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Introduction to Atomic Force Microscopy

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Single Molecule Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 783))

Abstract

Atomic force microscopy (AFM) is an invaluable tool not only to obtain high-resolution topographical images, but also to determine certain physical properties of specimens, such as their mechanical properties and composition. In addition to the wide range of applications, from materials science to biology, this technique can be operated in a number of environments as long as the specimen is attached to a surface, including ambient air, ultra high vacuum (UHV), and most importantly for biology, in liquids. The versatility of this technique is also reflected by the wide range of sizes of the sample that can dealt with, such as atoms, molecules, molecular aggregates, and cells. Indeed, this technique enables biological problems to be tackled from the single-molecule point of view and it allows not only to see but also to touch the material under study (i.e., mechanical manipulation at the nanoscale), a fundamental source of information for its characterization. In particular, the study of the mechanical properties at the nanoscale of biomolecular aggregates constitute an important source of data to elaborate mechano-chemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.

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References

  1. Binnig G & Rohrer H (1982) Scanning Tunneling Microscopy. Helvetica Physica Acta 55, 726–735.

    CAS  Google Scholar 

  2. Chen CJ (1993) Introduction to Scanning Tunneling Microscopy (Oxford University Press, Oxford).

    Google Scholar 

  3. Baro AM, Miranda R, Alaman J, Garcia N, Binnig G, Rohrer H, Gerber C, & Carrascosa JL (1985) Determination of Surface-Topography of Biological Specimens at High-Resolution by Scanning Tunnelling Microscopy. Nature 315, 253–254.

    Article  PubMed  CAS  Google Scholar 

  4. Binnig G, Quate CF, & Gerber C (1986) Atomic Force Microscope. Phys Rev Lett 56, 930–933.

    Article  PubMed  Google Scholar 

  5. Schmalz G (1929) Uber Glatte und Ebenheit als physikalisches und physiologishes Problem. Verein Deutscher Ingenieure.

    Google Scholar 

  6. Meyer G & Amer NM (1988) Novel Optical Approach to Atomic Force Microscopy. Applied Physics Letters 53, 1045–1047.

    Article  Google Scholar 

  7. Sader JE, Chon JWM, & Mulvaney P (1999) Calibration of rectangular atomic force microscope cantilevers. Review of Scientific Instruments 70, 3967–3969.

    Article  CAS  Google Scholar 

  8. Butt HJ & Jaschke M (1995) Calculation of Thermal Noise in Atomic-Force Microscopy. Nanotechnology 6, 1–7.

    Article  Google Scholar 

  9. Israelachvili J (2002) Intermolecular and surface forces (Academic Press, London).

    Google Scholar 

  10. Johnson KL (1985) Contact mechanics (Cambridge University Press, Cambridge).

    Google Scholar 

  11. Ohnesorge F & Binnig G (1993) True Atomic-Resolution by Atomic Force Microscopy through Repulsive and Attractive Forces. Science 260, 1451–1456.

    Article  PubMed  CAS  Google Scholar 

  12. Giessibl FJ (1995) Atomic-Resolution of the Silicon (111)-(7×7) Surface by Atomic-Force Microscopy. Science 267, 68–71.

    Article  PubMed  CAS  Google Scholar 

  13. Sugimoto Y, Pou P, Abe M, Jelinek P, Perez R, Morita S, & Custance O (2007) Chemical identification of individual surface atoms by atomic force microscopy. Nature 446, 64–67.

    Article  PubMed  CAS  Google Scholar 

  14. Villarrubia JS (1997) Algorithms for scanned probe microscope image simulation, surface reconstruction, and tip estimation. J Res Natl Inst Stan 102, 425–454.

    Google Scholar 

  15. Marti O, Drake B, Gould S, & Hansma PK (1988) Atomic Resolution Atomic Force Microscopy of Graphite and the Native Oxide on Silicon. Journal of Vacuum Science & Technology a-Vacuum Surfaces and Films 6, 287–290.

    Article  CAS  Google Scholar 

  16. Martin Y, Williams CC, & Wickramasinghe HK (1987) Atomic Force Microscope Force Mapping and Profiling on a Sub 100-a Scale. Journal of Applied Physics 61, 4723–4729.

