Skip to main content
Log in

Three Powerful Research Tools from Single Cells into Single Molecules: AFM, Laser Tweezers, and Raman Spectroscopy

  • Published:
Applied Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

By using three physical techniques (atomic force microscopy (AFM), laser tweezers, and Raman spectroscopy), many excellent works in single-cell/molecule research have been accomplished. In this review, we present a brief introduction to the principles of these three techniques, and their capabilities toward single-cell/molecule research are highlighted. Afterward, the advances in single-cell/molecule research that have been facilitated by these three techniques are described. Following this, their complementary assets for single-cell/molecule research are analyzed, and the necessity of integrating the functions of these three techniques into one instrument is proposed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Deniz, A. A., Mukhopadhyay, S., & Lemke, E. A. (2008). Single-molecule biophysics: At the interface of biology, physics and chemistry. Journal of the Royal Society Interface, 5, 15.

    Article  CAS  Google Scholar 

  2. Müller, D. J., & Dufrêne, Y. F. (2008). Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology. Nature Nanotechnology, 3, 261–269.

    Article  Google Scholar 

  3. Hormeno, S., & Arias-Gonzalez, J. R. (2006). Exploring mechanochemical processes in the cell with optical tweezers. Biology of the Cell, 98, 679–695.

    Article  CAS  Google Scholar 

  4. Kneipp, J., Kneipp, H., & Kneipp, K. (2008). SERS—a single-molecule and nanoscale tool for bioanalytics. Chemical Society Reviews, 37, 1052–1060.

    Article  CAS  Google Scholar 

  5. Neuman, K. C., & Nagy, A. (2008). Single-molecule force spectroscopy: Optical tweezers, magnetic tweezers and atomic force microscopy. Nature Methods, 5, 491–505.

    Article  CAS  Google Scholar 

  6. Muller, D. J. (2008). AFM: A nanotool in membrane biology. Biochemistry, 47, 7986–7998.

    Article  CAS  Google Scholar 

  7. Alsteens, D., Dague, E., Verbelen, C., Andre, G., Dupres, V., & Dufrêne, Y. F. (2009). Nanoscale imaging of microbial pathogens using atomic force microscopy. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 1, 168–180.

    Article  CAS  Google Scholar 

  8. Baumann, R. P., Schranz, M., & Hampp, N. (2010). Bending of purple membranes in dependence on the pH analyzed by AFM and single molecule force spectroscopy. Physical Chemistry Chemical Physics, 12, 4329–4335.

    Article  CAS  Google Scholar 

  9. Yu, J., Bippes, C. A., Hand, G. M., Muller, D. J., & Sosinsky, G. E. (2007). Aminosulfonate modulated pH-induced conformational changes in connexin26 hemichannels. The Journal of Biological Chemistry, 282, 8895.

    Article  CAS  Google Scholar 

  10. Dague, E., Alsteens, D., Latgé, J. P., & Dufrêne, Y. F. (2008). High-resolution cell surface dynamics of germinating Aspergillus fumigatus conidia. Biophysical Journal, 94, 656–660.

    Article  CAS  Google Scholar 

  11. Müller, D. J., Wu, N., & Palczewski, K. (2008). Vertebrate membrane proteins: Structure, function, and insights from biophysical approaches. Pharmacological Reviews, 60, 43.

    Article  Google Scholar 

  12. Krieg, M., Arboleda-Estudillo, Y., Puech, P. H., Käfer, J., Graner, F., Müller, D. J., et al. (2008). Tensile forces govern germ-layer organization in zebrafish. Nature cell biology, 10, 429–436.

    Article  CAS  Google Scholar 

  13. Dague, E., Alsteens, D., Latge, J. P., Verbelen, C., Raze, D., Baulard, A. R., et al. (2007). Chemical force microscopy of single live cells. Nano Letters, 7, 3026–3030.

