Skip to main content

Advertisement

Log in

Biophysics of single molecules

  • Analysis of Single Nanosystems
  • Published:
Biophysics Aims and scope Submit manuscript

Abstract

The modern methods of research on biological molecules which have led to the development of a new field of science, biophysics of single molecules, are reviewed. The measurement of the characteristics of single molecules enables one to reveal their individual features, and it is just for this reason that much more information can be obtained from one molecule than from the entire ensemble of molecules. The high sensitivity of the methods considered in detail makes it possible to come close to solving the basic problem of practical importance, namely, the determination of the nucleotide sequence of a single DNA molecule.

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.

Similar content being viewed by others

References

  1. I. N. Serdyuk, N. R. Zaccai, and J. Zaccai, Methods in Molecular Biophysics. Structure, Dynamics, Function (Cambridge Univ. Press, Cambridge, England, 2007; KDU, Moscow, 2009–2010).

    Google Scholar 

  2. U. Bockelmann, Curr. Opin. Struct. Biol. 14, 368 (2004).

    Article  Google Scholar 

  3. H. Clausen-Schaumann et al., Curr. Opin. Chem. Biol. 4, 524 (2000).

    Article  Google Scholar 

  4. K. Eom et al., Int. J. Mol. Sci. 10, 4009 (2009).

    Article  Google Scholar 

  5. Q. Peng and H. Li, Natl. Acad. Sci. USA 105, 1885 (2008).

    Article  ADS  Google Scholar 

  6. K. Ray et al., Virology 398, 224 (2010).

    Article  Google Scholar 

  7. K. C. Neuman and A. Nagy, Nat. Meth. 5, 491 (2008).

    Article  Google Scholar 

  8. G. Volpe, T. Brettschneider, L. Helden, and C. Bechinger, Opt. Express 17, 23975 (2009).

    Article  ADS  Google Scholar 

  9. N. Hertleinó et al., Langmuir 24, 1 (2008).

    Article  Google Scholar 

  10. M. J. Levene et al., Science 299, 682 (2003).

    Article  ADS  Google Scholar 

  11. W. E. Moerner and D. P. Fromm, Rev. Sci. Instrum. 74, 3597 (2003).

    Article  ADS  Google Scholar 

  12. E. Haustein and P. Schwille, Methods 29, 153 (2003).

    Article  Google Scholar 

  13. E. Cohen and W. E. Moerner, Appl. Phys. Lett. 86, 93 (2005).

    Google Scholar 

  14. R. Tsien, Annu. Rev. Biochem. 67, 509 (1998).

    Article  Google Scholar 

  15. Shelley R. McRae, Protein Expres. Purif. 41, 121 (2005).

    Article  Google Scholar 

  16. M. Fernandez-Suarez and A. Y. Ting, Nature Rev. 9, 929 (2008).

    Article  Google Scholar 

  17. P. Kukura, M. Celebrano, A. Renn, and V. Sandoghdar, Nanoletters 9, 926 (2009).

    Article  ADS  Google Scholar 

  18. S. Hohng and T. Ha, Chem. Phys. Chem. 6, 956 (2005).

    Article  Google Scholar 

  19. J. J. Lemasters et al., in Mitochondrial Dysfunction, Ed. by L.H. Lash, D.P. Jones (Academic Press, San Diego, 1993), p. 404.

