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Research Institute of Biomolecule Metrology Co., Ltd.
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High-Speed Atomic Force Microscope - Ando model -
Dynamic Visualization of nano-scale world
HS-AFM*1.0 - Ando model - is the High-Speed Atomic Force Microscope which was developed based on the research achievements accomplished by Prof. Ando in Kanazawa University. This is the world’s first instrument that broke through the weak point of conventional AFM “low-speed”, and realized the video rate scan. The high-speed scan enables us to capture swinging molecules in solution clearly without blurring. Consequently, the strong anchoring of a sample to the substrate is unnecessary and a dynamic observation is achieved without losing the activities of soft biomolecules.
*The HS-AFM was developed by Prof. Ando (Kanazawa Univ.) and commercialized by RIBM.
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walking myosin V(realtime) |
bacteriorhodopsinin response to light(x10) |
rotorless F1-ATPase(realtime) |
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Contents
- High-speed scanner
- Ultra small and soft cantilever with high resonance frequency
- High-speed and stable feedback control
- Movie Gallery
- Image Gallery
- Published Papers
- Reference List
- Standard System Specifications
- Options
High-speed scanner
- Active dumping and counter balance can suppress mechanical vibration.
- Compact and reliable design
In addition to Standard high-speed scanner, specialized scanners:
Injection type, Ultra high-speed, Wide scanner are optionally available.
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Ultra small and soft cantilever with high resonance frequency
- Cantilever for HS-AFM can realize the observation of any soft samples such as a protein.
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Ultra small cantilever Resonance frequency ：1500 kHz （in air ） Force constant ：0.1 N/m Tip radius ：< 10 nm |
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High-speed and stable feedback control
- Clear and fine images of surface structures can be obtained by using the high-speed scanning.
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Movie Gallery
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IgG antibodies Dynamic Imaging of the IgG antibodies |
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Plasmid DNA Dynamic Imaging of the Plasmid DNA on the mica-substrate |
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Dynamic Imaging of the DNA digestion process by DNase (DNA : λDNA , DNase： endonuclease) |
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DNA digestion by Nuclease Dynamic Imaging of the DNA digestion process (DNA : pUC18 plasmid DNA , DNA digestion： Bal31 nuclease) |
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DNA Polymerase reaction Dynamic Imaging of the DNA elongation process with Phi29 in liquid (DNA：λDNA , DNA polymerase： Phi29) |
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Point defect in streptavidin 2D crystal Dynamic Imaging of the diffusion on point defects in the crystal |
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Image Gallery
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IgG antibody150nm * 150nmStandard high-speed scanner |
plasmid DNA250nm * 250nmStandard high-speed scanner |
myosinⅡ500nm * 500nmStandard high-speed scanner |
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streptavidin90nm * 90nm(*1) |
GroEL90nm * 90nm(*1) |
bacteriorhodopsin40nm * 40nm(*1) |
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lipid membrane3500nm * 3500nmWide scanner |
350nm polystyrene beads3000nm * 3000nmWide scanner |
350nm polystyrene beads900nm * 900nmWide scanner |
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E.coli3000nm * 3000nmWide scanner |
(*1) Image courtesy of Prof. Ando (Kanazawa Univ.)
