JSEMAT  Vol.2 No.3 A , July 2012
Elucidation and Identification of Double-Tip Effects in Atomic Force Microscopy Studies of Biological Structures
Author(s) Yong Chen*
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.

Cite this paper
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. 3, 2012, pp. 238-247. doi: 10.4236/jsemat.2012.223037.
[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