    Article  CAS  Google Scholar 

  17. Carpick RW, Ogletree DF, & Salmeron M (1997) Lateral stiffness: A new nanomechanical measurement for the determination of shear strengths with friction force microscopy. Applied Physics Letters 70, 1548–1550.

    Article  CAS  Google Scholar 

  18. Garcia R & Perez R (2002) Dynamic atomic force microscopy methods. Surface Science Reports 47, 197–301.

    Article  CAS  Google Scholar 

  19. Legleiter J, Park M, Cusick B, & Kowalewski T (2006) Scanning probe acceleration microscopy (SPAM) in fluids: Mapping mechanical properties of surfaces at the nanoscale. P Natl Acad Sci USA 103, 4813–4818.

    Article  CAS  Google Scholar 

  20. Miyatani T, Horii M, Rosa A, Fujihira M, & Marti O (1997) Mapping of electrical double-layer force between tip and sample surfaces in water with pulsed-force-mode atomic force microscopy. Applied Physics Letters 71, 2632–2634.

    Article  CAS  Google Scholar 

  21. de Pablo PJ, Colchero J, Gomez-Herrero J, & Baro AM (1998) Jumping mode scanning force microscopy. Applied Physics Letters 73, 3300–3302.

    Article  Google Scholar 

  22. De Pablo PJ, Colchero J, Gomez-Herrero J, Baro AM, Schaefer DM, Howell S, Walsh B, & Reifenberger R (1999) Adhesion maps using scanning force microscopy techniques. Journal of Adhesion 71, 339–356.

    Article  Google Scholar 

  23. Hansma HG, Sinsheimer RL, Li MQ, & Hansma PK (1992) Atomic Force Microscopy of Single-Stranded and Double-Stranded DNA. Nucleic Acids Research 20, 3585–3590.

    Article  PubMed  CAS  Google Scholar 

  24. Lyubchenko YL, Jacobs BL, Lindsay SM, & Stasiak A (1995) Atomic-Force Microscopy of Nucleoprotein Complexes. Scanning Microscopy 9, 705–727.

    PubMed  CAS  Google Scholar 

  25. Dame RT, Wyman C, & Goosen N (2003) Insights into the regulation of transcription by scanning force microscopy. Journal of Microscopy-Oxford 212, 244–253.

    Article  CAS  Google Scholar 

  26. Janicijevic A, Ristic D, & Wyman C (2003) The molecular machines of DNA repair: scanning force microscopy analysis of their architecture. Journal of Microscopy-Oxford 212, 264–272.

    Article  CAS  Google Scholar 

  27. Dame RT, Wyman C, Wurm R, Wagner R, & Goosen N (2002) Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. Journal of Biological Chemistry 277, 2146–2150.

    Article  PubMed  CAS  Google Scholar 

  28. Wagner P, Hegner M, Guntherodt HJ, & Semenza G (1995) Formation and in-Situ Modification of Monolayers Chemisorbed on Ultraflat Template-Stripped Gold Surfaces. Langmuir 11, 3867–3875.

    Article  CAS  Google Scholar 

  29. Muller DJ, Amrein M, & Engel A (1997) Adsorption of biological molecules to a solid support for scanning probe microscopy. Journal of Structural Biology 119, 172–188.

    Article  PubMed  CAS  Google Scholar 

  30. Muller DJ, Janovjak H, Lehto T, Kuerschner L, & Anderson K (2002) Observing structure, function and assembly of single proteins by AFM. Progress in Biophysics & Molecular Biology 79, 1–43.

    Article  Google Scholar 

  31. Muller DJ, Schabert FA, Buldt G, & Engel A (1995) Imaging Purple Membranes in Aqueous-Solutions at Subnanometer Resolution by Atomic-Force Microscopy. Biophysical Journal 68, 1681–1686.

    Article  PubMed  CAS  Google Scholar 

  32. Viani MB, Pietrasanta LI, Thompson JB, Chand A, Gebeshuber IC, Kindt JH, Richter M, Hansma HG, & Hansma PK (2000) Probing protein-protein interactions in real time. Nature Structural Biology 7, 644–647.