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Published Papers
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Video imaging of walking myosin V 
a. and b. : Direct observation of walking myosin V. a. 130 nm x 65 nm, b. 125 nm x 62.5 nm. c. Scheme of myosin V walking. Myosin V is a two-headed processive motor and functions as cargo transporter in cells. The dynamic behaviors of myosin V translocating along actin filaments were visualized by HS-AFM. The high-resolution movies provided not only ‘visual evidence’ for previously speculated or demonstrated molecular behaviors, including lever-arm swing, but also more detailed behaviors of the molecules, leading to a comprehensive understanding of the motor mechanism. This direct and dynamic high-resolution visualization is a powerful new approach to studying the structure and dynamics of biomolecules in action. N. Kodera et al. Nature 468, 72 (2010). Kanazawa University |
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Dynamic molecular processes in photoactivated bacteriorhodopsin 
Structural change of bacteriorhodopsin (bR), which is known as light-driven proton pump, has been visualized by HS-AFM. The purple membrane composed of D96N bR mutant, which has a longer photocycle (10’s) than that of the wild type, was adsorbed on mica substrate. Upon illumination with green light (532nm), bR drastically changes its structure and returns to the unphotolysed state in a few seconds after light-off. This outcome is reproducible in repeated dark illumination cycles. M. Shibata et al. Nature Nanotech. 5, 208 (2010). Kanazawa University |
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Point defect in streptavidin 2D crystal 
a. Dynamic observation of the diffusion of point defects. b. Scheme of streptavidin arrays in a C222 crystal. Unit lattice vectors are indicated by red arrows. The diffusion of point defects in the crystals was successfully observed by HS-AFM. In Figure a, the trajectory tracking of two monovacancy defects was obviously anisotropic with respect to the two axes of the crystalline lattice. As a result, the diffusion constant D along each axis could be established to be Da = 20.5 nm2/s and Db = 48.8 nm2/s. This means, HS-AFM is useful for studying various dynamic process, such as the crystal growth and disintegration processes. D. Yamamoto et al. Nanotechnology 19, 384009 (2008). Kanazawa University |
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Reference List
| The authors | Title | Journal |
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| I. Casuso, N. Kodera, C. Le Grimellec, T. Ando and S. Scheuring | Contact-mode high-resolution high-speed atomic force microscopy movies of the purple membrane | Biophys., J. 97, 1354 (2009). |
| J. L. Gilmore, Y. Suzuki, G. Tamulaitis, V. Siksnys, K. Takeyasu and Y. L. Lyubchenko | Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy | Biochemistry, 48, 10492 (2009). |
| M.-C. Giocondi, D. Yamamoto, E. Lesniewska, P.-E. Milhiet, T. Ando, and C. L. Grimellec | Surface topography of membrane domains | BBA-Biomembranes, 1978, 703 (2010). |
| Y. L. Lyubchenko, L. S. Shlyakhtenko and A. A. Gall | Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: silatrane surface chemistry | Methods mol. Biol., 543, 337 (2009). |
| Y. L. Lyubchenko, L. S. Shlyakhtenko | AFM for analysis of structure and dynamics of DNA and protein-DNA complexes | Methods mol. Biol., 47, 206 (2009) |
| L. S. Shlyakhtenko, A. Y. Lushnikov, Y. L. Lyubchenko | Dynamics of Nucleosomes Revealed by Time-Lapse Atomic Force Microscopy | Biochemistry,48, 7842 (2009) |
| N. Kodera, D. Yamamoto, R. Ishikawa and T. Ando | Video imaging of walking myosin V by high-speed atomic force microscopy | Nature, 468, 72 (2010). |
| S. Sugimoto, K. Yamanaka, S. Nishikori, A. Miyagi, T. Ando and T. Ogura | AAA Chaperone ClpX Regulates Dynamics of Prokaryotic Cytoskeletal Protein FtsZ | J. Biol. Chem., 285, 6648 (2010). |
| D. Yamamoto, N. Nagura, S. Omote, M. Taniguchi and T. Ando | Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy | Biophys. J., 97, 2358 (2009). |
