Summary
Despite their rather recent invention, atomic force microscopes are widely available commercially. AFM and its special modifications (tapping mode and noncontact operation in solution) have been successfully used for topographic studies of a large number of biological objects including DNA, RNA, proteins, cell membranes, and even whole cells. AFM was also successfully applied to studies of nucleic acids and various protein DNA complexes. Part of this success is due to the development of reliable sample preparation procedures. This chapter describes one of the approaches based on chemical functionalization of mica surface with 1-(3-aminopropyl) silatrane (APS). One of the most important properties of APS-mica approach is that the sample can be deposited on the surface in a wide range of ionic strengths, in the absence of divalent cations and a broad range of pH. In addition to imaging of dried sample, APS-mica allows reliable and reproducible time lapse imaging in aqueous solutions. Finally, APS mica is terminated with reactive amino groups that can be used for covalent and ionic attachment of molecules for AFM force spectroscopy studies. The protocols for the preparation of APS, functionalization with APS mica and AFM probes, preparation of samples for imaging in air and in aqueous solutions, and force spectroscopy studies are outlined. All these applications are illustrated with a few examples.
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References
Binnig, G., Rohrer, H., Gerber, C., and Weibel, E. (1982). Surface Studies by Scanning Tunneling Microscopy, Phys Rev Lett 49, 57 60.
Binnig, G., Quate, C. F., and Gerber, C. (1986). Atomic force microscope, Phys Rev Lett 56, 930 933.
Clemmer, C. R., and Beebe, T. P., Jr. (1991). Graphite: a mimic for DNA and other biomolecules in scanning tunneling microscope studies, Science251, 640 642.
Heckl, W. M., and Binnig, G. (1992). Domain walls on graphite mimic DNA, Ultramicroscopy 42 44(Pt B), 1073 1078.
Bustamante, C., Vesenka, J., Tang, C. L., Rees, W., Guthold, M., and Keller, R. (1992). Circular DNA molecules imaged in air by scanning force microscopy, Biochemistry 31, 22 26.
Yang, J., Takeyasu, K., and Shao, Z. (1992). Atomic force microscopy of DNA molecules, FEBS Lett 301, 173 176.
Vesenka, J., Guthold, M., Tang, C. L., Keller, D., Delaine, E., and Bustamante, C. (1992). Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope, Ultramicroscopy 42 44(Pt B), 1243 1249.
Lyubchenko, Y. L., Gall, A. A., Shlyakhtenko, L. S., Harrington, R. E., Jacobs, B. L., Oden, P. I., and Lindsay, S. M. (1992). Atomic force microscopy imaging of double stranded DNA and RNA, J Biomol Struct Dyn 10, 589 606.
Allen, M. J., Dong, X. F., O'Neill, T. E., Yau, P., Kowalczykowski, S. C., Gatewood, J., Balhorn, R., and Bradbury, E. M. (1993). Atomic force microscope measurements of nucleosome cores assembled along defined DNA sequences, Biochemistry 32, 8390 8396.
Hegner, M., Wagner, P., and Semenza, G. (1993). Immobilizing DNA on gold via thiol modification for atomic force microscopy imaging in buffer solutions, FEBS Lett 336, 452 456.
Mou, J., Czajkowsky, D. M., Zhang, Y., and Shao, Z. (1995). High-resolution atomic-force microscopy of DNA: the pitch of the double helix, FEBS Lett 371, 279 282.
Bustamante, C., Erie, D., and Keller, D. (1994). Biochemical and structural applications of scanning force microscopy, Curr Opin Struct Biol 4, 750 760.
Bustamante, C., Rivetti, C., and Keller, D. J. (1997). Scanning force microscopy under aqueous solutions, Curr Opin Struct Biol 7, 709 716.
Lyubchenko, Y. L., Gall, A. A., and Shlyakhtenko, L. S. (2001). Atomic force microscopy of DNA and protein-DNA complexes using functionalized mica substrates, Methods Mol Biol 148, 569 578.
Lyubchenko, Y., Shlyakhtenko, L., Harrington, R., Oden, P., and Lindsay, S. (1993) Atomic force microscopy of long DNA: imaging in air and under water, Proc Natl Acad Sci U S A 90, 2137 2140.
Lyubchenko, Y. L., Jacobs, B. L., Lindsay, S. M., and Stasiak, A. (1995). Atomic force microscopy of nucleoprotein complexes, Scanning Microsc 9, 705 724; discussion 724 707.
Lyubchenko, Y. L., Blankenship, R. E., Gall, A. A., Lindsay, S. M., Thiemann, O., Simpson, L., and Shlyakhtenko, L. S. (1996). Atomic force microscopy of DNA, nucleoproteins and cellular complexes: the use of functionalized substrates, Scanning Microsc Suppl 10, 97 107; discussion 107 109.
Lyubchenko, Y. L., and Shlyakhtenko, L. S. (1997). Visualization of supercoiled DNA with atomic force microscopy in situ, Proc Natl Acad Sci U S A 94, 496 501.