    Google Scholar 

  20. M. N. Libenson, Soros. Obraz. Zh. 6, 99 (2000).

    Google Scholar 

  21. D. C. Mattis and J. Bardeen, Phys. Rev. 111, 412 (1958).

    Article  MATH  ADS  Google Scholar 

  22. P. Bharadwaj and L. Novotny, Optics Express 15, 14266 (2007).

    Article  ADS  Google Scholar 

  23. A. Egner et al., J. Struct. Biol. 147, 70 (2004).

    Article  Google Scholar 

  24. J. Bewersdorf, R. Schmidt, and S. W. Hell, J. Microscopy 222, 105 (2006).

    Article  MathSciNet  Google Scholar 

  25. O. A. Aktsipetrov, Soros. Obraz. Zh. 7, 109 (2001).

    Google Scholar 

  26. C. Xu et al., Proc. Natl. Acad. Sci. USA 20, 10763 (1996).

    Article  Google Scholar 

  27. V. Slabko, Soros. Obraz. Zh. 5, 105 (1999).

    Google Scholar 

  28. M. Hana, G. Giesec, and J. F. Billeb, Opt. Soc. Amer. 13(15), (2005).

  29. M. I. Stockman et al., Phys. Rev. Lett. 92, 057402 (2004).

    Article  ADS  Google Scholar 

  30. N. G. Walter et al., Nat. Meth. 5, 475 (2008).

    Article  Google Scholar 

  31. A Deniz, S. Mukhopadhyay, and E. A. Lemke, J. R. Soc. Interface 5, 15 (2008).

    Article  Google Scholar 

  32. S. W. Hell and J. Wichmann, Opt. Lett. 19, 780 (1994).

    Article  ADS  Google Scholar 

  33. K. I. Willig, New J. Phys. 8, 106 (2006).

    Article  ADS  Google Scholar 

  34. Klar et al., Proc. Natl. Acad. Sci. USA 97, 8206 (2000).

    Article  ADS  Google Scholar 

  35. A. Yildiz et al., J. Biol. Chem. 279, 37223 (2004).

    Article  Google Scholar 

  36. M. P. Gordon, T. Ha, and P. R. Selvin, Natl. Acad. Sci. USA 101, 6462 (2004).

    Article  ADS  Google Scholar 

  37. L. S. Churchman et al., Proc. Natl. Acad. Sci. USA 102, 1419 (2005).

    Article  ADS  Google Scholar 

  38. M. J. Rust, M. Bates, and X. W. Zhuang, Nat. Meth. 3, 793 (2006).

    Article  Google Scholar 

  39. B. Huang; W. Q. Wang, M. Bates, and X. W. Zhuang, Science 319, 810 (2008).

    Article  ADS  Google Scholar 

  40. S. T. Hess, T. P. K. Girirajan, and M. D. Mason, Biophys. J. 91, 4258 (2006).

    Article  ADS  Google Scholar 

  41. W. Min et al., Nature 461, 1105 (2009).

    Article  ADS  Google Scholar 

  42. R. Roy, S. Hohng, and T. Ha, Nat. Meth. 5, 507(2008).

    Article  Google Scholar 

  43. L. Stryer and R. P. Haugland, Proc. Natl. Acad. Sci. USA 58, 719 (1967).

    Article  ADS  Google Scholar 

  44. J. R. Lakowicz, in Principles of Fluorescence Spectroscopy (Kluwer Academic Plenum, New York, 1999).

    Google Scholar 

  45. Z. K. Majumdar et al., J. Mol. Biol. 351, 1123 (2005).

    Article  Google Scholar 

  46. G. Weber, Biochem. J. 75, 335 (1960).

    Google Scholar 

  47. I. H. Stein et al., Chem. Phys. Chem. 12, 689 (2011).

    Article  Google Scholar 

  48. Schuler et al., Proc. Natl. Acad. Sci. USA 102, 2754 (2005).

    Article  ADS  Google Scholar 

  49. S. Hohng, C. Joo, and T. Ha, Biophys. J. 87, 1328 (2004).

    Article  ADS  Google Scholar 

  50. S. Hohng et al., Science 318, 279 (2007).

    Article  ADS  Google Scholar 

  51. S. Lee, J. Lee, and S. Hohng, PLoS 5, 12270 (2010).

    ADS  Google Scholar 

