Watanabe Laboratory

*Iida, T., Shinoda, H., Yoshimura, M., Makino, A., Yoshimura, T., Nakazawa, M., Hayakawa, H., Kogo, Y., Miyauchi, K., Noda, T., Ban, t., Takeuchi, H., Toyoda, M., & *Watanabe, R.
"COWFISH2A+ as a Versatile and Accessible Platform for Digital Bioanalysis"

Cell Rep Phys Sci (2026)

Takezoe, N., Hanasaki, I., Watanabe, R., & Kazoe, Y.
"Simplified formation of ultrasmall lipid bilayer between parallel micrometer channels using Laplace pressure for assessing membrane instability under shear flow"

Biomicrofluidics (2026) 20, 054103

*Shinoda, H., Makino, A., Yoshimura, M., Iida, T., Yamazaki, D., Minagawa, N., Kogo, Y., Sano, T., Jinnai, M., Hishiki, T., Ohya, H., Nishimasu, H., & *Watanabe, R.
"Single-Molecule Characterization of CRISPR–Cas12a for Amplification-Free Genetic Testing"

Anal Chem (2026) 98(27):20145-20152

Sakamoto, S., Hiraide, H., Mizuno, T., Minoda, M., Nagano, N., Suzuki, M., Iwakura, N., Kashiro, A., Nara, S., Morizane, C., Hijioka, S., Honda, K., Kagami, Y., Watanabe, R., Urano, Y., & *Komatsu, T.
"Development of single-molecule protease activity analysis platform to elucidate disease-related alterations of circulating proteoform signatures"

Cell Biomaterials (2026) 100456

*Shinoda, H., Makino, A., Yoshimura, M., Minagawa, N., Iida, T., Nakano, M., Noda, T., Toyoda, M., & *Watanabe, R.
"Multicolor Amplification-Free RNA Detection with Cas13a and Cas13b"

Anal Chem (2026) 98(6):4705–4714

Furukawa, R., *Shinoda, H., *Tozaki, T., Makino, A., Yoshimura, M., Iida, T., Kawate, K., Kikuchi, M., Ishige, T., Takahashi, Y., Kato, T., Kakoi, H., Fukui, E., & *Watanabe, R.
"Direct Single-Molecule Detection of mRNA–LNP Drugs in Blood"

Anal Chem (2026) 98(1):756-765

*Ando, J., Murai, K., Michiyuki, T., Takahashi, I., Iida, T., Kogo, Y., Toyoda, M., Saito, Y., Maruyama, S., Kurihara, M., & *Watanabe, R.
"Digital SERS bioanalysis of single-enzyme biomarkers"

Proc Natl Acad Sci USA (2025) 122(36) e2510559122

Iida, T., Ando, J., Yoshimura, M., Makino, A., Nakano, M., Kogo, Y., Shinoda, H., Toyoda, M., Noda, T., & *Watanabe, R.
"Portable wide-field femtoliter-chamber imaging system for point-of-care digital bioanalysis"

iScience (2024) 110868

*Ando, J., Murai, K., Mori, M., Michiyuki, T., Iida, T., Makino, A., Shinoda, H., & *Watanabe, R.
"Exploring fluoropolymers for fabrication of femtoliter chamber arrays used in digital bioanalysis"

Sci Rep (2024) 14, 11442

Sakamoto, S., Hiraide, H., Minoda, M., Iwakura, N., Suzuki, M., Ando, J., Takahashi, C., Takahashi, I., Murai, K., Kagami, Y., Mizuno, T., Koike, T., Nara, S., Morizane, C., Hijioka, S., Kashiro, A., Honda, K., Watanabe, R., *Urano, Y., & *Komatsu, T.
"Identification of activity-based biomarkers for early-stage pancreatic tumors in blood using single-molecule enzyme activity screening"

Cell Rep Methods (2024) 100688

Ukegawa, T., *Komatsu, T., Minoda, M., Matsumoto, T., Iwasaka, T., Mizuno, T., Tachibana, R., Sakamoto, S., Hanaoka, K., Kusuhara, H., Honda, K., Watanabe, R., & *Urano, Y.
"Thioester-Based Coupled Fluorogenic Assays in Microdevice for the Detection of Single-Molecule Enzyme Activities of Esterases with Specified Substrate Recognition"

Adv Sci (2023) e2306559

Ando, J., & *Watanabe, R.
"Toward versatile digital bioanalysis"

Biomicrofluidics (2023) 17, 061303

Iida, T., Shinoda, H., & *Watanabe, R.
"SATORI: Amplification-free digital RNA detection method for the diagnosis of viral infections"

Biophys Physicobiol (2023) e200031

Ueda, T., *Shinoda, H., Makino, A., Yoshimura, M., Iida, T., & *Watanabe, R.
"Purification/Amplification-Free RNA Detection Platform for Rapid and Multiplex Diagnosis of Plant Viral Infections"

Anal Chem (2023) 95, 9680-9686

Kastian, RF., Baba, K., Kaewkascholkul, N., Sasaki, H., Watanabe, R., Toriyama, M., & *Inagaki, N.
"Dephosphorylation of neural wiring protein shootin1 by PP1 phosphatase regulates netrin-1-induced axon guidance"

