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Atomic Force Microscopy of DNA and Protein-DNA Complexes Using Functionalized Mica Substrates

  • Yuri L. Lyubchenko
  • Alexander A. Gall
  • Luda S. Shlyakhtenko
Part of the Methods in Molecular Biology book series (MIMB, volume 148)

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.

Keywords

Plastic Syringe Mica Surface Fluid Cell MultiMode System Nucleoprotein Complex 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Binnig, G., Quate, C. F., and Gerber, C. H. (1986) Atomic force microscope Phys. Rev. Lett. 56, 930–933.PubMedCrossRefGoogle Scholar
  2. 2.
    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.PubMedCrossRefGoogle Scholar
  3. 3.
    Bustamante, C., Erie, D. A., and Keller, D. (1994) Biochemical and structural applications of scanning force microscopy. Curr. Opin. Struct. Biol. 3, 750–760.CrossRefGoogle Scholar
  4. 4.
    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.PubMedCrossRefGoogle Scholar
  5. 5.
    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.PubMedCrossRefGoogle Scholar
  6. 6.
    Yang, J., Takeyasu, K., and Shao, Z. (1992) Atomic force microscopy of DNA molecules. FEBS Lett. 301, 173–176.PubMedCrossRefGoogle Scholar
  7. 7.
    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.PubMedCrossRefGoogle Scholar
  8. 8.
    Hansma, H., G., and Hoh, J. (1994) Biomolecular imaging with the atomic force microscopy. Ann. Rev. Biophys. Biochem. Struct. 23, 115–139.CrossRefGoogle Scholar
  9. 9.
    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.PubMedGoogle Scholar
  10. 10.
    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.Google Scholar
  11. 11.
    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.Google Scholar
  12. 12.
    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.PubMedCrossRefGoogle Scholar
  13. 13.
    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.CrossRefGoogle Scholar
  14. 14.
    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.PubMedCrossRefGoogle Scholar
  15. 15.
    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.PubMedCrossRefGoogle Scholar
  16. 16.
    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.PubMedCrossRefGoogle Scholar
  17. 17.
    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.PubMedCrossRefGoogle Scholar
  18. 18.
    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.Google Scholar
  19. 19.
    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.PubMedCrossRefGoogle Scholar
  20. 20.
    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.CrossRefGoogle Scholar
  21. 21.
    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.PubMedCrossRefGoogle Scholar
  22. 22.
    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.CrossRefGoogle Scholar
  23. 23.
    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.CrossRefGoogle Scholar
  24. 24.
    Hansma, H. G. (1996) A useful buffer for atomic force microscopy of DNA. Sci. Tools Pharmacia Biotech. 1(3), 7.Google Scholar
  25. 25.
    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.PubMedCrossRefGoogle Scholar
  26. 26.
    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.Google Scholar
  27. 27.
    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.PubMedCrossRefGoogle Scholar

General Reading

  1. Colton et al., (eds.) (1998) Procedures in Scanning Probe Microscopes. Wiley, Chichester.Google Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2001

Authors and Affiliations

  • Yuri L. Lyubchenko
    • 1
  • Alexander A. Gall
    • 2
  • Luda S. Shlyakhtenko
    • 3
  1. 1.Departments of Biology and MicrobiologyArizona State UniversityTempe
  2. 2.Seattle GeneticsBothell
  3. 3.Departments of Plant Biology and MicrobiologyArizona State UniversityTempe

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