• SPM Applications in Biology

    The last two decades of using AFM and related Scanning Probe Microscopy techniques in biology show that their popularity and power continue growing. Numerous reviews, both comprehensive and specialized, cited in the reference list and articles devoted to biological applications of Atomic Force Microscopy prove this fact. The state of today's activities in this field can be seen from the collection of latest abstracts from the Biophysical Journal: What Biologists Are Working On Using SPM?

    In biology Atomic Force Microscopy has traditionally been used to measure topography [, , , , , , , , , ] and nanomechanical properties of biological samples, such as elasticity [, , , , , , , , ]. Now the applications of AFM probing are far beyond these initial ones. AFM has been found to be useful in pharmacology [, ] biotechnology [], microbiology [, ], structural biology [, ], molecular biology [], genetics [, ] and other biology related fields.

    The variety of objects investigated using Atomic Force Microscopy in biology spans from the smallest biomolecules encompassing proteins, lipids, DNA, RNA and other nucleic acids, to the rather "big" human's platelets, viruses and living cells. The main advantage of AFM in biology as compared to other methods is that it usually does not require specific sample preparation and allows measuring in most of the physiological conditions biological objects are susceptible to. It is the most universal method in the sense that all the media including vacuum can be used for probing. The reason for choosing liquid media instead of air is not only because it is the natural physiological media for biological objects, but also due to the fact that all the interaction forces including unwanted ones are an order of magnitude smaller than in air allowing, for instance, to raise the resolution and to diminish image distortion. Although, it should be noted that measuring in liquids is much more complicated than imaging in air [].

    Because of their softness it is recommended that biological samples be investigated in intermittent-contact or tapping mode AFM. In this mode the probability of sample damage is lowered drastically compared to imaging in contact mode not excluding, though, it's displacement. Nevertheless, contact mode imaging in the beginning of the 21th century successfully deals with extralow loadings in the order of 100 pN []. What is more, the quality of AFM apparatus as well as the imaging techniques and data acquisition improves year after year [, , , , , , , ].

    Along with direct imaging of biological objects Atomic Force Microscopy plays a significant role among numerous biophysical methods for the investigation of specific and non-specific molecular interactions that all the biological processes are governed by [, ]. These are the protein-protein, enzyme-substrate, antigen-antibody, receptor-ligand interactions, drug-target associations, a diverse number of biocomplexes and many others. Being an instrument of choice for the investigation of biomolecule activities Atomic Force Microscopy is an ideal means for the visualization and real-time imaging of nucleation and crystallization of macromolecular crystals [, , , ], processes involved in the cell living cycle [357, 959, , , , , 979, 992, 1068], and the functioning of biomolecules [, ].

    Because of its capability to monitor biomolecular interactions on biosensor surfaces, Atomic Force Microscopy is applied successfully in biosensing applications [346, , , ]. The extended force range (theoretical limit estimated to be below 1 fN [360]) allows reaching unprecedented sensitivity at the nanoscale. For example, a special biosensor can be manufactured that is capable of detecting biological species at concentrations of 10-18 mol/l, which is approximately eight orders of magnitude more sensitive compared with conventional techniques [360].

    The high sensitivity achieved so far allows force measurements between individual biomolecules and complexes that have been substantial technical challenge a decade ago. For example, single-molecule atomic force spectroscopy has become standard practice. These advances give rise to developing a novel direction in biosensing techniques based on AFM as mentioned above. Actually, the AFM cantilever itself can be used to serve as the main sensitive element of biosensors. Such force measurements are usually performed using the AFM probe functionalized with a biomolecule of interest and its complementary molecule immobilized onto the sample surface [346, ].

    AFM by itself is, no doubt, a powerful instrument to explore micro- and nanoscopic biological objects. But since the early days of AFM the necessity of combining with other methods have been considered (see for instance []). For example, in biological applications the initial location of the target object is of great importance and the task of determining its position can be easily performed by conventional optical or fluorescence microscopy. It prevents from unnecessary scans and AFM tip contamination while locating, say, cells or subcell organelles such as chromosomes.

    It is not much of an exaggeration to say that the AFM prospects in biology are immense and who knows, may be some day in the future gene engineering will be provided with a useful tool for easy manipulating of genes inside a chromosome.

