.
    Yong-Woon Han*, Yasuo Tsunaka, Hiroaki Yokota, Tomoko Matsumoto, Gengo Kashiwazaki, Hironobu Morinaga, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama* and Yoshie Harada*
    Biomaterials Science 2014, 2 ,297-307 doi: 10.1039/C3BM60202H (link).

    2013
  13. ■Observing the rotational diffusion of nanodiamonds with arbitrary nitrogen vacancy center configurations.
    Yohsuke Yoshinari*, Ziya Kalay* and Yoshie Harada*
    Phys. Rev. B, 88, 235206 (2013) [8 pages] doi: 10.1103/PhysRevB.88.235206 http://dx.doi.org/10.1039/c3bm60202h (link).

  14. ■In vivo fluorescent adenosine 5'-triphosphate (ATP) imaging of Drosophila melanogaster and Caenorhabditis elegans by using a genetically encoded fluorescent ATP biosensor optimized for low temperatures.
    Taiichi Tsuyama†, Jun-ichi Kishikawa†, Yong-Woon Han, Yoshie Harada, Asako Tsubouchi, Hiroyuki Noji, Akira Kakizuka, Ken Yokoyama, Tadashi Uemura, and Hiromi Imamura*
    Analytical Chemistry 85(16):7889-96 doi: 10.1021/ac4015325.(link).

  15. ■Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5'-GCGC-3'.
    Yong-Woon Han*, Gengo Kashiwazaki, Hironobu Morinaga, Tomoko Matsumoto, Kaori Hashiya, Toshikazu Bando, Yoshie Harada*, and Hiroshi Sugiyama*
    Bioorganic & Medicinal Chemistry 21(17):5436-41 doi: 10.1016/j.bmc.2013.06.005.(link).

  16. ■ParA-mediated plasmid partition driven by protein pattern self-organization.
    Ling Chin Hwang†, Anthony G Vecchiarelli†, Yong-Woon Han, Michiyo Mizuuchi, Yoshie Harada, Barbara E Funnell and Kiyoshi Mizuuchi*
    The EMBO Journal 32(9):1238-49 doi: 10.1038/emboj.2013.34. (link).

  17. ■Single-Molecule Imaging of the Oligomer Formation of the Nonhexameric Escherichia coli UvrD Helicase.
    Hiroaki Yokota*, Yuko Ayabe Chujo and Yoshie Harada
    Biophysical Journal, (2013) Feb 19;104(4):924–33 doi: 10.1016/j.bpj.2013.01.014.(link).

Articles


    * corresponding author, † equal contribution

    2012
  1. ■Real-time background-free selective imaging of fluorescent nanodiamonds in vivo.
    Ryuji Igarashi†, Yousuke Yoshinari†, Hiroaki Yokota†, Takuma Sugi, Fuminori Sugihara, Kazuhiro Ikeda, Hitoshi Sumiya, Shigenori Tsuji, Ikue Mori, Hidehito Tochio, Yoshie Harada* and Masahiro Shirakawa*
    Nano Letters 12(11):5726-32 doi: 10.1021/nl302979d.(link).

  2. ■Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.
    Yong-Woon Han*, Tomoko Matsumoto, Hiroaki Yokota, Gengo Kashiwazaki, Hironobu Morinaga, Kaori Hashiya, Toshikazu Bando,
    Yoshie Harada and Hiroshi Sugiyama
    Nucleic Acids Research 40(22):11510-7 doi: 10.1093/nar/gks897. (link).

  3. ■Direct Visualization of the Movement of a Single T7 RNA Polymerase and Transcription on a DNA Nanostructure.
    Masayuki Endo*, Koichi Tatsumi, Kosuke Terushima, Yosuke Katsuda, Kumi Hidaka, Yoshie Harada and Hiroshi Sugiyama*
    Angew Chem Int Ed Engl., 2012 Aug 27;51(35):8778-8782 doi:10.1002/anie.201201890 (link).

  4. ■Direct observation of strand passage by DNA-topoisomerase and its micrometre processivity.
    Katsunori Yogo, Taisaku Ogawa, Masahito Hayashi, Yoshie Harada, Takayuki Nishizaka and Kazuhiko Kinosita Jr.*
    PLoS One., 2012;7(4):e34920 (link).

  5. ■Intracellular temperature mapping with a fluorescent polymeric thermometer and fluorescence lifetime imaging microscopy.
    Kohki Okabe, Noriko Inada, Chie Gota, Yoshie Harada, Takashi Funatsu and Seiichi Uchiyama*
    Nature Communications, 28(3):705 doi: 10.1038/ncomms1714.(link).

    2011
  6. ■Facilitated Intracellular Transport of TrkA by an Interaction with Nerve Growth Factor.
    Mami Nomura, Takeharu Nagai, Yoshie Harada and Tomomi Tani*
    Developmental Neurobiology, 71(7):634-649 doi:10.1002/dneu.20879 (link).

