Abstract
Atomic force microscopy (AFM; also called scanning force microscopy [SFM]) is a rather novel technique that offers unique advantages in the potential for the very high resolution of DNA and small ligands in the absence of stains, shadows, and labels (1,2). Furthermore, the scanning can be performed in air or liquid. The latter is particularly important for resolving fully hydrated structures. The AFM is theoretically capable of resolving structural details at the level of atomic dimensions, provided that the specimen is not dynamic.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Binnig, G., Quate, C. F., and Gerber, C. H. (1986) Atomic force microscope Phys. Rev. Lett. 56, 930–933.
Hansma, P. K., Elings, V. B., Marti, O., and Bracker, C. E. (1988) Scanning tunneling microscopy and atomic force microscopy: some applications to biology and technology. Science 242, 209–216.
Bustamante, C., Erie, D. A., and Keller, D. (1994) Biochemical and structural applications of scanning force microscopy. Curr. Opin. Struct. Biol. 3, 750–760.
Bustamante, C. and Rivetti, C. (1996) Visualizing protein-nucleic acid interactions on a large scale with scanning force microscope. Annu. Rev. Biophys. Biomol. Struct. 25, 395–429.
Vesenka, J., Guthold, M., Tang, C. L., Keller, D., and Bustamante, C. (1992) Substrate preparation for reliable imaging of DNA molecules with the scanning force microscopy. Ultramicroscopy 42-44, 1243–1249.
Yang, J., Takeyasu, K., and Shao, Z. (1992) Atomic force microscopy of DNA molecules. FEBS Lett. 301, 173–176.
Allen, M. J., Dong, X. F., O’Neil, T. E., Yau, P., Kowalczykowski, S. C., Gatewood, J., Balhorn, R., et al. (1993) Atomic force microscope measurements of nucleosome cores assembled along defined DNA sequences. Biochemistry 32, 8390–8396.
Hansma, H., G., and Hoh, J. (1994) Biomolecular imaging with the atomic force microscopy. Ann. Rev. Biophys. Biochem. Struct. 23, 115–139.
Lyubchenko Y. L., Jacobs B. L., Lindsay S. M., and Stasiak, A. (1995) Atomic force microscopy of protein-DNA complexes [Review]. Scanning Microsc. 9, 705–727.
Lyubchenko, Y. L., Gall, A. A., Shlyakhtenko, L. S., Harrington, R. E., Oden, P. I., Jacobs, B. L., et al. (1992) Atomic force microscopy imaging of double stranded DNA and RNA J. Biomolec. Struct. Dynam. 9, 589–606.
Lyubchenko, Y. L., Blankenship, R. E., Lindsay, S. M., Simpson, L., Shlyakhtenko, L. S. (1996) AFM studies of nucleic acids, nucleoproteins and cellular complexes: The use of functionalized substrates. Scanning Microsc. 10(Suppl.), 97–109.
Lyubchenko, Y. L., Jacobs, B. L., and Lindsay, S. M. (1992) Atomic force microscopy imaging of reovirus dsRNA: a routine technique for length measurements. Nucleic Acids Res. 20, 3983–3986.
Lyubchenko Y. L. and Shlyakhtenko, L. S. (1997) Visualization of supercoiled DNA with atomic force microscopyin situ. Proc. Natl. Acad. Sci. USA 94, 496–501.
Shlyakhtenko, L. S, Potaman, V. N., Sinden,. R., and Lyubchenko, Y. L. (1998) Structure and dynamics of supercoil-stabilized DNA cruciform. J. Mol. Biol. 280, 61–72.
Lyubchenko, Y. L., Oden, P. I., Lampner, D., Lindsay, S. M., and Dunker, K. (1993) Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces, Nucleic Acids Res. 21, 1117–1123.
Lyubchenko, Y. L., Shlyakhtenko, L. S., Aki, T., and Adhya, S. (1997) AFM visualization of GalR mediated DNA looping. Nucleic Acids Res. 25, 873–876.
Herbert A., Schade, M., Lowenkaupt, K., Alfken, J., Schwartz, T., Shlyakhtenko, L. S., et al. (1998) The Za domain from human ADAR1 binds to the Z-DNA conformer of many different sequences. Nucleic Acid Res. 26, 3486–3493.
Hansma, H. G., Laney, D. E., Bezanilla, M., Sinsheimer, R. L., and Hansma, P. K. (1995) Applications for atomic force microscopy of DNA. Biophys. J. 68, 672–1677.
Lyubchenko, Y. L., Shlyakhtenko, L. S., Harrington, R. E., Oden, P. I., and Lindsay, S. M. (1993) AFM imaging of long DNA in air and under water. Proc. Natl. Acad. Sci. USA 90, 2137–2140.
Hansma, P. K., Cleveland, J. P., Radmacher, M., Walters, D. A., and Hillner, P. (1994) Tapping mode atomic force microscopy in liquids. Appl. Phys. Lett. 64, 1738–1740.
Bezanilla, M., Drake, B., Nudler, E., Kashlev, M., Hansma, P. K., and Hansma, H. G. (1994) Motion and enzymatic degradation of DNA in the atomic force microscope Biophys. J. 67, 2454–2459.
Han, W. H., Lindsay, S. M., and Jing, T. W (1996) A magnetically-driven oscillating probe microscope for operation in liquids. Appl. Phys. Lett. 69, 4111–4114.
Bezanilla, M., Manne, S., Laney, D. E., Lyubchenko, Y. L., and Hansma, H. G (1995) Adsorption of DNA to mica, silylated mica, and minerals: characterization by atomic force microscopy. Langmuir 11, 655–659.
Hansma, H. G. (1996) A useful buffer for atomic force microscopy of DNA. Sci. Tools Pharmacia Biotech. 1(3), 7.
Kasas, S., Thomson, N. H., Smith, B. L., Hansma, H. G., Zhu, X., Guthold, M., et al. (1997) Escherichia coli RNA polymerase activity observed using atomic force microscopy. Biochemistry 36, 461–468.
Hansma, H. G. (1998) Atomic force microscopy of DNA on mica in air and fluid, in Procedures for Scanning Probe Microscope (Colton, R. J., et al., eds.), Wiley, Chichester, pp. 389–393.
van Noort, S. J. T., van der Werf, K. O., Eker, A. P. M., Wyman, C., Grooth, B. G., van Hulst, N. F., et al. (1998) Direct visualization of dynamic protein-DNA interactions with a dedicated atomic force microscope. Biophys. J. 74, 2840–2849.
General Reading
Colton et al., (eds.) (1998) Procedures in Scanning Probe Microscopes. Wiley, Chichester.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2001 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Lyubchenko, Y.L., Gall, A.A., Shlyakhtenko, L.S. (2001). Atomic Force Microscopy of DNA and Protein-DNA Complexes Using Functionalized Mica Substrates. In: Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 148. Humana Press. https://doi.org/10.1385/1-59259-208-2:569
Download citation
DOI: https://doi.org/10.1385/1-59259-208-2:569
Publisher Name: Humana Press
Print ISBN: 978-0-89603-625-3
Online ISBN: 978-1-59259-208-1
eBook Packages: Springer Protocols