    A cumulative list of articles devoted to biological applications of Atomic Force Microscopy and placed in the Biology section including subsections can be downloaded in PDF format:

    Biological Applications of Atomic Force Microscopy (Updated on January 14, 2003

    By now the amount of articles in the list exceeds 1000.

    Please, send all comments and suggestions concerning these pages to info@mikromasch.com

    ID Reference list (newly come references are marked red)
    Contact resonance imaging - a simple approach to improve the resolution of AFM for biological and polymeric materials
    D. Dunlap, A. Cattelino, I. de Curtis, F. Valtorta
    FEBS Letters, 382 (1996), 1-2, 65-72
    AFM studies of the nucleation and growth mechanisms of macromolecular crystals
    Y.G. Kuznetsov, A.J. Malkin, A. McPherson
    Journal of Crystal Growth, 196 (1999), 2-4, 489-502
    STM and AFM of bio/organic molecules and structures
    A. Ikai
    Surface Science Reports, 26 (1997), 261-332
    Application of atomic force microscopy to the study of micromechanical properties of biological materials
    W. Richard Bowen, Robert W. Lovitt, Chris J. Wright
    Biotechnology Letters, 22 (2000), 893-903
    Atomic force microscopy as a novel pharmacological tool1
    R.D.S. Pereira
    Biochemical Pharmacology, 62 (2001), 975-983
    Atomic force microscopy for characterization of the biomaterial interface
    C.A. Siedlecki, R.E. Marchant
    Biomaterials, 19 (1998), 4-5, 441-454
    Atomic force microscopy for the characterization of immobilized enzyme molecules on biosensor surfaces
    Peng Zhang, Weihong Tan
    Fresenius' Journal of Analytical Chemistry, 369 (2001), 3/4, 302-307
    Atomic force microscopy imaging of living cells: progress, problems and prospects
    Hong Xing You, Lei Yu.
    Methods in Cell Science, 21 (1999), 1, 1-17
    Atomic force microscopy in analytical biotechnology
    S. Allen, M.C. Davies, C.J. Roberts, S.J.B. Tendler, P.M. Williams
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    Atomic force microscopy of biomaterials surfaces and interfaces
    K.D. Jandt
    Surface Science, 491 (2001), 3, 303-332
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    Fractal Analysis of Pharmaceutical Particles by Atomic Force Microscopy
    Tonglei Li, Kinam Park
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    In situ atomic force microscopy studies of protein and virus crystal growth mechanisms
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    Journal of Crystal Growth, 168 (1996), 1-4, 63-73
    In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization
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    Measuring elasticity of biological materials by atomic force microscopy
    G. Semenza, A. Vinckier
    FEBS Letters, 430 (1998), 1-2, 12-16
    Probing the microelastic properties of nanobiological particles with tapping mode atomic force microscopy
    L. Shao, N.J. Tao, R.M. Leblanc
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    Submolecular resolution of single macromolecules with atomic force microscopy
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    Scanning force microscopy in the applied biological sciences
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    Biotechnology Advances, 19 (2001), 6, 451-485
    Atomic force microscopy for high-resolution imaging in cell biology
    Hoh J.H., Hansma P.K.
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    Imaging of living cells by atomic force microscopy
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    Biological applications of atomic force microscopy
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    Imaging surface and submembranous structures with the atomic force microscope: A study on living cancer cells, fibroblasts and macrophages
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    AFM review study on pox viruses and living cells
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    An integrated approach to the study of living cells by atomic force microscopy
    Nagao E., Dvorak J.A.
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    Scan speed limit in atomic force microscopy