Shlyakhtenko, L. S., Potaman, V. N., Sinden, R. R., Gall, A. A., and Lyubchenko, Y. L. (2000). Structure and dynamics of three-way DNA junctions: atomic force microscopy studies, Nucleic Acids Res 28, 3472 3477.
Lyubchenko, Y. L., Shlyakhtenko, L. S., Potaman, V. P. and Sinden, R. R. (2002). Global and local DNA structure and dynamics. Single molecule studies with AFM, Microsc Microanal 8, 170 171.
Yodh, J. G., Woodbury, N., Shlyakhtenko, L. S., Lyubchenko, Y. L., and Lohr, D. (2002). Mapping nucleosome locations on the 208 12 by AFM provides clear evidence for cooperativity in array occupation, Biochemistry 41, 3565 3574.
Kato, M., Hokabe, S., Itakura, S., Minoshima, S., Lyubchenko, Y. L., Gurkov, T. D., Okawara, H., Nagayama, K., and Shimizu, N. (2003). Interarm interaction of DNA cruciform forming at a short inverted repeat sequence, Biophys J 85, 402 408.
Potaman, V. N., Bissler, J. J., Hashem, V. I., Oussatcheva, E. A., Lu, L., Shlyakhtenko, L. S., Lyubchenko, Y. L., Matsuura, T., Ashizawa, T., Leffak, M., Benham, C. J., and Sinden, R. R. (2003). Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats, J Mol Biol 326, 1095 1111.
Shlyakhtenko, L. S., Gall, A. A., Filonov, A., Cerovac, Z., Lushnikov, A., and Lyubchenko, Y. L. (2003). Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials, Ultramicroscopy 97, 279 287.
Lushnikov, A. Y., Brown, B. A.,2nd, Oussatcheva, E. A., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (2004). Interaction of the Zalpha domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy, Nucleic Acids Res 32, 4704 4712.
Lyubchenko, Y. L. (2004). DNA structure and dynamics: an atomic force microscopy study, Cell Biochem Biophys 41, 75 98.
Tiner, W. J., Sr., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (2001). The structure of intramolecular triplex DNA: atomic force microscopy study, J Mol Biol 314, 353 357.
Kato, M., McAllister, C. J., Hokabe, S., Shimizu, N., and Lyubchenko, Y. L. (2002). Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy, Eur J Biochem 269, 3632 3636.
Dahlgren, P. R., Karymov, M. A., Bankston, J., Holden, T., Thumfort, P., Ingram, V. M., and Lyubchenko, Y. L. (2005). Atomic force microscopy analysis of the Huntington protein nanofibril formation, Dis Mon 51, 374 385.
Lonskaya, I., Potaman, V. N., Shlyakhtenko, L. S., Oussatcheva, E. A., Lyubchenko, Y. L., and Soldatenkov, V. A. (2005). Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding, J Biol Chem 280, 17076 17083.
Lushnikov, A. Y., Potaman, V. N., and Lyubchenko, Y. L. (2006). Site-specific labeling of supercoiled DNA, Nucleic Acids Res 34, 111 117.
Lushnikov, A. Y., Potaman, V. N., Oussatcheva, E. A., Sinden, R. R., and Lyubchenko, Y. L. (2006). DNA strand arrangement within the SfiI-DNA complex: Atomic force microscopy analysis, Biochemistry 45, 152 158.
McAllister, C., Karymov, M. A., Kawano, Y., Lushnikov, A. Y., Mikheikin, A., Uversky, V. N., and Lyubchenko, Y. L. (2005). Protein interactions and misfolding analyzed by AFM force spectroscopy, J Mol Biol 354, 1028 1042.
Kransnoslobodtsev, A. V., Shlyakhtenko, L. S., Ukraintsev, E., Zaikova, T. O., Keana, J. F., and Lyubchenko, Y. L. (2005). Nanomedicine and protein misfolding diseases, Nanomedicine 1, 300 305.
Lyubchenko, Y. L., Sherman, S., Shlyakhtenko, L. S., and Uversky, V. N. (2006). Nanoimaging for protein misfolding and related diseases, J Cell Biochem 99, 53 70 [Figure featured on journal cover].
Krasnoslobodtsev, A. V., Shlyakhtenko, L. S., and Lyubchenko, Y. L. (2007). Probing Interactions within the synaptic DNA-SfiI complex by AFM force spectroscopy, J Mol Biol 365, 1407 1418.
Shlyakhtenko, L. S., Yuan, B., Emadi, S., Lyubchenko, Y. L., and Sierks, M. R. (2007). Single-molecule selection and recovery of structure-specific antibodies using atomic force microscopy, Nanomedicine 3, 192 197.
Lushnikov, A. Y., Bogdanov, A., and Lyubchenko, Y. L. (2003). DNA recombination: Holliday junctions dynamics and branch migration, J Biol Chem 278, 43130 43134 [Figure featured on journal cover].
Mikheikin, A. L., Lushnikov, A. Y., and Lyubchenko, Y. L. (2006). Effect of DNA supercoiling on the geometry of Holliday junctions, Biochemistry 45, 12998 13006.