| M. Shibata, H. Yamashita, T. Uchihashi, H. Kandori and T. Ando | High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin | Nature Nanotech., 5, 208 (2010). |
| D. Yamamoto, T. Uchihashi, N. Kodera, H. Yamashita, S. Nishikori, T. Ogura, M. Shibata and T. Ando | High-speed atomic force microscopy techniques for observing dynamic biomolecular processes | Meth. Enzymol., 475, 541 (2010). |
| P.-E. Milhiet, D. Yamamoto, O. Berthoumieu, P. Dosset, C. L. Grimellec, J.-M. Verdier, S. Marchal, and T. Ando | Deciphering the structure, growth and assembly of amyloid-like fibrils using high-speed atomic force microscopy | PLos One, 5, e13240 (2010). |
| H. Yamashita, K. Voitchovsky, T. Uchihashi, S. A. Contera, J. F. Ryan , Ando T. | Dynamics of bacteriorhodopsin 2D crystal observed by high-speed atomic force microscopy | J. Struct. Biol., 167, 153 (2009). |
| D. Yamamoto, T. Uchihashi, N. Kodera and T. Ando | Anisotropic diffusion of point defects in a two-dimensional crystal of streptavidin observed by high-speed atomic force microscopy | Nanotechnology, 19, 384009 (2008). |
| T. Ando, T. Uchihashi, N. Kodera, D. Yamamoto, A. Miyagi, M. Taniguchi and H. Yamashita | High-speed AFM and nano-visualization of biomolecular processes | Eur. J. Physiol., 456, 211 (2008). |
| A. Miyagi, Y. Tsunaka, T. Uchihashi, K. Mayanagi, S. Hirose, K. Morikawa, and T. Ando | Visualization of Intrinsically Disordered Regions of Proteins by High-Speed Atomic Force Microscopy | Chemphyschem., 9, 1859 (2008). |
| K. Shinohara, N. Kodera and T. Ando | Single Molecular Imaging of a micro-Brownian Motion and a Bond Scission of a Supramolecular Chiral π-Conjugated Polymer as a Molecular Bearing Driven by Thermal Fluctuations | Chem. Lett., 36, 1378 (2007). |
| H. Yamashita, N. Kodera, A. Miyagi, T. Uchihashi, D. Yamamoto and T. Ando | Tip-sample distance control using photothermal actuation of a small cantilever for high-speed atomic force microscopy | Rev. Sci. Instrum. 78, 083702 (2007). |
| T. Ando, T. Uchihashi, N. Kodera, A. Miyagi, R. Nakakita, H. Yamashita and M. Sakashita | High-Speed Atomic Force Microscopy for Studying the Dynamic Behavior of Protein Molecules at Work | J. J. Appl. Phys., 45, 1897 (2006). |
| S. Morita, H. Yamada and T. Ando | Japan AFM roadmap 2006 | Nanotechnology, 18, 084001 (2007). |
| H. Koide, T. Kinoshita, Y. Tanaka, S. Tanaka, N. Nagura, G. Meyer zu Ho¨rste, A. Miyagi and T. Ando | Identification of the Single Specific IQ Motif of Myosin V from Which Calmodulin Dissociates in the Presence of Ca2+ | Biochemistry, 26, 11598 (2006). |
| Mikihiro Shibata, Takayuki Uchihashi, Hayato Yamashita, Hideki Kandori, and Toshio Ando | Structural Changes in Bacteriorhodopsin in Response to Alternate Ilumination Observed by High-Speed Atomic Force Microscopy | Angew. Chem. Int. Ed. 50, 4410-4413 (2011). |
| Takayuki Uchihashi, Ryota Iino, Toshio Ando Hiroyuki Noji | High-Speed Atomic Force Microscopy Reveals Rotary Catalysis of Rotorless F1-ATPase | Science 333, 1279 (2011). |
| Y. Shinozaki, A. M. Siitonen, K. Sumitomo, K. Furukawa, and K. Torimitsu | Effect of Ca2+ on Vesicle Fusion on Solid Surface: An In vitro Model of Protein-Accelerated Vesicle Fusion | Jpn. J. Appl. Phys., 47, 6164 (2008). |
| Y. Shinozaki, K. Sumitomo, M. Tsuda, S. Koizumi, K. Inoue, K. Torimitsu | Direct Observation of ATP-Induced Conformational Changes in Single P2X4 Receptors | Plos Biol. 7, e1000103 (2009). |
| Y. Shinozaki, K. Sumitomo, K. Furukawa, H. Miyashita, Y. Tamba, N. Kasai, H. Nakashima and K. Torimitsu | Visualization of Single Membrane Protein Structure in Stretched Lipid Bilayer Suspended over Nanowells | Appl. Phys. Express. 3. 027002 (2010) |
| H. Sugasawa, Y. Sugiyama, T. Morii and T. Okada | Dynamic Observation of 2686bp DNA-BAL 31 Nuclease Interaction with Single Molecule Level Using High-Speed Atomic Force Microscopy | Jpn. J. Appl. Phys., 47, 6168 (2008). |
| S.-I. Yamamoto, T. Okada, Y. Uraoka, I. Yamashita and S. Hasegawa | Static and dynamic observation of supermolecular protein, ferritin, using high-speed atomic force microscope. | J. Appl. Phys., 109, 034901 (2011) |