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    Relative microelastic mapping of living cells by atomic force microscopy
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    Biophys. J. 74 (1998), 1564-1578
    Measuring the elastic properties of biological samples with the AFM
    Radmacher M.
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    Combining optical and atomic force microscopy for life sciences research
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    Studying the surface of soft materials (live cells) at high resolution by scanning probe microscopy: Challenges faced
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    Thin Solid Films, 331 (1998), 1-2, 194-202
    Rapid biochemical detection and differentiation with magnetic force microscope cantilever arrays
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    Sensors and Actuators A: Physical, 83 (2000), 1-3, 256-262
    Applications for Atomic Force Microscopy of DNA
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    Atomic force microscopy of biomolecules
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    Potential applications of atomic force microscopy of DNA to the human genome project
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    Probing biopolymers with the atomic force microscope: a review
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    Recent Advances in Atomic force Microscopy of DNA
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    Recent Highlights from Atomic Force Microscopy of DNA
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    Conversation 11 (2000), 271-276
    Surface Biology of DNA by Atomic Force Microscopy
    Hansma H.G.
    Ann. Rev. Physical Chemistry 52 (2001), 71-92
    Varieties of imaging with scanning probe microscopes
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    Basement Membrane Macromolecules: Insights from Atomic Force Microscopy
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    Biomolecular imaging with the atomic force microscope
    Hansma, H. G., and J. Hoh.
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    Biological applications of the AFM: from single molecules to organs
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    Translating biomolecular recognition into nanomechanics
    Fritz J., Baller M.K., Lang H.P., Rothuizen H., Vettiger P., Meyer E., Guntherodt H.-J., Gerber Ch, Gimzewski J.K.
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    Micromechanical cantilever-based biosensors
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    Sensors and Actuators B: 79 (2001), 115-126
    Advances in the characterization of supported lipid films with the atomic force microscope
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    Biochimica et Biophysica Acta (BBA)/Biomembranes, 1509 (2000), 1-2, 14-41
    A relocated technique of atomic force microscopy (AFM) samples and its application in molecular biology
    Aiguo Wu, Zhuang Li, Lihua Yu, Hongda Wang and Erkang Wang
    Ultramicroscopy, Vol. 92 (2002) 3-4, pp. 201-207
    Atomic force microscopy in the study of macromolecular crystal growth
    A. McPherson, A. J. Malkin, and Yu. G. Kuznetsov
    Annu. Rev. Biophys. Biomol. Struct., 29 (2000) 361 - 410
    Biomolecular interactions measured by atomic force microscopy
    Oscar H. Willemsen, Margot M. E. Snel, Alessandra Cambi, Jan Greve, Bart G. De Grooth, and Carl G. Figdor
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    A metal-chelating microscopy tip as a new toolbox for single-molecule experiments by atomic force microscopy
    Lutz Schmitt, Markus Ludwig, Hermann E. Gaub, and Robert Tampe
    Biophys. J., 78 (2000) 3275 - 3285
    From images to interactions: high-resolution phase imaging in tapping-mode atomic force microscopy
    Martin Stark, Clemens Moller, Daniel J. Muller, and Reinhard Guckenberger
    Biophys. J., 80 (2001) 3009 - 3018
    Determination of elastic moduli of thin layers of soft material using the atomic force microscope
    Emilios K. Dimitriadis, Ferenc Horkay, Julia Maresca, Bechara Kachar, and Richard S. Chadwick
    Biophys. J., 82 (2002) 2798 - 2810
    Atomic force microscopy, a powerful tool in microbiology