  7. ■Real time monitoring of endogenous cytoplasmic mRNA using linear antisense 2′-O-methyl RNA probes in living cells.
    Kohki Okabe, Yoshie Harada, Junwei Zhang, Hisashi Tadakuma, Tokio Tani and Takashi Funatsu*
    Nucleic Acids Research, 39(4): e20 doi:10.1093/nar/gkq1196

  8. 2010
  9. ■Strain through the neck linker ensures processive runs: a DNA-kinesin hybrid nanomachine study.
    Yuya Miyazono, Masahito Hayashi, Peter Karagiannis, Yoshie Harada and Hisashi Tadakuma*
    EMBO Journal 29,1,93-106, doi: 10.1038/emboj.2009.319. (link)

    2009
  10. ■Single-molecule Visualization of Binding Modes of Helicase to DNA on PEGylated Surfaces.
    Hiroaki Yokota*, Yong-Woon Han, Jean-Francois Allemand, Xu.-Guang Xi, David Bensimon,Vincent Croquette,Yoshihiro Ito and Yoshie Harada
    Chemistry Letters 38,4,308【Abstract】

  11. ■Hydrophilic fluorescent nanogel thermometer for intracellular thermometry
    Chie Gota, Kohki Okabe, Takashi Funatsu, Yoshie Harada and Seiichi Uchiyama*
    J. Am. Chem. Soc. 131 (8), 2766–2767, doi: 10.1021/ja807714j.(link).

    2008
  12. ■Single-Cell Chemical Lysis Method for Analyses of Intracellular Molecules Using an Array of Picoliter-Scale Microwells.
    Yasuhiro Sasuga, Tomoyuki Iwasawa, Kayoko Terada, Yoshihiro Oe, Hiroyuki Sorimachi, Osamu Ohara* and Yoshie Harada
    Analytical Chemistry80,23,9141-9149, doi: 10.1021/ac8016423. 【Abstract】

  13. 2007
  14. ■Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide.
    Masahito Hayashi* and Yoshie Harada
    Nucleic Acids Research 35(19), e125, doi: 10.1093/nar/qkm529(link).

  15. ■Inhibition of Reversed Electron Transfer and Proton Transport in the Beef Heart Cytochrome bc1 Complex by Chemical Modification.
    Toshiaki Miki*, Masato Umeda and Yoshie Harada
    J. Biochem.141(3), 377-387, doi: 10.1093/jb/mvm042 (link).

  16. ■Visualization of RecA filaments and DNA by fluorescence microscopy.
    Taro Nishinaka*, Yuko Doi, Makiko Hashimoto, Reiko Hara, Takehiko Shibata, Yoshie Harada, Kazuhiko Kinosita Jr,
    Hiroyuki Noji and Eiji Yashima
    J. Biochem. 141(2), 147-156, doi: 10.1093/jb/mvm033 (link).

  17. 2006
    ■Direct observation of DNA rotation during branch migration of Holliday junction DNA by Escherichia coli RuvA-RuvB protein complex.
    Yong-Woon Han, Tomomi Tani, Masahito Hayashi, Takashi Hishida, Hiroshi Iwasaki, Hideo Shinagawa and Yoshie Harada*
    Proc. Natl. Acad. Sci. USA. 103 (31), 11544-11548, doi: 10.1073/pnas.0600753103 (link).

    ■Development of a microscopic platform for real-time monitoring of biomolecular interactions.
    Yasuhiro Sasuga, Tomomi Tani, Masahito Hayashi, Hisashi Yamakawa, Osamu Ohara* and Yoshie Harada
    Genome Res. 16, 132-139, doi: 10.1101/gr.4235806 (link).

Articles


    * corresponding author, † equal contribution

    2005
    ■Structure-function analysis of the three domains of RuvB DNA motor protein.
    Takayuki Ohnishi, Takashi Hishida, Yoshie Harada, Hiroshi Iwasaki and Hideo Shinagawa*
    J. Biol. Chem. 280, 30504-30510, doi: 10.1074/jbc.M502400200 (link).

    ■Trafficking of a ligand-receptor complex on the growth cones as an essential step for the uptake of nerve growth factor at the distal end of axon: a single-molecule analysis.
    Tomomi Tani*, Yoshikazu Miyamoto, Kazuhiro E. Fujimori, Takahisa Taguchi, Toshio Yanagida, Yasushi Sako and Yoshie Harada
    J. Neurosci. 25, 2181-2191, doi: 10.1523/JNEUROSCI.4570-04.2005 (link).

    2004
    ■Studies on biomolecules using single molecule imaging and manipulation techniques.
    Yoshie Harada*
    Sci. Tech. Adv. Mat. 5,709-713, doi: 10.1016/j.stam.2004.02.014 (link).

    2001
    ■Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase.
    Yoshie Harada*, Osamu Ohara, Akira Takatsuki, Hiroyasu Itoh, Nobuo Shimamoto and Kazuhiko Kinosita Jr.
    Nature 409, 113-115, doi:10.1038/35051126 (link).

    2000
    ■Stepping rotation of F1-ATPase visualized through angle-resolved single-fluorophore imaging.
    Kengo Adachi, Ryohei Yasuda, Hiroyuki Noji, Hiroyasu Itoh, Yoshie Harada, Masasuke Yoshida and Kazuhiko Kinosita Jr. *
    Proc. Natl. Acad.Sci. USA97, 7243-7247, doi: 10.1073/pnas.120174297 (link).

