Laboratory of Nanobiology

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Professor
Yoshie HARADA
mail harada.yoshie.4r@kyoto-u.ac.jp
Associate Professor
Madoka Suzuki
mail suzu_mado@protein.osaka-u.ac.jp
Assistant Professor
Hisashi Tadakuma
mail tadakuma@protein.osaka-u.ac.jp
Fields

Signal Transduction Biology

Belong

Institute for Protein Research

Location

Suita

Research Theme

Biomolecules are constantly perturbed by the surrounding environment. Thus, in contrast to the artificial system, biomolecules harness thermal fluctuation, achieving high energy efficiency. For example, without using chemical energy such as ATP, RNA polymerases diffuse one-dimensionally on DNA to search the promoter sequence. Our ultimate goal is to elucidate the sophisticated molecular mechanism of biomolecules. Imaging and manipulating individual molecules are powerful technique. We have developed novel technology such as single-molecule imaging and have visualized the motion and/or structural change of biomolecules at single molecule level, revealing some secrets of the nature. Our current topics are developing novel tools to investigate the thermal-biology and genetics.

Quantum imaging using fluoresccent nano-diamonds

Conventional fluorescent probes have intrinsic problems such as 1) photo-bleaching, blinking, 2) hindered by auto-fluorescence of the biological sample, 3) low resolution of angle variation and rotational motion. To resolve such problems, we have developed fluorescent nano-diamonds (FNDs). Upon 560 nm visible light excitation, Nitrogen-Vacancy Center (NVC) of the diamond emit fluorescent signal. In contrast to the conventional fluorescent probes, fluorescence from NVC is not photo-bleached or blinked, allowing us prolonged observation of biological samples. Furthermore, using optically detected magnetic resonance (ODMR) technique, we have succeed in distinguishing FNDs's fluorescent signal from that of auto-fluorescence in the C. elegans. We are currently developing the high sensitive measurement methods of rotational motion.

Thermal-biology

Temperature is the fundamental parameter of biology, affecting metabolism and biorhythm. Although past efforts, local temperature fluctuation inside the individual cell is enigmatic. We have developed thermometer using high-molecular-weight polymer and FNDs. With quantitative measurements, we tackle the biological relevance of the thermal fluctuation. With proofing the concept of "Temperature-signaling", we aim to establish the "Thermal-biology".

Epigenetic imaging

The maximum fluorescent signal concentration of conventional single molecule technique such as TIRF microscopy is about 50 nM, limiting the versatility of their application. To overcome these issue, we have developed new techniques using zero-mode waveguides (ZMWs), which allows us to observe single molecule interaction under micro-M fluorescent signals. We applied ZMWs to elucidate the molecular mechanism of gene expression control.

0Fluorescent nano-diamonds

1Intracellular temperature imaging

2Zero-mode waveguides (ZMWs)

Bibliography

Sotoma, S. et al. Enrichment of ODMR-active nitrogen-vacancy centres in five-nanometre-sized detonation-synthesized nanodiamonds: Nanoprobes for temperature, angle and position. Scientific reports 8 (1) , 5463 - 3802 (2018)

Hou, Y. et al. Ca<sup>2+</sup>-associated triphasic pH changes in mitochondria during brown adipocyte activation. Molecular metabolism 6(8) , 797 - 808 (2017)

Marino, A. et al. Gold Nanoshell-Mediated Remote Myotube Activation. ACS nano 11(3) , 2494 - 2508 (2017)

Shimomura, T. et al. A Beetle Flight Muscle Displays Leg Muscle Microstructure. Biophysical journal 111(6) , 1295 - 1303 (2016)

Suzuki, M. et al. The 10(5) gap issue between calculation and measurement in single-cell thermometry. Nature Methods 12 , 802 - 803 (2015)

Iwasa, T. et al. Synergistic effect of ATP for RuvA-RuvB-Holiday junction DNA complex formation. Scientific Reports 5 , 18177 - (2015)

Yao, C. et al. Single-Molecule Analysis of the Target Cleavage Reaction by the Drosophila RNAi Enzyme Complex. Molecular Cell 59 , 125 - 132 (2015)

Contact

Osaka Univ. IPR Bldg. 6F
3-2 Yamadaoka, Suita-shi
Osaka, 565-0871

Tel: +81-6-6879-8627
Fax: +81-6-6879-8629
E-mail: yharada(at)protein.osaka-u.ac.jp

https://www.ccc.osaka-u.ac.jp/protein/nanobiology/

https://www.ccc.osaka-u.ac.jp/protein/nanobiology/