High-speed AFM and nano-visualization of biomolecular processes

Conventional atomic force microscopes (AFMs) take at least 30–60 s to capture an image, while dynamic biomolecular processes occur on a millisecond timescale or less. To narrow this large difference in timescale, various studies have been carried out in the past decade. These efforts have led to a maximum imaging rate of 30–60 ms/frame for a scan range of ~250 nm, with a weak tip–sample interaction force being maintained. Recent imaging studies using high-speed AFM with this capacity have shown that this new microscope can provide straightforward and prompt answers to how and what structural changes progress while individual biomolecules are at work. This article first compares high-speed AFM with its competitor (single-molecule fluorescence microscopy) on various aspects and then describes high-speed AFM instrumentation and imaging studies on biomolecular processes. The article concludes by discussing the future prospects of this cutting-edge microscopy.

[1]  M. Anderson,et al.  A Raman-atomic force microscope for apertureless-near-field spectroscopy and optical trapping , 2002 .

[2]  Georg Schitter,et al.  High-Speed Atomic Force Microscopy , 2006, Science.

[3]  Mervyn J Miles,et al.  A mechanical microscope: High speed atomic force microscopy , 2005 .

[4]  A. Horwich,et al.  The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex , 1997, Nature.

[5]  Todd Sulchek,et al.  Parallel atomic force microscopy with optical interferometric detection , 2001 .

[6]  C. Quate,et al.  AUTOMATED PARALLEL HIGH-SPEED ATOMIC FORCE MICROSCOPY , 1998 .

[7]  D. Lohr,et al.  Single-molecule recognition imaging microscopy. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Todd Sulchek,et al.  Dual integrated actuators for extended range high speed atomic force microscopy , 1999 .

[9]  Toshio Ando,et al.  Tip-sample distance control using photothermal actuation of a small cantilever for high-speed atomic force microscopy. , 2007, The Review of scientific instruments.

[10]  V. Dravid,et al.  Nanoscale Imaging of Buried Structures via Scanning Near-Field Ultrasound Holography , 2005, Science.

[11]  Todd Sulchek,et al.  High speed tapping mode atomic force microscopy in liquid using an insulated piezoelectric cantilever , 2003 .

[12]  Jeffrey A. Reimer,et al.  Efficient visible luminescence from hydrogenated amorphous silicon , 1983 .

[13]  J. Sellers,et al.  The prepower stroke conformation of myosin V , 2002, The Journal of cell biology.

[14]  Andrzej Joachimiak,et al.  THE CRYSTAL STRUCTURE OF THE BACTERIAL CHAPERONIN GROEL AT 2.8 ANGSTROMS , 1995 .

[15]  Satoshi Kawata,et al.  Application of tip-enhanced microscopy for nonlinear Raman spectroscopy , 2004 .

[16]  Y. Dufrêne,et al.  Detection and localization of single molecular recognition events using atomic force microscopy , 2006, Nature Methods.

[17]  J. Joo,et al.  Raman Study of Polymer–Metal Hybrid Nanotubes Using Atomic Force/Confocal Combined Microscope , 2007 .

[18]  E. Krementsova,et al.  Differential labeling of myosin V heads with quantum dots allows direct visualization of hand-over-hand processivity. , 2005, Biophysical journal.

[19]  S. Jarvis,et al.  Direct imaging of lipid-ion network formation under physiological conditions by frequency modulation atomic force microscopy. , 2007, Physical review letters.

[20]  P K Hansma,et al.  Escherichia coli RNA polymerase activity observed using atomic force microscopy. , 1997, Biochemistry.

[21]  Kiwamu Saito,et al.  Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous solution , 1995, Nature.

[22]  RosemanAM ChenS FurtakK FentonWA SaibilHR HorwichAL RyeHS GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings. , 1999 .

[23]  S. Kawata,et al.  Tip-enhanced coherent anti-stokes Raman scattering for vibrational nanoimaging. , 2004, Physical review letters.

[24]  W. Jhe,et al.  High-speed near-field scanning optical microscopy with a quartz crystal resonator , 2002 .

[25]  Masashi Kitazawa,et al.  Batch Fabrication of Sharpened Silicon Nitride Tips , 2003 .

[26]  Toshio Ando,et al.  High-Speed Atomic Force Microscopy for Studying the Dynamic Behavior of Protein Molecules at Work , 2006 .

[27]  A. Nagy,et al.  Spatially and temporally synchronized atomic force and total internal reflection fluorescence microscopy for imaging and manipulating cells and biomolecules. , 2006, Biophysical journal.

[28]  M. Stark,et al.  Fast low-cost phase detection setup for tapping-mode atomic force microscopy , 1999 .

