Papers

2025

■Microalgae-Mediated Synthesis of Functionalized Gold Nanoparticles with High Photothermal Stability

Reham Samir Hamida, Shingo Sotoma, James Chen Yong Kah, Yoshie Harada, and Madoka Suzuki*

ACS Sustainable Chemistry & Engineering, Articles ASAP (Research Article)

Publication Date (Web):November 7, 2025

■Fluorescent Thermometers Based on Carbon Quantum Dots with Various Detection Modes for Intracellular Temperature Measurement. 

Yuki S Kato, Yukiho Shimazaki, Shunsuke Chuma, Kota Shiraya, Yurina Nakane, Takuma Sugi, Kohki Okabe, Yoshie Harada, Shingo Sotoma

Nano letters 2025年3月25日

■Evaluation of the microenvironment formed by interferon-β 

Mai Yamagishi, Yutaka Hori, Nobutake Suzuki, Yu Peng, Yoshie Harada, Takashi Funatsu, Osamu Ohara, Yoshitaka Shirasaki

Frontiers in Chemical Biology 3 2025年1月21日

2024

■Organ-Specific Gene Expression Control Using DNA Origami-Based Nanodevices 

Yuxiang Liu、Ruixuan Wang、Qimingxing Chen、Yan Chang、Qi Chen、Kodai Fukumoto、Bingxun Wang、 Jianchen Yu、Changfeng Luo、Jiayuan Ma、Xiaoxia Chen、Yuko Murayama、Kenichi Umeda、Noriyuki Kodera、 Yoshie Harada、Shun-ichi Sekine、Jianfeng Li、Hisashi Tadakuma

Nano Letters 24(27) 8410-8417 2024年6月26日  

■Implication of thermal signaling in neuronal differentiation revealed by manipulation and measurement of intracellular temperature. 

Shunsuke Chuma, Kazuyuki Kiyosue, Taishu Akiyama, Masaki Kinoshita, Yukiho Shimazaki, Seiichi Uchiyama, Shingo Sotoma, Kohki Okabe, Yoshie Harada

Nature communications 15(1) 3473-3473 2024年5月9日

2023

■Evaluating the effect of two-dimensional molecular layout on DNA origami-based transporters 

Kodai Fukumoto, Yuya Miyazono, Takuya Ueda, Yoshie Harada, Hisashi Tadakuma

Nanoscale Advances 5(9) 2590-2601 2023年4月19日

■Highly Dispersed 3C Silicon Carbide Nanoparticles with a Polydopamine/Polyglycerol Shell for Versatile Functionalization 

Shingo Sotoma, Hiroshi Abe, Yohei Miyanoiri, Takeshi Ohshima, Yoshie Harada

ACS Applied Materials & Interfaces 15 21413-21424 2023年4月18日

2022

■Heat-hypersensitive mutants of ryanodine receptor type 1 revealed by microscopic heating

Kotaro Oyama†*, Vadim Zeeb†*, Toshiko Yamazawa†, Nagomi Kurebayashi, Fuyu Kobirumaki-Shimozawa, Takashi Murayama, Hideto Oyamada, Satoru Noguchi, Takayoshi Inoue, Yukiko U. Inoue, Ichizo Nishino, Yoshie Harada, Norio Fukuda*, Shin’ichi Ishiwata, Madoka Suzuki*

Proceedings of the National Academy of Sciences of the United States of America, 119(32), e2201286119 (2022). 

■Modulation of local cellular activities using a photothermal dye-based subcellular-sized heat spot

Ferdinandus, Madoka Suzuki, Cong Quang Vu, Yoshie Harada, Satya Ranjan Sarker, Shin’ichi Ishiwata, Tetsuya Kitaguchi, and Satoshi Arai

ACS Nano , 16, 6, 9004–9018（2022). 

■Opto-thermal technologies for microscopic analysis of cellular temperature-sensing systems

Kotaro Oyama†*, Shuya Ishii†, and Madoka Suzuki*

Biophysical Reviews, 14, 41-5 (2022). 

■Nanaomycin E inhibits NLRP3 inflammasome activation by preventing mitochondrial dysfunction

Yudai Matsui, Naoki Takemura, Yoshitaka Shirasaki, Michihiro Takahama, Yoshihiko Noguchi, Kenta Ikoma, Yixi Pan, Shuhei Nishida, Manabu Taura, Akiyoshi Nakayama, Takashi Funatsu, Takuma Misawa, Yoshie Harada, Toshiaki Sunazuka, Tatsuya Saitoh

International Immunology, dxac028 

■Cell-autonomous control of intracellular temperature by unsaturation of phospholipid acy1 chains