J Biol Chem (2023) 299, 1046687

Nagano, N., Ichihashi, Y., Komatsu, T., Matsuzaki, H., Hata, K., Watanabe, T., Misawa, Y., Suzuki, M., Sakamoto, S., Kagami, Y., Kashiro, A., Takeuchi, K., Kanemitsu, Y., Ochiai, H., Watanabe, R., Honda, K., & *Urano, Y.
"Development of fluorogenic substrates for colorectal tumor-related neuropeptidases for activity-based diagnosis"

Chem Sci (2023) 14, 4495-4499

Iida, T., Ando, J., Shinoda, H., Makino, A., Yoshimura, M., Murai, K., Mori, M., Takaeuchi, H., Noda, T., Nishimasu, H., & *Watanabe, R.
"Compact wide-field femtoliter-chamber imaging system for high-speed and accurate digital bioanalysis"

Lab Chip (2023) 23, 684-691

Shinoda, H., Iida, T., Makino, A., Yoshimura, M., Ishikawa, J., Ando, J., Murai, K., Sugiyama, K., Muramoto, Y., Nakano, M., Kiga, K., Cui, L., Nureki, O., Takaeuchi, H., Noda, T., *Nishimasu, H., & *Watanabe, R.
"Automated amplification-free digital RNA detection platform for rapid and sensitive SARS-CoV-2 diagnosis"

Commun Biol (2022) 5, 473

Shinoda, H., Taguchi, Y., Nakagawa, R., Makino, A., Okazaki, S., Nakano, M., Muramoto, Y., Takahashi, C., Takahashi, I., Ando, J., Noda, T., *Nureki, O., *Nishimasu, H., & *Watanabe, R.
"Amplification-free RNA detection with CRISPR-Cas13"

Commun Biol (2021) 4, 476

Soga, N., Ota, A., Nakajima, K., Watanabe, R., Ueno, H., & *Noji, H.
"Monodisperse Liposomes with Femtoliter Volume Enable Quantitative Digital Bioassays of Membrane Transporters and Cell-Free Gene Expression"

ACS Nano (2020) 14, 11700-11711

Sakamoto, S., *Komatsu, T., *Watanabe, R., Zhang, Y., Inoue, T., Kawaguchi, M., Nakagawa, H., Ueno, T., Okusaka, T., Honda, K., *Noji, H., & *Urano, Y.
"Multiplexed single-molecule enzyme activity analysis for counting disease-related proteins in biological samples"

Sci Adv (2020) 6, eaay0888

*Watanabe, R., Komatsu, T., Sakamoto, S., Urano, Y., & *Noji, H.
"High-throughput single-molecule bioassay using micro-reactor arrays with a concentration gradient of target molecules"

Lab Chip (2018) 18, 2849-2853

Baba, K., Yoshida, W., Toriyama, M., Shimada, T., Manning, C., Saito, M., Kohno, K., Trimmer, J., Watanabe, R., & *Inagaki, N.
"Gradient-reading and mechano-effector machinery for netrin-1–induced axon guidance"

eLife (2018) 7, e34593

Moriizumi, Y., *Tabata, KV., Watanabe, R., Doura, T., Kamiya, M., Urano, Y., & *Noji, H.
"Hybrid cell reactor system from Escherichia coli protoplast cells and arrayed lipid bilayer chamber device"

Sci Rep (2018) 8, 11757

*Watanabe, R., Sakuragi, T., *Noji, H., & *Nagata, S.
"Single molecule analysis of phospholipid scrambling by TMEM16F"

Proc Natl Acad Sci USA (2018b) 115, 3066-3071

Abe, K., Katsuno, H., Toriyama, M., Baba, K., Mori, T., Hakoshima, T., Kanemura, Y., Watanabe, R., & *Inagaki, N.
"Grip and slip of L1-CAM on adhesive substrates direct growth cone haptotaxis"

Proc Natl Acad Sci USA (2018a) 115, 2764-2769

*Watanabe, R., Soga, N., Ohdate, S., & *Noji, H.
"Single molecule analysis of membrane transporter activity by using a microsystem"

Methods Mol Biol (2018) 1700, 321-330

*Watanabe, R., Genda, M., Kato-Yamada, Y., & *Noji, H.
"Essential role of the epsilon subunit for reversible chemo-mechanical coupling in F1-ATPase"

Biophys J (2018) 114, 178-187

Tamiya, Y., Watanabe, R., Noji, H., *Li, C., & *Komatsuzaki, T.
"Effects of non-equilibrium angle fluctuation on F1-ATPase kinetics induced by temperature increase"

Phys Chem Chem Phys (2018) 20, 1872-1880

*Watanabe, R., Soga, N., Hara, M., & *Noji, H.
"Arrayed water-in-oil droplet bilayers for membrane transport analysis"

Lab Chip (2016) 16, 3043-3048

*Watanabe, R., Soga, N., & *Noji, H.
"Novel nano-device to measure voltage-driven membrane transporter activity"