    Article  PubMed  CAS  Google Scholar 

  33. Moreno-Herrero F, Colchero J, Gomez-Herrero J, & Baro AM (2004) Atomic force microscopy contact, tapping, and jumping modes for imaging biological samples in liquids. Physical Review E 69.

    Google Scholar 

  34. Xu X, Carrasco C, de Pablo PJ, Gomez-Herrero J, & Raman A (2008) Unmasking imaging forces on soft biological samples in liquids when using dynamic atomic force microscopy: A case study on viral capsids. Biophysical Journal 95, 2520–2528.

    Article  PubMed  CAS  Google Scholar 

  35. Kasas S, Thomson NH, Smith BL, Hansma HG, Zhu XS, Guthold M, Bustamante C, Kool ET, Kashlev M, & Hansma PK (1997) Escherichia coli RNA polymerase activity observed using atomic force microscopy. Biochemistry 36, 461–468.

    Article  PubMed  CAS  Google Scholar 

  36. Moreno-Herrero F, de Jager M, Dekker NH, Kanaar R, Wyman C, & Dekker C (2005) Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA. Nature 437, 440–443.

    Article  PubMed  CAS  Google Scholar 

  37. Plomp M, Rice MK, Wagner EK, McPherson A, & Malkin AJ (2002) Rapid visualization at high resolution of pathogens by atomic force microscopy – Structural studies of herpes simplex virus-1. American Journal of Pathology 160, 1959–1966.

    Article  PubMed  CAS  Google Scholar 

  38. Carrasco C, Carreira A, Schaap IAT, Serena PA, Gomez-Herrero J, Mateu MG, & Pablo PJ (2006) DNA-mediated anisotropic mechanical reinforcement of a virus. P Natl Acad Sci USA 103, 13706–13711.

    Article  CAS  Google Scholar 

  39. Carrasco C, Castellanos M, de Pablo PJ, & Mateu MG (2008) Manipulation of the mechanical properties of a virus by protein engineering. P Natl Acad Sci USA 105, 4150–4155.

    Article  CAS  Google Scholar 

  40. Ando T, Kodera N, Takai E, Maruyama D, Saito K, & Toda A (2001) A high-speed atomic force microscope for studying biological macromolecules. P Natl Acad Sci USA 98, 12468–12472.

    Article  CAS  Google Scholar 

  41. Ivanovska IL, de Pablo PJ, Ibarra B, Sgalari G, MacKintosh FC, Carrascosa JL, Schmidt CF, & Wuite GJL (2004) Bacteriophage capsids: Tough nanoshells with complex elastic properties. Proc. Natl. Acad. Sci. U. S. A. 101, 7600–7605.

    Article  PubMed  CAS  Google Scholar 

  42. Melcher J, Carrasco C, Xu X, Carrascosa JL, Gomez-Herrero J, de Pablo PJ, Raman A (2009) Origins of phase constrat in the atomic forces microscopy in liquids. P Natl Acad Sci USA 106, 13655–13660.

    Google Scholar 

  43. Hoogenboom BW, Hug HJ, Pellmont Y, Martin S, Frederix PLTM, Fotiadis D, & Engel A (2006) Quantitative dynamic-mode scanning force microscopy in liquid. Applied Physics Letters 88, 193109.

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain

    Pedro J. de Pablo

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  1. Pedro J. de Pablo
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Correspondence to Pedro J. de Pablo .

Editor information

Editors and Affiliations

  1. Dept. Physics & Astronomy, Section Physics of Complex Systems, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, Netherlands

    Erwin J. G. Peterman

  2. Dept. Physics & Astronomy, Section Physics of Complex Systems, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, Netherlands

    Gijs J. L. Wuite

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de Pablo, P.J. (2011). Introduction to Atomic Force Microscopy. In: Peterman, E., Wuite, G. (eds) Single Molecule Analysis. Methods in Molecular Biology, vol 783. Humana Press. https://doi.org/10.1007/978-1-61779-282-3_11

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  • DOI: https://doi.org/10.1007/978-1-61779-282-3_11

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-281-6

  • Online ISBN: 978-1-61779-282-3

  • eBook Packages: Springer Protocols

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