| Y. Suzuki, Y. Higuchi, K. Hizume, M. Yokokawa, S. H. Yoshimura, K. Yoshikawa and K. Takeyasu | Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy | Ultramicrosc., 110, 682 (2010) |
| M. Yokokawa, C. Wada, T. Ando, N. Sakai, A. Yagi, S. H. Yoshimura and K. Takeyasu | Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL | EMBO J., 25, 4567 (2006). |
| N. Crampton, M. Yokokawa, D. T. F. Dryden, J. M. Edwardson, D. N. Rao, K. Takeyasu, S. H. Yoshimura, and R. M. Henderson | Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping | PNAS, 104, 12755 (2007). |
| F. Tanaka, T. Mochizuki, X. Liang, H. Asanuma, S. Tanaka, K. Suzuki, S. Kitamura, A. Nishikawa, K. Ui-Tei and M. Hagiya | Robust and photocontrollable DNA capsules using azobenzenes | Nano Lett., 10, 3560 (2010). |
| K. Igarashi, A. Koivula, M. Wada, S. Kimura, M. Penttila and M. Samejima | High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose | J. Biol. Chem., 284, 36186 (2009). |
| Kiyohiko Igarashi, Takayuki Uchihashi, Anu Koivula, Masahisa Wada, Satoshi Kimura,Tetsuaki Okamoto, Merja Penttila, Toshio Ando, Masahiro Samejima1 | Traffic Jams Reduce Hydrolytic Efficiency of Cellulase on Cellulose Surface | Science 333, 755 (2011) |
| Toshio Ando | Observation of the protein molecule by HS-AFM | Applied physics, 77, 1181 (2008). |
| M. Endo and H. Sugiyama | Three-dimensional DNA nanostructures constructed by folding of multiple rectangles | Nucleic Acids Symposium Series, 53, 81 (2009). |
| M. Endo, Y. Katsuda, K. Hidaka and H. Sugiyama | Regulation of DNA Methylation Using Different Tensions of Double Strands Constructed in a Defined DNA Nanostructure | J. Am. Chem. Soc., 132, 1592 (2010). |
| M. Endo, T Sugita, Y. Katsuda, K. Hidaka and H. Sugiyama | Programmed-assembly system using DNA jigsaw pieces | Chem.-Eur. J., 16, 5362 (2010). |
| M. Endo and H. Sugiyama | Chemical Approaches to DNA Nanotechnology. | ChemBioChem, 10, 2420 (2009). |
| M. Endo, T. Sugita, A. Rajendran, Y. Katsuda, T. Emura, K. Hidaka and H. Sugiyama | Two-dimensional DNA origami assemblies using a four-way connector. | Chem. Commun., 47, 3213 (2011) |
| Y. Sannohe, M. Endo, Y. Katsuda, K. Hidaka and H. Sugiyama | Visualization of Dynamic Conformational Switching of the G-Quadruplex in a DNA Nanostructure | J. Am. Chem. Soc., 132. 16311 (2010) |
| M. Endo, K. Hidaka and H. Sugiyama | Direct AFM observation of an opening event of a DNA cuboid constructed via a prism structure | Org. Biomol. Chem., DOI: 10.1039/ c0ob01093f (2011) |
| A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka and H. Sugiyama | Programmed Two-Dimensional Self-Assembly of Multiple DNA Origami Jigsaw Pieces | ACS Nano, 5, 665 (2011) |
| Wickham SF, Endo M, Katsuda Y, Hidaka K, Bath J, Sugiyama H, Turberfield AJ | Direct observation of stepwise movement of a synthetic molecular transporter. | Nat Nanotechnol. 2011 Feb 6. |
| The authors | Title | Journal |
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| T. Itani and J. J. Santillan | In situ Characterization of Photoresist Dissolution | Appl. Phys. Exp., 3, 061601 (2010). |
| T. Itani and J. J. Santillan | Dissolution Behavior of Photoresists: An In-situ Analysis | J. Photopoly. Sci. Technol., 23, 639 (2010). |
| Shigeto Inoue,a Takayuki Uchihashi, Daisuke Yamamotob and Toshio Ando | Direct observation of surfactant aggregate behavior on a mica surface using high-speed atomic force microscopy | Chem. Commun., 47, 4974 4976 (2011) |
| KEN-ICHI SHINOHARA, NORIYUKI KODERA, TAKASHI OOHASHI | Single-Molecule Imaging of Photodegradation Reaction in a Chiral Helical π-Conjugated Polymer Chain | Polymer Chemistry, 48, 4103 4107 (2010) |
| The authors | Title | Journal |
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| T. Fukuma, Y. Okazaki, N. Kodera, T. Uchihashi and T. Ando | High resonance frequency force microscope scanner using inertia balance support | Appl. Phys. Lett., 92, 243119 (2008) |
| T. Ando, T. Uchihashi and T. Fukuma | High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes | Prog. Surf. Sci., 83, 337 (2008). |