    1999
    ■Tying a molecular knot with optical tweezers.
    Yasuharu Arai, Ryohei Yasuda, Ken-ichirou Akashi, Yoshie Harada*, Hidetake Miyata, Kazuhiko Kinosita Jr and Hiroyasu Itoh
    Nature 399, 446-448, doi:10.1038/20894 (link).

    ■Single molecule imaging of RNA polymerase-DNA interactions in real time.
    Yoshie Harada*, Takashi Funatsu, Katsuhiko Murakami, Yoshikazu Nonoyama, Akira Ishihama and Toshio Yanagida
    Biophys. J. 76, 709-715, doi: 10.1016/S0006-3495(99)77237-1 (link).

    1997
    ■Imaging and nano-manipulation of single bio-molecules.
    Takashi Funatsu*, Yoshie Harada, Hideo Higuchi, Makio Tokunaga, Kiwamu Saito,Yoshiharu Ishii, Ron D. Vale and Toshio Yanagida
    Biophys. Chem.68, 63-72, doi: 10.1016/S0301-4622(97)00008-2 (link).

    ■Single molecular assay of the individual ATP turnovers by a myosin-GFP fusion protein expressed in vitro.
    Atsuko Hikikoshi Iwane*, Takashi Funatsu, Yoshie Harada, Makio Tokunaga, Osamu Ohara, Sayuri Morimoto and Toshio Yanagida
    FEBS Letters 407, 235-238, doi: 10.1016/S0014-5793(97)00359-1 (link).

    ■Coupling of protein surface hydrophobicity change to ATP hydrolysis by myosin motor domain.
    Makoto Suzuki*, Junji Shigematsu, Yoshifumi Fukunishi, Yoshie Harada, Toshio Yanagida and Takao Kodama
    Biophys. J. 72, 18-23 doi: 10.1016/S0006-3495(97)78643-0 (link).

    1996
    ■Direct inhibition of the actomyosin motility by local anesthetics in vitro.
    Yuri Tsuda*, Takashi Mashimo, Ikuto Yoshiya, Kuniyoshi Kaseda, Yoshie Harada and Toshio Yanagida
    Biophys. J.71, 2733-2741 doi: 10.1016/S0006-3495(96)79466-3 (link).

    ■Direct observation of single kinesin molecules moving along microtubules.
    Ron D. Vale*, Takashi Funatsu, Laura Romberg, Dan W. Pierce, Yoshie Harada and Toshio Yanagida
    Nature 380, 451-453 doi: 10.1038/380451a0 (link).

    ■Multiple and single-molecule analysis of the actomyosin motor by nanometer- piconewton manipulation with a microneedle: Unitaly steps and forces.
    Akihiko Ishijima*, Hiroaki Kojima, Hideo Higuchi, Yoshie Harada, Takashi Funatsu and Toshio Yanagida
    Biophys. J. 70, 383-400 doi: 10.1016/S0006-3495(96)79582-6 (link).
    1995
    ■ Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous solution
    Takashi Funatsu, Yoshie Harada, Makio Tokunaga, Kiwamu Saito and Toshio Yanagi Nature 374, 555-559 (1995) doi:10.1038/374555a0 (link).

    1994
    ■ Single-molecule analysis of the actomyosin motor using nano-manipulation.
    Akihiko Ishijima, Yoshie Harada, Hiroaki Kojima, Takashi Funatsu, Hideo Higuchi and Toshio Yanagida
    Biochem. Biophys. Res. Commun 99, 1057-1063 (1994) doi:10.1006/bbrc.1994.1336

    1993
    ■ Force-generating domain of myosin motor.
    Shinji Itakura, Hisashi Yamakawa, Yoko Yano Toyoshima, Akihiko Ishijima, Hiroaki Kojima, Yoshie Harada, Toshio Yanagida, Takeyuki Wakabayashi and Kazuo Sutoh*
    Biochem. Biophys. Res. Commun.196(3), 1504-1510 (1993) doi:10.1006/bbrc.1993.2422 (link).

    1990
    ■ Mechanochemical coupling in actomyosin energy transduction studied by in vitro movement assay.
    Yoshie Harada, Katsuhiko Sakurada, Toshiaki Aoki, David D. Thomas and Toshio Yanagida
    J. Mol. Biol. 216(1), 49-68 (1990) doi:10.1016/S0022-2836(05)80060-90 (link).

    1988
    ■ Direct observation of molecular motility by light microscopy.
    Yoshie Harada and Toshio Yanagida
    Cell Motility and the Cytoskeleton 10, 71-76 (1988) (link).

    1987
    ■ Sliding movement of single actin filaments on one-headed myosin filaments.
    Yoshie Harada, Akira Noguchi, Akiyoshi Kishino and Toshio Yanagida
    Nature326, 805-808 (1987)
    NEWS AND VIEWS Nature326, 746-747 (1987) (link).