    Yves F. Dufrene
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    Atomic force microscopy in structural biology: from the subcellular to the submolecular
    Danie M. Czajkowsky, Hideki Iwamoto, and Zhifeng Shao
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    Atomic force microscopy proposes a 'kiss and pull' mechanism for enhancer function
    Shige H. Yoshimura, Chikashi Yoshida, Kazuhiko Igarashi, and Kunio Takeyasu
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    The application of the atomic force microscope to studies of medically important protozoan parasites
    James A. Dvorak, Seiki Kobayashi, Kazuhiro Abe, Tatsushi Fujiwara, Tsutomu Takeuchi, and Eriko Nagao
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    The atomic force microscope as a new microdissecting tool for the generation of genetic probes
    Thalhammer, S., Stark, R. Muller, S., Wienberg, J. and Heckl, W.M.
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    Imaging and manipulation of biological structures with the AFM
    Dimitrios Fotiadis, Simon Scheuring , Shirley A. Muller, Andreas Engel and Daniel J. Muller
    Micron, 33 (2002), 4, 385-397
    Biological cryo atomic force microscopy: a brief review
    Z. Shao, Y. Zhang
    Ultramicroscopy, 66 (1996) 3-4, 141-152
    Progress in the application of scanning probe microscopy to biology
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    Scanning force microscopy of biological samples
    M. Lekka, J. Lekki, A. P. Shoulyarenko, B. Cleff, J. Stachura, Z. Stachura
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    Striving for atomic resolution in biomolecular topography: the scanning force microscope (SFM)
    A. Schaper, T. M. Jovin
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    The role of scanning probe microscopy in drug delivery research
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    Adsorption of biological molecules to a solid support for scanning probe microscopy
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    J. Struct. Biol., 119 (1997) 2, 172-188
    High resolution imaging of native biological sample surfaces using scanning probe microscopy
    A. Engel, C. A. Schoenenberger, D. J. Muller
    Current Opinion in Structural Biology, 7 (1997) 2, 279-284
    Imaging of individual biopolymers and supramolecular assemblies using noncontact atomic force microscopy
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    Biopolymers, 42 (1997) 2, 133-146
    Scanning force microscopy for imaging biostructures at high-resolution
    A. Diaspro, R. Rolandi
    Eur. J. Histochem., 41 (1997) 1, 7-16
    Scanning probe microscopy for the characterization of biomaterials and biological interactions
    M. D. Garrison, B. D. Ratner
    Ann. N. Y. Acad. Sci., 831 (1997) 101-113
    Subpiconewton intermolecular force microscopy
    M. Tokunaga, T. Aoki, M. Hiroshima, K. Kitamura, T. Yanagida
    Biochemical and Biophysical Research Communications, 231 (1997) 3, 566-569
    Evaluating the interaction of bacteria with biomaterials using atomic force microscopy
    A. Razatos, Y. L. Ong, M. M. Sharma, G. Georgiou
    J. Biomater. Sci. Polym. Ed., 9 (1998) 12, 1361-1373
    Analysis of indentation: implications for measuring mechanical properties with atomic force microscopy
    K. D. Costa, F. C. Yin
    J. Biomech. Eng., 121 (1999) 5, 462-471
    Atomic force microscopy imaging of dried or living bacteria
    D. Robichon, J. C. Girard, Y. Cenatiempo, J. F. Cavellier
    C. R. Acad. Sci. III, 322 (1999) 8, 687-693
    Atomic force microscopy: a forceful way with single molecules
    A. Engel, H. E. Gaub, D. J. Muller
    Curr. Biol., 9 (1999) 4, R133-R136
    Chemical and biochemical analysis using scanning force microscopy
    H. Takano, J. R. Kenseth, S. S. Wong, J. C. O'Brien, M. D. Porter
    Chem. Rev., 99 (1999) 10, 2845-2890
    Chemical Force Microscopy Study of Adhesion and Friction between Surfaces Functionalized with Self-Assembled Monolayers and Immersed in Solvents
    S. C. Clear, P. F. Nealey
    J. Colloid. Interface. Sci., 213 (1999) 1, 238-250
    High speed atomic force microscopy of biomolecules by image tracking
    S. J. van Noort, K. O. van Der Werf, B. G. de Grooth, J. Greve