Akira Murakami,Kohjiro Nagao,Reiko Sakaguchi,Keisuke Kida,Yuji Hara,Yasuo Mori,Kohki Okabe,Yoshie Harada,Masato Umeda

Cell Report (March 15, 2022) 

■Quantum nanodiamonds for sensing of biological quantities: Angle, temperature, and thermal conductivity 

Shingo Sotoma, Hirotaka Okita, Shunsuke Chuma, Yoshie Harada

Biophysics and Physicobiology 19 n/a-n/a 2022年

2021

■Microscopic temperature control reveals cooperative regulation of actin–myosin interaction by drebrin E

Hiroaki Kubota†, Hiroyuki Ogawa†, Makito Miyazaki†, Shuya Ishii, Kotaro Oyama, Yuki Kawamura, Shin’ichi Ishiwata*, and Madoka Suzuki*

Nano Letters, 21, 9526-9533 (2021). 

■Opportunities for hybrid diamond nanosensors targeting photothermal applications in biological systems

Madoka Suzuki*, and Taras Plakhotnik*

Applied Physics Letters, 119, 190502 (2021). 

■Pressure-induced changes on the morphology and gene expression in mammalian cells.

Kazuko Okamoto , Tomonobu M. Watanabe, Masanobu Horie, Masayoshi Nishiyama, Yoshie Harada, and Hideaki Fujita

Biology Open, 10, bio058544 (2021). 

■In situ measurement of intracellular thermal conductivity using heater-thermometer hybrid diamond nanosensors.

Shingo Sotoma, Chongxia Zhong (co-first), James Chen Yong Kah, Hayato Yamashita, Taras Plakhotnik*, Yoshie Harada* and Madoka Suzuki*

Science Advances, 7, eabd7888 (2021). 

2020

■Tracking the 3D Rotational Dynamics in Nanoscopic Biological Systems.

Ryuji Igarashi*, Takuma Sugi, Shingo Sotoma, Takuya Genjo, Yuta Kumiya, Erik Walinda, Hiroshi Ueno, Kazuhiro Ikeda, Hitoshi Sumiya, Hidehito Tochio, Yohsuke Yoshinari, Yoshie Harada* and Masahiro Shirakawa*

Journal of the American Chemical Society, 142, 7542-7554 (2020). 

■In situ measurement of intracellular thermal conductivity using heater-thermometer hybrid diamond nanosensor.

Shingo Sotoma, Chongxia Zhong, James Chen Yong Kah, Hayato Yamashita, Taras Plakhotnik*, Yoshie Harada* and Madoka Suzuki*

bioRxiv, https://doi.org/10.1101/2020.06.03.126789. 

■The challenge of intracellular temperature.

Madoka Suzuki* and Taras Plakhotnik

Biophysical Reviews, 142, 593-600 (2020). 

2019

■Multifunctional temozolomide-loaded lipid superparamagnetic nanovectors: Dual targeting and disintegration of glioblastoma spheroids by synergic chemotherapy and hyperthermia treatment.

Attilio Marino, Alice Camponovo, Andrea degl’Innocenti, Martina Bartolucci, Christos Tapeinos, Chiara Martinelli, Daniele de Pasquale, Francesca Santoro, Valentina Mollo, Satoshi Arai, Madoka Suzuki, Yoshie Harada, Andrea Petretto and Gianni Ciofani

Nanoscale, 11, 21227-21248 (2019)

doi: 10.1039/C9NR07976A.

■Polydopamine Coating as a Scaffold for Ring-Opening Chemistry To Functionalize Gold Nanoparticles.

Shingo Sotoma* and Yoshie Harada

Langmuir. 35, 8357-8362 (2019).

doi: 10.1021/acs.langmuir.9b00762. (link) 

■HCV IRES captures an actively translating 80S ribosome.

Takeshi Yokoyama, Kodai Machida†, Wakana Iwasaki†, Tomoaki Shigeta, Madoka Nishimoto, Mari Takahashi, Ayako Sakamoto, Mayumi Yonemochi, Yoshie Harada, Hideki Shigematsu, Mikako Shirouzu, Hisashi Tadakuma*, Hiroaki Imataka* and Takuhiro Ito*

Molecular Cell. 74(6), 1205-1214 (2019).

doi: 10.1016/j.molcel.2019.04.022. 

2018

■Magnetic Field Imaging of Superparamagnetic Particles Using High-Density, Perfectly Oriented NV Centers in Diamond CVD Film.

Yuji Hatano*, Takeharu Sekiguchi, Takayuki Iwasaki, Mutsuko Hatano and Yoshie Harada

Physica Status Solidi (a), 215(22), pssa.201800254 (2018).

doi: 10.1002/pssa.201800254  

■Fluorescent nanodiamonds as a robust temperature sensor inside a single cell.