    Article  CAS  Google Scholar 

  14. Alsteens, D., Dague, E., Rouxhet, P. G., Baulard, A. R., & Dufrêne, Y. F. (2007). Direct measurement of hydrophobic forces on cell surfaces using AFM. Langmuir, 23, 11977–11979.

    Article  CAS  Google Scholar 

  15. Rico, F., Roca-Cusachs, P., Sunyer, R., Farré, R., & Navajas, D. (2007). Cell dynamic adhesion and elastic properties probed with cylindrical atomic force microscopy cantilever tips. Journal of Molecular Recognition, 20, 459–466.

    Article  CAS  Google Scholar 

  16. Cuerrier, C. M., Lebel, R., & Grandbois, M. (2007). Single cell transfection using plasmid decorated AFM probes. Biochemical and Biophysical Research Communications, 355, 632–636.

    Article  CAS  Google Scholar 

  17. Cross, S. E., Jin, Y. S., Rao, J., & Gimzewski, J. K. (2007). Nanomechanical analysis of cells from cancer patients. Nature Nanotechnology, 2, 780–783.

    Article  CAS  Google Scholar 

  18. Suresh, S. (2007). Nanomedicine: Elastic clues in cancer detection. Nature Nanotechnology, 2, 748–749.

    Article  CAS  Google Scholar 

  19. Li, Q. S., Lee, G. Y. H., Ong, C. N., & Lim, C. T. (2008). AFM indentation study of breast cancer cells. Biochemical and Biophysical Research Communications, 374, 609–613.

    Article  CAS  Google Scholar 

  20. Kienberger, F., Costa, L. T., Zhu, R., Kada, G., Reithmayer, M., Chtcheglova, L., et al. (2007). Dynamic force microscopy imaging of plasmid DNA and viral RNA. Biomaterials, 28, 2403–2411.

    Article  CAS  Google Scholar 

  21. Hamon, L., Pastré, D., Dupaigne, P., Le Breton, C., Le Cam, E., & Piétrement, O. (2007). High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein—DNA complexes. Nucleic Acids Research, 35, e58.

    Article  Google Scholar 

  22. Elie-Caille, C., Severin, F., Helenius, J., Howard, J., Muller, D. J., & Hyman, A. A. (2007). Straight GDP-tubulin protofilaments form in the presence of taxol. Current Biology, 17, 1765–1770.

    Article  CAS  Google Scholar 

  23. Bash, R., Wang, H., Anderson, C., Yodh, J., Hager, G., Lindsay, S. M., et al. (2006). AFM imaging of protein movements: histone H2A–H2B release during nucleosome remodeling. FEBS Letters, 580, 4757–4761.

    Article  CAS  Google Scholar 

  24. Li, B. S., Sattin, B. D., & Goh, M. C. (2006). Direct and real-time visualization of the disassembly of a single RecA-DNA-ATPγS complex using AFM imaging in fluid. Nano Letters, 6, 1474–1478.

    Article  CAS  Google Scholar 

  25. Zhang, W., Dillingham, M. S., Thomas, C. D., Allen, S., Roberts, C. J., & Soultanas, P. (2007). Directional loading and stimulation of PcrA helicase by the replication initiator protein RepD. Journal of Molecular Biology, 371, 336–348.

    Article  CAS  Google Scholar 

  26. Yokokawa, M., Wada, C., Ando, T., Sakai, N., Yagi, A., Yoshimura, S. H., et al. (2006). Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL. The EMBO Journal, 25, 4567–4576.

    Article  CAS  Google Scholar 

  27. Kienberger, F., Ebner, A., Gruber, H. J., & Hinterdorfer, P. (2006). Molecular recognition imaging and force spectroscopy of single biomolecules. Accounts of Chemical Research, 39, 29–36.

    Article  CAS  Google Scholar 

  28. Hinterdorfer, P., & Dufrêne, Y. F. (2006). Detection and localization of single molecular recognition events using atomic force microscopy. Nature Methods, 3, 347–355.