    Biophys. J., 77 (1999) 4, 2295-2303
    Novel polymer substrates for SFM investigations of living cells, biological membranes, and proteins
    A. Linder, U. Weiland, H. J. Apell
    J. Struct. Biol., 126 (1999) 1, 16-26
    Probing Nanometer Structures with Atomic Force Microscopy
    Z. Shao
    News Physiol. Sci., 14 (1999) 142-149
    The micro-mechanics of single molecules studied with atomic force microscopy
    T. E. Fisher, P. E. Marszalek, A. F. Oberhauser, M. Carrion-Vazquez, J. M. Fernandez
    J. Physiol., 520 (1999) 1, 5-14
    Aspects of the physical chemistry of polymers, biomaterials and mineralised tissues investigated with atomic force microscopy (AFM)
    K. D. Jandt, M. Finke, P. Cacciafesta
    Colloids. Surf. B. Biointerfaces, 19 (2000) 4, 301-314
    Atomic force microscopy measurements of intermolecular binding strength
    G. N. Misevic
    Methods Mol. Biol., 139 (2000) 111-117
    Chemical force microscopy of microcontact-printed self-assembled monolayers by pulsed-force-mode atomic force microscopy
    Y. Okabe, M. Furugori, Y. Tani, U. Akiba, M. Fujihira
    Ultramicroscopy, 82 (2000) 1-4, 203-212
    Monitoring biomolecular interactions by time-lapse atomic force microscopy
    M. Stolz, D. Stoffler, U. Aebi, C. Goldsbury
    J. Struct. Biol., 131 (2000) 3, 171-180
    Quantification of bacterial adhesion forces using atomic force microscopy (AFM)
    H. H. Fang, K. Y. Chan, L. C. Xu
    J. Microbiol. Methods, 40 (2000) 1, 89-97
    Structural biology with carbon nanotube AFM probes
    A. T. Woolley, C. L. Cheung, J. H. Hafner, C. M. Lieber
    Chem. Biol., 7 (2000) 11, R193-R204
    The importance of molecular structure and conformation: learning with scanning probe microscopy
    B. L. Smith
    Prog. Biophys. Mol. Biol., 74 (2000) 1-2, 193-113
    Application of atomic force microscopy to study initial events of bacterial adhesion
    A. Razatos
    Methods Enzymol., 337 (2001) 276-285
    Atomic force microscopy and its related techniques in biomedicine
    T. Ushiki
    Ital. J. Anat. Embryol., 106 (2001) 2 Suppl 1, 3-8
    Atomic force microscopy applications in macromolecular crystallography
    A. McPherson, A. J. Malkin, Y. G. Kuznetsov, M. Plomp
    Acta Crystallogr. D: Biol. Crystallogr., 57 (2001) 8, 1053-1060
    Atomic force microscopy of macromolecular interactions
    C. M. Yip
    Current Opinion in Structural Biology, 11 (2001) 5, 567-572
    Chemical force microscopy with active enzymes
    M. Fiorini, R. McKendry, M. A. Cooper, T. Rayment, C. Abell
    Biophys. J., 80 (2001) 5, 2471-2476
    Comparative studies of bacteria with an atomic force microscopy operating in different modes
    A. V. Bolshakova, O. I. Kiselyova, A. S. Filonov, O. Y. Frolova, Y. L. Lyubchenko, I. V. Yaminsky
    Ultramicroscopy, 86 (2001) 1-2, 121-128
    Novel methods for studying lipids and lipases and their mutual interaction at interfaces. Part I. Atomic force microscopy
    K. Balashev, T. R. Jensen, K. Kjaer, T. Bjornholm
    Biochimie, 83 (2001) 5, 387-397
    Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology
    A. J. Malkin, M. Plomp, A. McPherson
    Acta Crystallogr. D: Biol. Crystallogr., 58 (2002) 1, 1617-1621
    Biomolecular imaging using atomic force microscopy
    D. J. Muller, K. Anderson
    Trends in Biotechnology, 20 (2002) 8, S45-S49
    Biotechnological applications of atomic force microscopy
    G. Charras, P. Lehenkari, M. Horton
    Methods Cell Biol., 68 (2002) 171-191
    Cryo-atomic force microscopy
    S. Sheng, Z. Shao
    Methods Cell Biol., 68 (2002) 243-256
    Methods for biological probe microscopy in aqueous fluids
    J. H. Kindt, J. C. Sitko, L. I. Pietrasanta, E. Oroudjev, N. Becker, M. B. Viani, H. G. Hansma
    Methods Cell Biol., 68 (2002) 213-229
    Supported lipid bilayers as effective substrates for atomic force microscopy
    D. M. Czajkowsky, Z. Shao
    Methods Cell Biol., 68 (2002) 231-241
    Dynamic force microscopy imaging of native membranes
    F. Kienberger, C. Stroh, G. Kada, R. Moser, W. Baumgartner, V. Pastushenko, C. Rankl, U. Schmidt, H. Mueller, E. Orlova, C. LeGrimellec, D. Drenckhahn, D. Blaas, P. Hinterdorfer
    Ultramicroscopy, 97 (2003) 229-237