Takeharu Sekiguchi, Shingo Sotoma† and Yoshie Harada*

Biophysics and Physicobiology, 15, 229-234 (2018),

doi: 10.2142/biophysico.15.0_229 

■Construction of integrated gene logic-chip.

Takeya Masubuchi, Masayuki Endo*, Ryo Iizuka, Ayaka Iguchi, Dong Hyun Yoon, Tetsushi Sekiguchi, Hao Qi, Ryosuke Iinuma, Yuya Miyazono, Shuichi Shoji, Takashi Funatsu, Hiroshi Sugiyama*, Yoshie Harada, Takuya Ueda* and Hisashi Tadakuma*

Nature Nanotechnology. 13(10), 933-940 (2018).

doi: 10.1038/s41565-018-0202-3. 

■Enrichment of ODMR-active nitrogen-vacancy centres in five-nanometre-sized detonation-synthesized nanodiamonds: Nanoprobes for temperature, angle and position.

Shingo Sotoma, Daiki Terada, Takuya F. Segawa, Ryuji Igarashi*, Yoshie Harada* and Masahiro Shirakawa*

Scientific Reports, 8(1), pp 5463 (2018),

doi: 10.1038/s41598-018-23635-5 

■Commonly stabilized cytochromes c from deep-sea Shewanella and Pseudomonas.

Sotaro Fujii, Misa Masanari-Fujii, Shinya Kobayashi, Chiaki Kato, Masayoshi Nishiyama, Yoshie Harada, Satoshi Wakai and Yoshihiro Sambongi*

Biosci Biotechnol Biochem., 82(5), pp 792-799 (2018),

doi: 10.1080/09168451.2018.1448255 

■Morphological Control of Microtubule-Encapsulating Giant Vesicles by Changing Hydrostatic Pressure.

Kingo Takiguchi*, Masahito Hayashi, Yuki Kazayama, Taro Toyota, Yoshie Harada and Masayoshi Nishiyama

Biol Pharm Bull., 41(3), pp 288-293 (2018),

doi: 10.1248/bpb.b17-00366  

2017

■Live Cell Imaging Using Photoswitchable Diarylethene-Doped Fluorescent Polymer Dots.

Yasuko Osakada*, Tuyoshi Fukaminato*, Yuma Ichinose, Mamoru Fujitsuka*, Yoshie Harada and Tetsuro Majima*

Chem Asian J., 12(20), pp 2660-2665 (2017),

doi: 10.1002/asia.201701038 

2016

■Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein.

Seiichiro Kizaki, Tingting Zou, Yue Li, Yong‐Woon Han, Yuki Suzuki, Yoshie Harada and Hiroshi Sugiyama*

Chemistry, 22(46), pp 16598-16601 (2016),

doi: 10.1002/chem.201602435 

■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 , 32 (15), pp 3794–3802 (2016), doi:10.1021/acs.langmuir.6b00799 

■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 , Advance Article (2016), doi:10.1039/C5BM00214A 

2015

■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 Harada*

Scientific Reports , 5, 18177 (2015), doi:10.1038/srep18177 

■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  

■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*

Nucleic Acids Res., 43(19), e126 (2015), doi:10.1093/nar/gkv614  

■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 

■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 

2014

■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 , 34(17), 3272-3290 (2014), doi:10.1128/MCB.00087-14 

■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*  

■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 Reports, 4, 4736 (2014), doi:10.1038/srep04736 

■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), 50, 3549-3551 (2014), doi:10.1039/c3cc48661c 

■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 , 2 ,297-307 (2014), doi:10.1039/C3BM60202H 

2013

■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), doi:10.1103/PhysRevB.88.235206 http://dx.doi.org/10.1039/c3bm60202h 

■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 (2013), doi:10.1021/ac4015325 

■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 (2013), doi:10.1016/j.bmc.2013.06.005

■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 (2013), doi:10.1038/emboj.2013.34.

■Single-Molecule Imaging of the Oligomer Formation of the Nonhexameric Escherichia coli UvrD Helicase.

Hiroaki Yokota*, Yuko Ayabe Chujo and Yoshie Harada

Biophysical Journal, 104(4), 924–33 (2013), doi:10.1016/j.bpj.2013.01.014. 

2012

■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 (2012), doi:10.1021/nl302979d

■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 (2012), doi:10.1093/nar/gks897

■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., 51(35), 8778-8782 (2012), doi:10.1002/anie.201201890 (link).  

■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., 7(4), e34920 (2012), doi:10.1371/journal.pone.0034920

■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 (2012), doi:10.1038/ncomms1714

2011

■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 (2011), doi:10.1002/dneu.20879 (link). 

