Elucidation and Identification of Double-Tip Effects in Atomic Force Microscopy Studies of Biological Structures

Abstract

While atomic force microscopy (AFM) has been increasingly applied to life science, artifactual measurements or images can occur during nanoscale analyses of cell components and biomolecules. Tip-sample convolution effect is the most common mechanism responsible for causing artifacts. Some deconvolution-based methods or algorithms have been developed to reconstruct the specimen surface or the tip geometry. Double-tip or double-probe effect can also induce artifactual images by a different mechanism from that of convolution effect. However, an objective method for identifying the double-tip/probe-induced artifactual images is still absent. To fill this important gap, we made use of our expertise of AFM to analyze artifactual double-tip images of cell structures and biomolecules, such as linear DNA, during AFM scanning and imaging. Mathematical models were then generated to elucidate the artifactual double-tip effects and images develop during AFM imaging of cell structures and biomolecules. Based on these models, computational formulas were created to measure and identify potential double-tip AFM images. Such formulas proved to be useful for identification of double-tip images of cell structures and DNA molecules. The present studies provide a useful methodology to evaluate double-tip effects and images. Our results can serve as a foundation to design computer-based automatic detection of double-tip AFM images during nanoscale measuring and imaging of biomolecules and even non-biological materials or structures, and then personal experience is not needed any longer to evaluate artifactual images induced by the double-tip/probe effect.

Share and Cite:

Y. Chen, "Elucidation and Identification of Double-Tip Effects in Atomic Force Microscopy Studies of Biological Structures," Journal of Surface Engineered Materials and Advanced Technology, Vol. 2 No. 3A, 2012, pp. 238-247. doi: 10.4236/jsemat.2012.223037.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] R. F. Service, “Nanotechnology: Biology Offers Nanotechs a Helping Hand,” Science, Vol. 298, No. 5602, 2002, pp. 2322-2323. doi:10.1126/science.298.5602.2322
[2] S. W. Schneider, K. C. Sritharan, J. P. Geibel, et al., “Surface Dynamics in Living Acinar Cells Imaged by Atomic Force Microscopy: Identification of Plasma Membrane Structures Involved in Exocytosis,” Proceedings of the National Academy of Sciences of USA, Vol. 94, No. 1, 1997, pp. 316-321. doi:10.1126/science.298.5602.2322
[3] D. Fotiadis, Y. Liang, S. Filipek, et al., “Atomic-Force Microscopy: Rhodopsin Dimers in Native Disc Membranes,” Nature, Vol. 421, No. 6919, 2003, pp. 127-128. doi:10.1126/science.298.5602.2322
[4] J. L. Alonso and W. H. Goldmann, “Feeling the Forces: Atomic Force Microscopy in Cell Biology,” Life Sciences, Vol. 72, No. 23, 2003, pp. 2553-2560. doi:10.1016/S0024-3205(03)00165-6
[5] J. A. Dvorak, “The Application of Atomic Force Micros-copy to the Study of Living Vertebrate Cells in Culture,” Methods, Vol. 29, No. 1, 2003, pp. 86-96. doi:10.1016/S1046-2023(02)00284-0
[6] Y. Chen, J. Cai, “Membrane Deformation of Unfixed Erythrocytes in Air with Time Lapse Investigated by Tapping Mode Atomic Force Microscopy,” Micron, Vol. 37, No. 4, 2006, pp. 339-346. doi:10.1016/j.micron.2005.11.011
[7] Y. Chen, J. Cai, C. Wang, et al., “Atomic Force Microscopy Imaging and 3-D Reconstructions of Serial Thin Sections of a Single Cell and Its Interior Structures,” Ul- tramicroscopy, Vol. 103, No. 3, 2005, pp. 173-182. doi:10.1016/j.ultramic.2004.11.019
[8] L. F. Jimenez-Garcia and R. Fragoso-Soriano, “Atomic Force Microscopy of the Cell Nucleus,” Journal of Structural Biology, Vol. 129, No. 2-3, 2000, pp. 218-222. doi:10.1006/jsbi.2000.4233
[9] J. G. Forbes and G. H. Lorimer, “Structural Biology: Unraveling a Membrane Protein,” Science, Vol. 288, No. 5463, 2000, pp. 63-64. doi:10.1126/science.288.5463.63
[10] G. H. Thomas, “New Routes to Membrane Protein Struc- tures. Practical Course: Current Methods in Membrane Protein Research,” EMBO Re-port, Vol. 2, No. 3, 2001, pp. 187-191. doi:10.1093/embo-reports/kve049
[11] T. Osada, A. Itoh and A. Ikai, “Mapping of the Receptor- Associated Protein (RAP) Binding Proteins on Living Fibroblast Cells Using an Atomic Force Microscope,” Ultramicroscopy, Vol. 97, No. 1-4, 2003, pp. 353-357. doi:10.1016/S0304-3991(03)00060-3
[12] Y. Yang, H. Wang and D. A. Erie, “Quantitative Characterization of Biomolecular Assemblies and Interactions Using Atomic Force Microscopy,” Methods, Vol. 29, No. 2, 2003, pp. 175-187. doi:10.1016/S1046-2023(02)00308-0
[13] Y. Chen, J. Cai, Q. Xu and Z. W. Chen, “Atomic Force Bio-Analytics of Polymer-ization and Aggregation of phy-coerythrin-Conjugated Immu-noglobulin G Molecules,” Molecular Immunology, Vol. 41, No. 12, 2004, pp. 1247- 1252. doi:10.1016/j.molimm.2004.05.012
[14] P. E. Marszalek, H. Li and J. M. Fernandez, “Fingerprinting Polysaccharides with Single-Molecule Atomic Force Microscopy,” Nature Biotechnology, Vol. 19, No. 3, 2001, pp. 258-262. doi:10.1038/85712
[15] J. Tamayo and M. Miles, “Scanning Probe Microscopy for Chromosomal Research,” Archives of Histology and Cytology, Vol. 65, No. 5, 2002, pp. 369-376. doi:10.1679/aohc.65.369
[16] Y. Chen, L. Shao, Z. Ali, J. Cai and Z. W. Chen, “NSOM/ QD-Based Nanoscale Immunofluo-rescence Imaging of An-tigen-Specific T-Cell Receptor Responses during an in Vivo Clonal Vg2Vd2 T-Cell Expansion,” Blood, Vol. 111, No. 8, 2008, pp. 4220-4232. doi:10.1182/blood-2007-07-101691