IEEE Trans Nanotechnol (2016) 15, 70-73

*McMiillan, D. G., Watanabe, R., Ueno, H., Cook, G. M., & *Noji, H.
"Biophysical Characterization of a Thermoalkaliphilic Molecular Motor with a High Stepping-Torque Gives Insight into Evolutionary ATP Synthase Adaptation"

J Biol Chem (2016) 291, 23965-23977

Li, C. B., Ueno, H., Watanabe, R., Noji, H., & *Komatsuzaki, T.
"ATP hydrolysis assists Phosphate release and promotes reaction ordering in F1-ATPase"

Nat Commun (2015) 6, 10223

Soga, N., *Watanabe, R., & *Noji, H.
"Attolitre-sized lipid bilayer chamber array for rapid detection of single transporters"

Sci Rep (2015) 5, 11025

Watanabe, R., Koyasu, K., You, H., Tanigawara, M., & *Noji, H.
"Torque transmission mechanism via DELSEED loop of F1-ATPase"

Biophys J (2015) 108, 1144-52

Yukawa, A., *Watanabe, R., & *Noji, H.
"Effects of an ATP analogue, adenosine 5'-[α-thio]triphosphate, on F1-ATPase rotary catalysis, torque generation, and inhibited intermediated formation"

Biochem Biophys Res Commun (2015) 458, 515-9

Yukawa, A., Iino, R., Watanabe, R., Hayashi, H., & *Noji, H.
"Key Chemical Factors of Arginine Finger Catalysis of F1-ATPase Clarified by an Unnatural Amino Acid Mutation"

Biochemistry (2015) 54, 472-80

*Watanabe, R., Soga, N., Yamanaka, T., & *Noji, H.
"High-throughput formation of lipid bilayer membrane arrays with an asymmetric lipid composition"

Sci Rep (2014) 4, 7076

Watanabe, R., Minagawa, Y., & *Noji, H.
"Thermodynamic analysis of F1-ATPase rotary catalysis using high-speed imaging"

Protein Sci (2014) 23, 1773-1779

*Watanabe, R., Soga, N., Fujita, D., Tabata, K. V., Yamauchi, L., Kim, SH., Asanuma, D., Kamiya, M., Urano, Y., *Suga, H., & *Noji, H.
"Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity"

Nat Commun (2014b) 5, 4519

Watanabe, R., Matsukage, Y., Yukawa, A., Tabata, K. V., & *Noji, H.
"Robustness of the Rotary Catalysis Mechanism of F1-ATPase"

J Biol Chem (2014) 289, 19331-19340

Arai, HC., Yukawa, A., Iwatate, RJ., Kamiya, M., Watanabe, R., Urano, Y., & *Noji, H.
"Torque generation mechanism of F1-ATPase upon NTP binding"

Biophys J (2014) 107, 156-64

Watanabe, R., & *Noji, H.
"Characterization of the temperature-sensitive reaction of F1-ATPase by using single-molecule manipulation"

Sci Rep (2014) 4, 4962

Watanabe, R., & *Noji, H.
"Timing of inorganic phosphate release modulates the catalytic activity of ATP-driven rotary motor protein"

Nat Commun (2014a) 5, 3486

Watanabe, R., Hayashi, K., Ueno, H., & *Noji, H.
"Catalysis-enhancement via rotary fluctuation of F1-ATPase"

Biophys J (2013) 105, 2385-91

Watanabe, R., Tabata, KV., Iino, R., Ueno, H., Iwamoto, M., Oiki, S., & *Noji, H.
"Biased Brownian stepping rotation of FoF1-ATP synthase driven by proton motive force"

Nat Commun (2013) 4, 1631

Tanigawara, M., Tabata, KV., Ito, Y., Ito, J., Watanabe, R., Ueno, H., Ikeguchi, M., & *Noji, H.
"Role of the DELSEED Loop in Torque Transmission of F1-ATPase"

Biophys J (2012) 103, 970-8

You, H., Iino, R., Watanabe, R., & *Noji, H.
"Winding single-molecule double-stranded DNA on a nanometer-sized reel"

Nucleic Acids Res (2012) 40, e151

Watanabe, R., Okuno, D., Sakakihara, S., Shimabukuro, K., Iino, R., Yoshida, M., & *Noji, H.
"Mechanical modulation of catalytic power on F1-ATPase"

Nat Chem Biol (2012) 1, 86-92

Watanabe, R., Iino, R., & *Noji, H.
"Phosphate release in F1-ATPase catalytic cycle follows ADP release."

Nat Chem Biol (2010) 6, 814-20

Enoki, S., Watanabe, R., Iino, R., & *Noji, H.
"Single-molecule study on the temperature-sensitive reaction of F1-ATPase with a hybrid F1 carrying a single beta(E190D)."

J Biol Chem (2009) 284, 23169-76

Watanabe, R., Iino, R., Shimabukuro, K., Yoshida, M., & *Noji, H.
"Temperature-sensitive reaction intermediate of F1-ATPase."

EMBO Rep (2008) 9, 84-90