■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 (2011), doi:10.1093/nar/gkq1196 

2010

■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 (2010), doi:10.1038/emboj.2009.319. (link) 

2009

■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), 308-309 (2009), doi:10.1246/cl.2009.308 

■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 (2009), doi:10.1021/ja807714j   

2008

■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 Chemistry, 80(23), 9141-9149 (2008), doi:10.1021/ac8016423    

2007

■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    

■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   

■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    

■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    

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 \

■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 

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 

■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 

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 

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  

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   

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    

■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     

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   

■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 

■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  

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  

■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 

■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 

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  

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 

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 

1988

■  Direct observation of molecular motility by light microscopy.

Yoshie Harada and Toshio Yanagida

Cell Motility and the Cytoskeleton 10, 71-76 (1988) 

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)  

Review, Books, etc.

原田 慶恵, 石渡 信一
『1分子生物学』
化学同人 第8章 DNA結合タンパク質 102-112, 第15章 1分子イメージングのプローブ 195-204 (2014)

横田 浩章、原田 慶恵
『光ピンセット. 生命科学のための機器分析実験ハンドブック (実験医学別冊) 第3章顕微解析4』
羊土社, 99-104 (2007)

原田 慶恵
『DNAモーター. 非侵襲・可視化技術ハンドブック─ナノ・バイオ・医療から情報システムまで─』
第7章1分子可視化と操作 第5節 （エヌ・ティー・エス）, 738-747 (2007)

原田 慶恵
『一分子蛍光法』
化学と生物(日本農芸化学会 会誌) 45(5), 340-346 (2007)

原田 慶恵
『モーター. 生物物理学ハンドブック』
朝倉書店 6.5, 353-356 (2007)

原田 慶恵
『一分子観察，蛍光顕微鏡，蛍光色素，光ピンセット』
ナノバイオ大辞典 (テクノシステム), 56-58, 147-148, 149-151, 449-450 (2007)

原田 慶恵、横田 浩章
『バイオマシン・生物分子モーター』
細胞工学 （秀潤社）25(8), 878-883 (2006)

谷 知己、原田 慶恵
『神経細胞の軸索伸長反応を引き起こす神経成長因子のふるまい：その１分子解析』
生物物理45(6),320-323 (2005)

原田 慶恵
『1個の生体分子の運動を観る』
総研大ジャーナル, 8, 13-15(2005)

原田 慶恵
『細胞運動解析法. 細胞生物学実験法 Ⅲ 細胞解析法-Ⅳ』
大熊勝治 編、廣川書店 94-105 (2005)

原田 慶恵
『ビーズを用いた生体分子間相互作用解析技術の開発』
BIO INDUSTRY（ シーエムシー出版）22(10), 66-74 (2005)

Yoshie Harada
『Microbead Arrays』
The Japan Journal, September,27(2005)

原田 慶恵
『1分子イメージング. ソフトナノテクノロジー－バイオマテリアル革命－』
田中順三，下村政嗣 監修 第5編 第4章. （シーエムシー出版） 314-324 (2005)

貴家 康尋, 原田 慶恵
『分子イメージングによる分子間相互作用解析法の開発』
バイオテクノロジージャーナル　5(3), 303-305 (2005)

谷 知己, 原田 慶恵
『蛍光1分子イメージング』
蛋白質 核酸 酵素　49(11), 1647-1651 (2004)

貴家 康尋, 原田 慶恵
『生体分子機能を観察できる光学顕微鏡システムの開発』
月刊薬事　46(5), 149-154 (2004)

原田 慶恵
『熱ゆらぎを利用して動く？ ─ モータータンパク質の新しい運動モデル─』
化学58(11), 48-49 (2003)

原田 慶恵
『生物学実験法講座「１分子生理学」DNAモーターの１分子機能解析』日生誌65(7,8), 225-231 (2003)

原田 慶恵
『RNAポリメラーゼによるDNAの回転をみる(イメージングで解き明かす生命機能 第3回)』実験医学 21(13), 1800-1801 (2003)

原田 慶恵
『1分子の動きを見て生体分子の機能を探る』
光技術コンタクト 40(12), 19-26 (2002)

原田 慶恵
『RNAポリメラーゼはDNAを回転させて転写する』
化学と生物 39(7), 420-421 (2001)

原田 慶恵
『RNAポリメラーゼによるDNAの回転の可視化』
細胞工学 20(5), 636-637 (2001)

原田 慶恵
『エバネッセント波を用いたポリメラーゼ１分子相互作用のイメージング』
精密工学会誌 65, 205-208(1999)

原田 慶恵、木下 一彦
『RNA分子に結び目をつくる』
遺伝 53(10), 10-12 (1999)

原田　慶恵、船津　高志
『蛍光顕微鏡で単一分子を見る方法』
細胞工学 17(4), 626-633(1998)