[17] Y. Chen, J. Qin and Z. W. Chen, “Fluorescence-Topog-raphic NSOM Directly Visu-alizes Peak-Valley Polarities of GM1/GM3 Rafts in Cell Mem-brane Fluctuations,” The Journal of Lipid Research, Vol. 49, No. 10, 2008, pp. 2268-2275. doi:10.1194/jlr.D800031-JLR200
[18] Y. Chen, J. Qin, J. Cai and Z. W. Chen, “Cold Induces Micro- and Nano-Scale Reor-ganization of Lipid Raft Markers at Mounds of Cell-Membrane Fluctuations,” PLoS One, Vol. 4, No. 4, 2009, p. e5386. doi:10.1371/journal.pone.0005386
[19] S. Bunk, “Better Mi-croscopes will Be Instrumental in Nanotechnology Develop-ment,” Nature, Vol. 410, No. 6824, 2001, pp. 127-129. doi:10.1038/35065204
[20] K. Keren, M. Krueger, R. Gilad, et al., “Sequence-Specific Molecular Lithography on Single DNA Molecules,” Science, Vol. 297, No. 5578, 2002, pp. 72-75. doi:10.1126/science.1071247
[21] J. K. Horber and M. J. Miles, “Scanning Probe Evolution in Biology,” Science, Vol. 302, No. 5647, 2003, pp. 1002- 1005. doi:10.1126/science.1067410
[22] K. L. Westra, A. W. Mitchell and D. J. Thomson, “Tip Artifacts in Atomic-Force Microscope Imaging of Thin-Film Surfaces,” Journal of Applied Physics, Vol. 74, No. 5, 1993, pp. 3608-3610. doi:10.1063/1.354498
[23] D. Nyyssonen, L. Landstein and E. Coombs, “2-Dimen- sional Atomic Force Microprobe Trench Metrology System,” Journal of Vacuum Science & Technology B, Vol. 9, No. 6, 1991, pp. 3612-3616. doi:10.1116/1.585855
[24] D. J. Keller and C. C. Chou, “Imaging Steep, High Structures by Scanning Force Microscopy with Electron-Beam Deposited Tips,” Surface Science, Vol. 358, No. 1-3, 1992, pp. 333-339. doi:10.1016/0039-6028(92)90973-A
[25] P. Grutter, W. Zimmermannedling and D. Brodbeck, “Tip Artifacts of Microfabricated Force Sensors for Atomic Force Microscopy,” Applied Physics Letters, Vol. 60, No. 22, 1992, pp. 2741-2743. doi:10.1063/1.106862
[26] S. N. Magonov, A. Y. Gorenberg and H. J. Cantow, “Atomic Force Microscopy on Polymers and Polymer Related- Compounds,” Polymer Bulletin, Vol. 28, No. 5, 1992, pp. 577-584. doi:10.1007/BF00296049
[27] U. D. Schwarz, H. Haefke, P. Reimann and H. J. Guntherodt, “Tip Artifacts in Scanning Force Microscopy,” Journal of Microscopy, Vol. 173, No. 3, 1994, pp. 183- 197. doi:10.1111/j.1365-2818.1994.tb03441.x
[28] J. S. Villarrubia, “Morphological Estimation of Tip Ge- ometry for Scanned Probe Microscopy,” Surface Science, Vol. 321, No. 3, 1994, pp. 287-300. doi:10.1016/0039-6028(94)90194-5
[29] J. S. Villarrubia, “Algorithms for Scanned Probe Microscope Image Simulation, Surface Reconstruction, and Tip Estimation,” Journal of Re-search of the National Institute of Standards and Technology, Vol. 102, No. 4, 1997, pp. 425-454. doi:10.6028/jres.102.030
[30] Y. Chen, J. Cai, M. Liu, et al., “Research on Double- Probe, Double- and Triple-Tip Effects during Atomic Force Microscopy Scanning,” Scanning, Vol. 26, No. 4, 2004, pp. 155-161. doi:10.1002/sca.4950260402
[31] N. C. Santos, E. Ter-Ovanesyan, J. A. Zasadzinski and M. A. Castanho, “Reconstitution of Phospholipid Bilayer by an Atomic Force Microscope Tip,” Biophysical Journal, Vol. 75, No. 4, 1998, pp. 2119-2120. doi:10.1016/S0006-3495(98)77654-4
[32] N. H. Thomson, B. L. Smith, N. Almqvist, et al., “Oriented, Active Escherichia coli RNA Polymerase: An Atomic Force Microscope Study,” Biophysical Journal, Vol. 76, No. 2, 1999, pp. 1024-1033. doi:10.1016/S0006-3495(99)77267-X
[33] F. J. Giessibl, S. Hembacher, H. Bielefeldt and J. Mannhart, “Subatomic Features on the Silicon (111)-(7×7) Surface Observed by Atomic Force Microscopy,” Science, Vol. 289, No. 5478, 2000, pp. 422-426. doi:10.1126/science.289.5478.422
[34] J. Jass, T. Tjarnhage and G. Puu, “From Liposomes to Sup- ported, Planar Bilayer Structures on Hydrophilic and Hydrophobic Surfaces: An Atomic Force Microscopy Study,” Biophysical Journal, Vol. 79, No. 6, 2000, pp. 3153- 3163. doi:10.1016/S0006-3495(00)76549-0

Copyright © 2021 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.