Liu, R., McAllister, C., Lyubchenko, Y., and Sierks, M. R. (2004). Residues 17-20 and 30-35 of beta-amyloid play critical roles in aggregation, J Neurosci Res 75, 162 171.
Liu, R., McAllister, C., Lyubchenko, Y., and Sierks, M. R. (2004). Proteolytic antibody light chains alter beta-amyloid aggregation and prevent cytotoxicity, Biochemistry 43, 9999 10007.
Liu, R., Yuan, B., Emadi, S., Zameer, A., Schulz, P., McAllister, C., Lyubchenko, Y., Goud, G., and Sierks, M. R. (2004). Single chain variable fragments against beta-amyloid (Abeta) can inhibit Abeta aggregation and prevent abeta-induced neurotoxicity, Biochemistry 43, 6959 6967.
Emadi, S., Liu, R., Yuan, B., Schulz, P., McAllister, C., Lyubchenko, Y., Messer, A., and Sierks, M. R. (2004). Inhibiting aggregation of alpha-synuclein with human single chain antibody fragments, Biochemistry 43, 2871 2878.
Yamin, G., Munishkina, L. A., Karymov, M. A., Lyubchenko, Y. L., Uversky, V. N., and Fink, A. L. (2005). Forcing nonamyloidogenic beta-synuclein to fibrillate, Biochemistry 44, 9096 9107.
Watson, D., Castano, E., Kokjohn, T. A., Kuo, Y. M., Lyubchenko, Y., Pinsky, D., Connolly, E. S., Jr., Esh, C., Luehrs, D. C., Stine, W. B., Rowse, L. M., Emmerling, M. R., and Roher, A. E. (2005). Physicochemical characteristics of soluble oligomeric Abeta and their pathologic role in Alzheimer's disease, Neurol Res 27, 869 881.
Uversky, V. N., Yamin, G., Munishkina, L. A., Karymov, M. A., Millett, I. S., Doniach, S., Lyubchenko, Y. L., and Fink, A. L. (2005). Effects of nitration on the structure and aggregation of alpha-synuclein, Brain Res Mol Brain Res 134, 84 102.
Uversky, V. N., Kabanov, A. V., and Lyubchenko, Y. L. (2006). Nanotools for megaproblems: probing protein misfolding diseases using nanomedicine modus operandi, J Proteome Res 5, 2505 2522.
Dahlgren, P. R., Bankston, J., Holden, T., Karymov, M. A., Thumfort, P., Ingram, V. M., and Lyubchenko, Y. L. (2005). Atomic force microscopy analysis of the Huntington protein nanofibril formation, Nanomedicine 1, 52 57.
Riener, C. K., Stroh, C. M., Ebner, A., Gall, A. A., Klampfl, C., Romanin, C., Lyubchenko, Y. L., Hinterdorfer, P., and Gruber, H. J. (2003). A simple test system for single molecule recognition force microscopy, Anal Chim Acta 479, 59 75.
US Patent 3,118,921.
Hansma, H. G., and Hoh, J. H. (1994). Biomolecular imaging with the atomic force microscope, Annu Rev Biophys Biomol Struct 23, 115 139.
Lyubchenko, Y. L., Oden, P. I., Lampner, D., Lindsay, S. M., and Dunker, K. A. (1993). Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces, Nucleic Acids Res 21, 1117 1123.
Potaman, V. N., Lushnikov, A. Y., Sinden, R. R., and Lyubchenko, Y. L. (2002). Site-specific labeling of supercoiled DNA at the AÂ +Â T rich sequences, Biochemistry 41, 13198 13206.
Shlyakhtenko, L. S., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (1998). Structure and dynamics of supercoil-stabilized DNA cruciforms, J Mol Biol 280, 61 72.
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.
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.
Crampton, N., Yokokawa, M., Dryden, D. T., Edwardson, J. M., Rao, D. N., Takeyasu, K., Yoshimura, S. H., and Henderson, R. M. (2007). Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping, Proc Natl Acad Sci U S A 104, 12755 12760.
Hansma, H. G., and Laney, D. E. (1996). DNA binding to mica correlates with cationic radius: assay by atomic force microscopy, Biophys J 70, 1933 1939.
Kasas, S., Thomson, N. H., Smith, B. L., Hansma, H. G., Zhu, X., Guthold, M., Bustamante, C., Kool, E. T., Kashlev, M., and Hansma, P. K. (1997). Escherichia coli RNA polymerase activity observed using atomic force microscopy, Biochemistry 36, 461 468.
Acknowledgments
This work was supported by the grants GM 54991 (NIH) and PHY-06155909 (NSF) to YLL.
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Lyubchenko, Y.L., Shlyakhtenko, L.S., Gall, A.A. (2009). Atomic Force Microscopy Imaging and Probing of DNA, Proteins, and Protein-DNA Complexes: Silatrane Surface Chemistry. In: Leblanc, B., Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 543. Humana Press. https://doi.org/10.1007/978-1-60327-015-1_21
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