[29]  J. Buchner,et al.  Review: a structural view of the GroE chaperone cycle. , 2001, Journal of structural biology.

[30]  V. Dupres,et al.  Sample preparation procedures for biological atomic force microscopy , 2005, Journal of microscopy.

[31]  V. Elings,et al.  Fractured polymer/silica fiber surface studied by tapping mode atomic force microscopy , 1993 .

[32]  C F Quate,et al.  Imaging crystals, polymers, and processes in water with the atomic force microscope. , 1989, Science.

[33]  Jonathan D. Adams,et al.  Components for high speed atomic force microscopy. , 2006, Ultramicroscopy.

[34]  C. Quate,et al.  Centimeter scale atomic force microscope imaging and lithography , 1998 .

[35]  A. Noy,et al.  Combined force and photonic probe microscope with single molecule sensitivity , 2003 .

[36]  Paul K. Hansma,et al.  Fast imaging and fast force spectroscopy of single biopolymers with a new atomic force microscope designed for small cantilevers , 1999 .

[37]  Marcus Dyba,et al.  Concepts for nanoscale resolution in fluorescence microscopy , 2004, Current Opinion in Neurobiology.

[38]  Toshio Ando,et al.  Japan AFM roadmap 2006 , 2007 .

[39]  Georg Schitter,et al.  Data acquisition system for high speed atomic force microscopy , 2005 .

[40]  I. Reviakine,et al.  Formation of Supported Phospholipid Bilayers from Unilamellar Vesicles Investigated by Atomic Force Microscopy , 2000 .

[41]  A. Horovitz,et al.  Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL. , 1995, Biochemistry.

[42]  W. Baumeister,et al.  Functional significance of symmetrical versus asymmetrical GroEL-GroES chaperonin complexes , 1995, Science.

[43]  E. Sackmann,et al.  Supported Membranes: Scientific and Practical Applications , 1996, Science.

[44]  M. Kessel,et al.  Characterization of a functional GroEL14(GroES7)2 chaperonin hetero-oligomer. , 1994, Science.

[45]  Keith Bonin,et al.  A combined atomic force/fluorescence microscopy technique to select aptamers in a single cycle from a small pool of random oligonucleotides , 2007, Microscopy research and technique.

[46]  T. Ando,et al.  High-speed Atomic Force Microscopy for Capturing Dynamic Behavior of Protein Molecules at Work , 2005 .

[47]  A. Horwich,et al.  Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL , 1997, Nature.

[48]  Georg Schitter,et al.  Identification and open-loop tracking control of a piezoelectric tube scanner for high-speed scanning-probe microscopy , 2004, IEEE Transactions on Control Systems Technology.

[49]  A. Aydınlı,et al.  Visible photoluminescence from low temperature deposited hydrogenated amorphous silicon nitride , 1996 .

[50]  Toshio Ando,et al.  Active damping of the scanner for high-speed atomic force microscopy , 2005 .

[51]  Yale E. Goldman,et al.  Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization , 2003, Nature.

[52]  T. Ando,et al.  A high-speed atomic force microscope for studying biological macromolecules , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[53]  S. Burgess,et al.  Dynein structure and power stroke , 2003, Nature.

[54]  Aufried T. M. Lenferink,et al.  Combined AFM and confocal fluorescence microscope for applications in bio‐nanotechnology , 2005, Journal of microscopy.

[55]  T. Ha,et al.  A survey of single-molecule techniques in chemical biology. , 2007, ACS chemical biology.

[56]  T. Creighton,et al.  Protein Folding , 1992 .

[57]  Mime Kobayashi,et al.  Real-time imaging of DNA-streptavidin complex formation in solution using a high-speed atomic force microscope. , 2007, Ultramicroscopy.

[58]  R. Jaenicke,et al.  Symmetric complexes of GroE chaperonins as part of the functional cycle. , 1994, Science.

[59]  P. Vadgama 2 Surface biocompatibility , 2005 .

[60]  Mervyn J Miles,et al.  Ultrahigh-speed scanning near-field optical microscopy capable of over 100 frames per second , 2003 .

[61]  P K Hansma,et al.  Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. , 1999, Biophysical journal.

[62]  Paul R. Selvin,et al.  Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization , 2003, Science.

[63]  Hiroto Tanaka,et al.  Simultaneous Observation of Individual ATPase and Mechanical Events by a Single Myosin Molecule during Interaction with Actin , 1998, Cell.

[64]  V. Lulevich,et al.  An atomic force microscope tip as a light source , 2005 .

[65]  M. Horton,et al.  Breaking the speed limit with atomic force microscopy , 2007 .