    Article  CAS  Google Scholar 

  29. Puntheeranurak, T., Wildling, L., Gruber, H. J., Kinne, R. K. H., & Hinterdorfer, P. (2006). Ligands on the string: single-molecule AFM studies on the interaction of antibodies and substrates with the Na+–glucose co-transporter SGLT1 in living cells. Journal of Cell Science, 119, 2960–2967.

    Article  CAS  Google Scholar 

  30. Gilbert, Y., Deghorain, M., Wang, L., Xu, B., Pollheimer, P. D., Gruber, H. J., et al. (2007). Single-molecule force spectroscopy and imaging of the vancomycin/D-Ala-D-Ala interaction. Nano Letters, 7, 796–801.

    Article  CAS  Google Scholar 

  31. Sapra, K. T., Besir, H., Oesterhelt, D., & Muller, D. J. (2006). Characterizing molecular interactions in different bacteriorhodopsin assemblies by single-molecule force spectroscopy. Journal of Molecular Biology, 355, 640–650.

    Article  CAS  Google Scholar 

  32. Kedrov, A., Ziegler, C., & Muller, D. J. (2006). Differentiating ligand and inhibitor interactions of a single antiporter. Journal of Molecular Biology, 362, 925–932.

    Article  CAS  Google Scholar 

  33. Liu, N., Peng, B., Lin, Y., Su, Z., Niu, Z., Wang, Q., et al. (2010). Pulling genetic RNA out of tobacco mosaic virus using single-molecule force spectroscopy. Journal of the American Chemical Society, 132, 11036–11038.

    Article  CAS  Google Scholar 

  34. Dietz, H., Berkemeier, F., Bertz, M., & Rief, M. (2006). Anisotropic deformation response of single protein molecules. Proceedings of the National Academy of Sciences, 103, 12724.

    Article  CAS  Google Scholar 

  35. Lee, G., Abdi, K., Jiang, Y., Michaely, P., Bennett, V., & Marszalek, P. E. (2006). Nanospring behaviour of ankyrin repeats. Nature, 440, 246–249.

    Article  CAS  Google Scholar 

  36. Linke, W. A., & Grützner, A. (2008). Pulling single molecules of titin by AFM—recent advances and physiological implications. Pflügers Archiv—European Journal of Physiology, 456, 101–115.

    Article  CAS  Google Scholar 

  37. Kedrov, A., Appel, M., Baumann, H., Ziegler, C., & Muller, D. J. (2008). Examining the dynamic energy landscape of an antiporter upon inhibitor binding. Journal of Molecular Biology, 375, 1258–1266.

    Article  CAS  Google Scholar 

  38. Tsapikouni, T. S., & Missirlis, Y. F. (2010). Measuring the force of single protein molecule detachment from surfaces with AFM. Colloids and Surfaces. B: Biointerfaces, 75, 252–259.

    Article  CAS  Google Scholar 

  39. Kufer, S. K., Puchner, E. M., Gumpp, H., Liedl, T., & Gaub, H. E. (2008). Single-molecule cut-and-paste surface assembly. Science, 319, 594.

    Article  CAS  Google Scholar 

  40. Titushkin, I., & Cho, M. (2006). Distinct membrane mechanical properties of human mesenchymal stem cells determined using laser optical tweezers. Biophysical Journal, 90, 2582–2591.

    Article  CAS  Google Scholar 

  41. Xu, G., & Shao, J. Y. (2008). Human neutrophil surface protrusion under a point load: location independence and viscoelasticity. American Journal of Physiology. Cell Physiology, 295, C1434.

    Article  CAS  Google Scholar 

  42. Wei, M. T., Zaorski, A., Yalcin, H. C., Wang, J., Hallow, M., Ghadiali, S. N., et al. (2008). A comparative study of living cell micromechanical properties by oscillatory optical tweezers. Optics Express, 16, 8594–8603.