| T. Ando, T. Uchihashi1, N. Kodera, D. Yamamoto, M. Taniguchi, A. Miyagi1 and H. Yamashita | High-speed atomic force microscopy for observing dynamic biomolecular processes | J. Mol. Recognit., 20, 448 (2007). |
| T. Uchihashi, N. Kodera, H. Itoh, H. Yamashita and T. ANDO | Feed-Forward Compensation for High-Speed Atomic Force Microscopy Imaging of Biomolecules | J. J. Appl. Phys. 45, 1904 (2006). |
| N. Kodera, M. Sakashita and T. Ando | Dynamic proportional-integral-differential controller for high-speed atomic force microscopy | Rev. Sci. Instrum., 77, 083704 (2006). |
| N. Kodera, H. Yamashita and T. Ando | Active damping of the scanner for high-speed atomic force microscopy | Rev. Sci. Instrum., 76, 053708 (2005). |
| T. Ando, N. Kodera, T. Uchihashi, A. Miyagi, R. Nakakita, H. Yamashita and K. Matada | High-speed Atomic Force Microscopy for Capturing Dynamic Behavior of Protein Molecules at Work | J. Surf. Sci. Nanotech., 3 384 (2005). |
| T. Ando, N. Kodera, Y. Naito, T. Kinoshita, K. Furuta and Y. Y. Toyoshima | A High-speed Atomic Force Microscope for Studying Biological Macromolecules in Action | Chemphyschem., 4, 1196 (2003). |
| N. Kodera, T. Kinoshita, T. Ito and T. Ando | High-resolution imaging of myosin motor in action by a high-speed atomic force microscope | Adv. Exp. Med. Biol., 538, 119 (2003). |
| T. Ando, N. Kodera, D. Maruyama, E. Takai, K. Saito and A. Toda | A High-Speed Atomic Force Microscope for Studying Biological Macromolecules in Action | Jpn. J. Appl. Phys., 41, 4851 (2002). |
| T. Ando, N. Kodera, E. Takai, D. Maruyama, K. Saito and A. Toda | A high-speed atomic force microscope for studying biological macromolecules | PNAS, 98, 12468 (2001). |
| Toshio Ando, Noriyuki Kodera | High speed video rate, AFM | Measurement and control, 45, 2 |
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Standard system Specifications
| Scan Speed | 80 ms / frame (12.5 frames / sec) |
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| Piezo Range | X: 0.7 μm, Y: 0.7 μm, Z: 0.4 μm |
| Sample Size | 1.5 mm in diameter |
| Detection Method | Optical lever method |
| Scanning Method | Sample scan |
| Environment | In liquid |
| Control System | PID control, Dynamic PID control |
| Measurement Mode | AC mode. Topography and phase image |
| Significant Function | Scanner active dumpingDrift correction for cantilever excitation |
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Options
- Units
| Light irradiation Unit | Light irradiation unit for the experiments with caged compounds.Variable wavelength : 350 - 560 nm |
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| Circulation unit | The observation solutions can be exchanged while continuing AFM observation. The pH value and/or the buffer composition can be gradually changed during the measurement. |
| Heat control unit | From room temperature to 50℃*Under developments |
- Scanners
| Ultra high-speed scanner |
Suitable for observing reactions between molecules .
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| Wide scanner |
Suitable for relatively large samples with a high scanning rate.
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| Mechanically amplified ultra wider scanner |
Suitable for observing whole body of large samples such as cells.
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Contact
Research Institute of Biomolecule Metrology Co., Ltd.
807-133 Enokido, Tsukuba, Ibaraki 305-0853, Japan
Tel: +81-29-839-4611 Fax: +81-29-839-4612
E-mail: world-sales@ribm.co.jp
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Research Institute of Biomolecule Metrology Co., Ltd. is a trading, R&D and manufacturing-type venture capital organization. Our aim is to lead the technological advancement for measurements in nano-biology, a field which integrates biotechnology and nanotechnology. Through our bio-molecular measurement division, we develop various scanning probe microscopes that have unique features and reliable functionalities. With each device, our skilled staff can also provide operation software that is specialized to the customer’s need. |
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