[66]  P Rolfe,et al.  Physical and biological properties of compound membranes incorporating a copolymer with a phosphorylcholine head group. , 1998, Biomaterials.

[67]  Martin Stark,et al.  Inverting dynamic force microscopy: From signals to time-resolved interaction forces , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[68]  A. Clarke,et al.  The origins and consequences of asymmetry in the chaperonin reaction cycle. , 1995, Journal of molecular biology.

[69]  T. Yanagida,et al.  Single-molecule visualization in cell biology. , 2003, Nature reviews. Molecular cell biology.

[70]  T. Ando,et al.  Dynamic proportional-integral-differential controller for high-speed atomic force microscopy , 2006 .

[71]  Paul K. Hansma,et al.  Studies of vibrating atomic force microscope cantilevers in liquid , 1996 .

[72]  M. Wallace,et al.  Combined single-molecule force and fluorescence measurements for biology , 2003, Journal of biology.

[73]  Toshio Ando,et al.  Fast phase imaging in liquids using a rapid scan atomic force microscope , 2006 .

[74]  I. Reviakine,et al.  Streptavidin 2D crystals on supported phospholipid bilayers: Toward constructing anchored phospholipid bilayers , 2001 .

[75]  S Devasia,et al.  CONTROL ISSUES IN HIGH‐SPEED AFM FOR BIOLOGICAL APPLICATIONS: COLLAGEN IMAGING EXAMPLE , 2004, Asian journal of control.

[76]  Jacqueline A. Cutroni,et al.  Rigid design of fast scanning probe microscopes using finite element analysis. , 2004, Ultramicroscopy.

[77]  A. Ikai,et al.  High sensitivity detection of protein molecules picked up on a probe of atomic force microscope based on the fluorescence detection by a total internal reflection fluorescence microscope , 2004, FEBS letters.

[78]  P. Hansma,et al.  The scanning ion-conductance microscope. , 1989, Science.

[79]  P. Selvin,et al.  Adaptability of myosin V studied by simultaneous detection of position and orientation , 2006, The EMBO journal.

[80]  Calvin F. Quate,et al.  High-speed, large-scale imaging with the atomic force microscope , 1991 .

[81]  Franz J. Giessibl,et al.  Atomic Force Microscopy-(7x7) Surface by Atomic Force Microscopy , 1995 .

[82]  M Yokokawa,et al.  Fast-scanning atomic force microscopy reveals the molecular mechanism of DNA cleavage by ApaI endonuclease. , 2006, IEE proceedings. Nanobiotechnology.

[83]  Christian Eggeling,et al.  Macromolecular-scale resolution in biological fluorescence microscopy. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Masatoshi Yokokawa,et al.  Fast‐scanning atomic force microscopy reveals the ATP/ADP‐dependent conformational changes of GroEL , 2006, The EMBO journal.

[85]  J. Martín,et al.  Asymmetrical interaction of GroEL and GroES in the ATPase cycle of assisted protein folding , 1995, Science.

[86]  Helen R. Saibil,et al.  GroEL-GroES Cycling ATP and Nonnative Polypeptide Direct Alternation of Folding-Active Rings , 1999, Cell.

[87]  B. Rogers,et al.  Improving tapping mode atomic force microscopy with piezoelectric cantilevers. , 2004, Ultramicroscopy.

[88]  A. Engel,et al.  Imaging streptavidin 2D crystals on biotinylated lipid monolayers at high resolution with the atomic force microscope , 1999, Journal of microscopy.

[89]  Yongho Seo,et al.  Fast-scanning shear-force microscopy using a high-frequency dithering probe , 2000 .

[90]  D. Dryden,et al.  Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping , 2007, Proceedings of the National Academy of Sciences.

[91]  Karl Meller,et al.  Atomic force microscopy and confocal laser scanning microscopy on the cytoskeleton of permeabilised and embedded cells. , 2006, Ultramicroscopy.

[92]  G. Lorimer Protein folding Folding with a two-stroke motor , 1997, Nature.

[93]  M. Stark,et al.  Stabilized atomic force microscopy imaging in liquids using second harmonic of cantilever motion for setpoint control , 2004 .

[94]  T. Ando,et al.  A high-speed atomic force microscope for studying biological macromolecules in action. , 2003, Chemphyschem : a European journal of chemical physics and physical chemistry.

[95]  Hideki Taguchi,et al.  Single-molecule observation of protein–protein interactions in the chaperonin system , 2001, Nature Biotechnology.

[96]  Takeshi Fukuma,et al.  Development of liquid-environment frequency modulation atomic force microscope with low noise deflection sensor for cantilevers of various dimensions , 2006 .