    Article  CAS  Google Scholar 

  43. Nascimento, J. M., Shi, L. Z., Chandsawangbhuwana, C., Tam, J., Durrant, B. S., Botvinick, E. L., et al. (2008). Use of laser tweezers to analyze sperm motility and mitochondrial membrane potential (Journal Paper). Journal of Biomedical Optics, 13, 014002.

    Article  Google Scholar 

  44. Volpe, G., Singh, G. P., & Petrov, D. (2006). Dynamics of a growing cell in an optical trap. Applied Physics Letters, 88, 231106.

    Article  Google Scholar 

  45. Rancourt-Grenier, S., Wei, M. T., Bai, J. J., Chiou, A., Bareil, P. P., Duval, P. L., et al. (2010). Dynamic deformation of red blood cell in dual-trap optical tweezers. Optics Express, 18, 10462–10472.

    Article  CAS  Google Scholar 

  46. Allioux-Guérin, M., Icard-Arcizet, D., Durieux, C., Hénon, S., Gallet, F., Mevel, J. C., et al. (2009). Spatiotemporal analysis of cell response to a rigidity gradient: a quantitative study using multiple optical tweezers. Biophysical Journal, 96, 238–247.

    Article  Google Scholar 

  47. Abbondanzieri, E. A., Shaevitz, J. W., & Block, S. M. (2005). Picocalorimetry of transcription by RNA polymerase. Biophysical Journal, 89, L61–L63.

    Article  CAS  Google Scholar 

  48. McNerney, G. P., Hübner, W., Chen, B. K., & Huser, T. (2010). Manipulating CD4+ T cells by optical tweezers for the initiation of cell-cell transfer of HIV-1. Journal of Biophotonics, 3, 216–223.

    Article  CAS  Google Scholar 

  49. Dame, R. T., Noom, M. C., & Wuite, G. J. L. (2006). Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature, 444, 387–390.

    Article  CAS  Google Scholar 

  50. Cecconi, C., Shank, E. A., Bustamante, C., & Marqusee, S. (2005). Direct observation of the three-state folding of a single protein molecule. Science, 309, 2057.

    Article  CAS  Google Scholar 

  51. Woodside, M. T., Anthony, P. C., Behnke-Parks, W. M., Larizadeh, K., Herschlag, D., & Block, S. M. (2006). Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science, 314, 1001.

    Article  CAS  Google Scholar 

  52. Woodside, M. T., Behnke-Parks, W. M., Larizadeh, K., Travers, K., Herschlag, D., & Block, S. M. (2006). Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. PNAS, 103, 6190–6195.

    Article  CAS  Google Scholar 

  53. Li, P. T. X., Bustamante, C., & Tinoco, I. (2007). Real-time control of the energy landscape by force directs the folding of RNA molecules. Proceedings of the National Academy of Sciences, 104, 7039.

    Article  CAS  Google Scholar 

  54. Moffitt, J. R., Chemla, Y. R., Aathavan, K., Grimes, S., Jardine, P. J., Anderson, D. L., et al. (2009). Intersubunit coordination in a homomeric ring ATPase. Nature, 457, 446–450.

    Article  CAS  Google Scholar 

  55. Galburt, E. A., Grill, S. W., Wiedmann, A., Lubkowska, L., Choy, J., Nogales, E., et al. (2007). Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature, 446, 820–823.

    Article  CAS  Google Scholar 

  56. Herbert, K. M., La Porta, A., Wong, B. J., Mooney, R. A., Neuman, K. C., Landick, R., et al. (2006). Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell, 125, 1083–1094.

    Article  CAS  Google Scholar 

  57. Dumont, S., Cheng, W., Serebrov, V., Beran, R. K., Tinoco, I., Pyle, A. M., et al. (2006). RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature, 439, 105–108.

    Article  CAS  Google Scholar 

  58. Dalal, R. V., Larson, M. H., Neuman, K. C., Gelles, J., Landick, R., & Block, S. M. (2006). Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing. Molecular Cell, 23, 231–239.