  52. X. Michalet, S. Weiss, and M. Jager, Chem. Rev. 106, 1785 (2006).

    Article  Google Scholar 

  53. B. Schuler, E. A. Lipman, and W. A. Eaton, Nature 419, 743 (2002).

    Article  ADS  Google Scholar 

  54. E. V. Kuzmenkina, C. D. Heyes, and G. U. Nienhaus, Proc. Natl. Acad. Sci. USA 102, 15471 (2005).

    Article  ADS  Google Scholar 

  55. B. D. Slaughter et al., J. Phys. Chem. 108, 10388 (2004).

    Article  Google Scholar 

  56. Y. Sun, H. Wallrabe, R.N. Day, and A. Periasamy, Biophys. J. 99, 1274 (2010).

    Article  ADS  Google Scholar 

  57. U. Stephan et al., Forster Resonance Energy Transfer 12(3), 421 (2011).

    Google Scholar 

  58. E. Bailo and V. Deckert, Angew. Chem. Int. Ed. 47, 1658 (2008).

    Article  Google Scholar 

  59. X. M. Qian and S. M. Nie, Chem. Soc. Rev. 37, 912 (2008).

    Article  Google Scholar 

  60. K. Kneipp et al., Phys. Rev. Lett. 78, 1667 (1997).

    Article  ADS  Google Scholar 

  61. B. S. Yeo et al., J. Phys. Chem. 112, 4867 (2008).

    Google Scholar 

  62. D. Cialla et al., J. Raman Spectrosc. 40, 240 (2009).

    Article  ADS  Google Scholar 

  63. M. Bon et al., FASEB J. 20, 1721 (2006).

    Article  Google Scholar 

  64. M. K. Nahas et al., Nat. Struct. Mol. Biol. 11, 1107 (2004).

    Article  Google Scholar 

  65. W. J. Greenleaf, M. T. Woodside, and S. M. Block, Annu. Rev. Biophys. Biomol. Struct. 36, 171 (2007).

    Article  Google Scholar 

  66. U. M. Mirsaidov, D. Wang, W. Timp, and G. Timp, Nanomed. Nanobiotechnol. 2, 367 (2010).

    Article  Google Scholar 

  67. L. B. Freund, Proc. Natl. Acad. Sci. USA 106, 8818 (2009)

    Article  ADS  Google Scholar 

  68. R. Trefferl and V. Deckert, Curr. Opin. Biotechnol. 21, 4 (2010).

    Article  Google Scholar 

  69. K. Dorre et al., Bioimaging 5, 139 (1997).

    Article  Google Scholar 

  70. T. D. Harris et al., Science 320, 106 (2008).

    Article  ADS  Google Scholar 

  71. http://visgenbio.com

  72. J. Korlach et al., Proc. Natl. Acad. Sci. USA 105, 1176 (2008).

    Article  ADS  Google Scholar 

  73. J. Clarke et al., Nat. Nano. 4, 265 (2009).

    Article  Google Scholar 

  74. http://www.reveo.com

  75. http://zsgenetics.com

  76. M. Ronaghi et al., Anal. Biochem. 242, 84 (1996).

    Article  Google Scholar 

  77. W. J. Greenleaf and S. M. Block, Science 313, 801 (2006).

    Article  Google Scholar 

  78. A. Rasmussen and V. Deckert, J. Raman Spectrosc. 37, 311 (2006).

    Article  ADS  Google Scholar 

  79. K. F. Domke, D. Zhang, and B. Pettinger, J. Am. Chem. Soc. 129, 6708 (2007).

    Article  Google Scholar 

  80. B. R. Packer et al., Nucl. Acids Res. 30, 158 (2002).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to I. N. Serdyuk.

Additional information

Original Russian Text © I.N. Serdyuk, E.I. Deryusheva, 2011, published in Biofizika, 2011, Vol. 56, No. 5, pp. 899–927.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Serdyuk, I.N., Deryusheva, E.I. Biophysics of single molecules. BIOPHYSICS 56, 858–882 (2011). https://doi.org/10.1134/S0006350911050186

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0006350911050186

Keywords

Navigation