    Article  CAS  Google Scholar 

  59. Maier, B., Chen, I., Dubnau, D., & Sheetz, M. P. (2004). DNA transport into Bacillus subtilis requires proton motive force to generate large molecular forces. Nature Structural & Molecular Biology, 11, 643–649.

    Article  CAS  Google Scholar 

  60. Larson, M. H., Greenleaf, W. J., Landick, R., & Block, S. M. (2008). Applied force reveals mechanistic and energetic details of transcription termination. Cell, 132, 971–982.

    Article  CAS  Google Scholar 

  61. Mao, H., & Ricardo, A. G. (2005). Temperature control methods in a laser tweezers system. Biophysical Journal, 89, 1308–1316.

    Article  CAS  Google Scholar 

  62. Tam, J. M., Biran, I., & Walt, D. R. (2006). Parallel microparticle manipulation using an imaging fiber-bundle-based optical tweezer array and a digital micromirror device. Applied Physics Letters, 89, 194101.

    Article  Google Scholar 

  63. Konorov, S. O., Glover, C. H., Piret, J. M., Bryan, J., Schulze, H. G., Blades, M. W., et al. (2007). In situ analysis of living embryonic stem cells by coherent anti-Stokes Raman microscopy. Analytical Chemistry, 79, 7221–7225.

    Article  CAS  Google Scholar 

  64. Chan, J. W., Lieu, D. K., Huser, T., & Li, R. A. (2009). Label-free separation of human embryonic stem cells and their cardiac derivatives using Raman spectroscopy. Analytical Chemistry, 81, 1324–1331.

    Article  CAS  Google Scholar 

  65. Oshima, Y., Shinzawa, H., Takenaka, T., Furihata, C., & Sato, H. (2010). Discrimination analysis of human lung cancer cells associated with histological type and malignancy using Raman spectroscopy. Journal of Biomedical Optics, 15, 017009.

    Article  Google Scholar 

  66. Kaczor, A., Turnaub, K., & Baranskaa, M. (2011). In situ Raman imaging of astaxanthin in a single microalgal cell. Analyst, 136, 1109–1112.

    Article  CAS  Google Scholar 

  67. Hu, Q., Tay, L. L., Noestheden, M., & Pezacki, J. P. (2007). Mammalian cell surface imaging with nitrile-functionalized nanoprobes: biophysical characterization of aggregation and polarization anisotropy in SERS imaging. Journal of the American Chemical Society, 129, 14–15.

    Article  CAS  Google Scholar 

  68. Kneipp, J., Kneipp, H., McLaughlin, M., Brown, D., & Kneipp, K. (2006). In vivo molecular probing of cellular compartments with gold nanoparticles and nanoaggregates. Nano Letters, 6, 2225–2231.

    Article  CAS  Google Scholar 

  69. Li, J. F., Huang, Y. F., Ding, Y., Yang, Z. L., Li, S. B., Zhou, X. S., et al. (2010). Shell-isolated nanoparticle-enhanced Raman spectroscopy. Nature, 464, 392–395.

    Article  CAS  Google Scholar 

  70. Inya-Agha, O., Klauke, N., Davies, T., Smith, G., & Cooper, J. M. (2007). Spectroscopic probing of dynamic changes during stimulation and cell remodeling in the single cardiac myocyte. Analytical Chemistry, 79, 4581–4587.

    Article  CAS  Google Scholar 

  71. Huang, W. E., Bailey, M. J., Thompson, I. P., Whiteley, A. S., & Spiers, A. J. (2007). Single-cell Raman spectral profiles of Pseudomonas fluorescens SBW25 reflects in vitro and in planta metabolic history. Microbial Ecology, 53, 414–425.

    Article  CAS  Google Scholar 

  72. Qian, X. M., & Nie, S. M. (2008). Single-molecule and single-nanoparticle SERS: from fundamental mechanisms to biomedical applications. Chemical Society Reviews, 37, 912–920.

    Article  CAS  Google Scholar 

  73. Delfino, I., Bizzarri, A. R., & Cannistraro, S. (2005). Single-molecule detection of yeast cytochrome C by surface-enhanced Raman spectroscopy. Biophysical Chemistry, 113, 41–51.

    Article  CAS  Google Scholar 

  74. Koo, T. W., Chan, S., & Berlin, A. A. (2005). Single-molecule detection of biomolecules by surface-enhanced coherent anti-Stokes Raman scattering. Optics Letters, 30, 1024–1026.

    Article  CAS  Google Scholar 

  75. Xie, C., Nguyen, N., Zhu, Y., & Li, Y. (2007). Detection of the recombinant proteins in single transgenic microbial cell using laser tweezers and Raman spectroscopy. Analytical Chemistry, 79, 9269–9275.

    Article  CAS  Google Scholar 

  76. Chen, D., Shelenkova, L., Li, Y., Kempf, C. R., & Sabelnikov, A. (2009). Laser tweezers Raman spectroscopy potential for studies of complex dynamic cellular processes: single cell bacterial lysis. Analytical Chemistry, 81, 3227–3238.

    Article  CAS  Google Scholar 

  77. Chan, J. W., Taylor, D. S., Lane, S. M., Zwerdling, T., Tuscano, J., & Huser, T. (2008). Nondestructive identification of individual leukemia cells by laser trapping Raman spectroscopy. Analytical Chemistry, 80, 2180–2187.

    Article  CAS  Google Scholar 

  78. Wu, H., Volponi, J. V., Oliver, A. E., Parikh, A. N., Simmons, B. A., & Singh, S. (2011). In vivo lipidomics using single-cell Raman spectroscopy. Proceedings of the National Academy of Sciences, 108, 3809–3814.

    Article  CAS  Google Scholar 

  79. Rong, X., Huang, S. S., Kuang, X. C., & Liu, H. (2010). Real–time detection of single–living pancreatic β–cell by laser tweezers Raman spectroscopy: High glucose stimulation. Biopolymers, 93, 587–594.

    Article  CAS  Google Scholar 

  80. Ye A & Zhang Y (2009) Micro-Raman spectroscopy of optically trapped single cell. In SPIE, pp. 750704.

  81. Liu, R., Taylor, D. S., Matthews, D. L., & Chan, J. W. (2010). Parallel analysis of individual biological cells using multifocal laser tweezers Raman spectroscopy. Applied Spectroscopy, 64, 1308–1310.

    Article  CAS  Google Scholar 

  82. Zhang, P., Kong, L., Setlow, P., & Li, Y. (2010). Multiple-trap laser tweezers Raman spectroscopy for simultaneous monitoring of the biological dynamics of multiple individual cells. Optics Letters, 35, 3321–3323.

    Article  CAS  Google Scholar 

  83. Böhme, R., Richter, M., Cialla, D., Rösch, P., Deckert, V., & Popp, J. (2009). Towards a specific characterisation of components on a cell surface—combined TERS-investigations of lipids and human cells. Journal of Raman Spectroscopy, 40, 1452–1457.

    Article  Google Scholar 

  84. Böhme, R., Cialla, D., Richter, M., Rösch, P., Popp, J., & Deckert, V. (2010). Biochemical imaging below the diffraction limit—probing cellular membrane related structures by tip-enhanced Raman spectroscopy (TERS). Journal of Biophotonics, 3, 455–461.

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by The National Natural Sciences Foundation of China (10974025, 30700181), Young Teacher Culture Foundation of Dalian University of Technology (893228), and the Doctoral Fund of the Ministry of Education of China (20070141055).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kun Liu.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wu, Y., Liu, K., Song, K. et al. Three Powerful Research Tools from Single Cells into Single Molecules: AFM, Laser Tweezers, and Raman Spectroscopy. Appl Biochem Biotechnol 165, 485–496 (2011). https://doi.org/10.1007/s12010-011-9267-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12010-011-9267-2

Keywords

Navigation