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Accurately determining single molecule trajectories of molecular motion on surfaces

J. Chem. Phys. 130, 164710 (2009); doi:10.1063/1.3118982

Published 28 April 2009

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Kevin Claytor,1 Saumyakanti Khatua,1 Jason M. Guerrero,1 Alexei Tcherniak,1 James M. Tour,1 and Stephan Link1,2
1Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, USA
2Department of Electrical and Computer Engineering, Rice University, 6100 Main Street, Houston, Texas 77005, USA
This paper presents a method for simultaneously determining multiple trajectories of single molecules from sequential fluorescence images in the presence of photoblinking. The tracking algorithm is computationally nondemanding and does not assume a model for molecular motion, which allows one to determine correct trajectories even when a distribution of movement speeds is present. We applied the developed procedure to the important problem of monitoring surface motion of single molecules under ambient conditions. By limiting the laser exposure using sample scanning confocal microscopy, long-time trajectories have been extracted without the use of oxygen scavengers for single fluorescent molecules. Comparison of the experimental results to simulations showed that the smallest diffusion constants extracted from the trajectories are limited by detector shot noise giving error in locating the positions of the individual molecules. The simulations together with the single molecule trajectories and distributions of diffusion constants allowed us therefore to distinguish between mobile and immobile molecules. Because the analysis algorithm only requires a time series of images, the procedure presented here can be used in conjunction with various imaging methodologies to study a wide range of diffusion processes. ©2009 American Institute of Physics
History: Received 25 January 2009; accepted 17 March 2009; published 28 April 2009
Permalink: http://link.aip.org/link/?JCPSA6/130/164710/1
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KEYWORDS and PACS

Keywords
PACS
  • 33.50.Dq
    Molecular fluorescence and phosphorescence spectra
  • 68.35.Fx
    Diffusion; interface formation (solid surfaces)
  • 07.79.-v
    Scanning probe microscopes and components
  • YEAR: 2009

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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REFERENCES (38)
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For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. W. Ho, J. Chem. Phys. 117, 11033 (2002).
  2. C. Joo, H. Balci, Y. Ishitsuka, C. Buranachai, and T. Ha, Annu. Rev. Biochem. 77, 51 (2008).
  3. W. E. Moerner and D. P. Fromm, Rev. Sci. Instrum. 74, 3597 (2003).
  4. X. S. Xie and J. K. Trautman, Annu. Rev. Phys. Chem. 49, 441 (1998).
  5. T. Schmidt, G. J. Shultz, W. Baumgartner, H. J. Gruber, and H. Schindler, Proc. Natl. Acad. Sci. U.S.A. 93, 2926 (1996).
  6. C. Hellriegel, J. Kirstein, C. Braeuchle, V. Latour, T. Pigot, R. Olivier, S. Lacombe, R. Brown, V. Guieu, C. Payrastre, A. Izquierdo, and P. Mocho, J. Phys. Chem. B 108, 14699 (2004).
  7. B. Takimoto, H. Nabika, and K. Murakoshi, Jpn. J. Appl. Phys., Part 1 45, 6039 (2006).
  8. E. Mei, A. Sharonov, F. Gaio, J. H. Ferris, and R. M. Hochstrasser, J. Phys. Chem. A 108, 7339 (2004).
  9. G. Sazaki, M. Okada, T. Matsui, T. Watanabe, H. Higuchi, K. Tsukamoto, and K. Nakajima, Cryst. Growth Des. 8, 2024 (2008).
  10. J. C. Crocker and B. D. Hoffman, Methods Cell Biol. 83, 141 (2007).
  11. A. D. Mehta, M. Rief, J. A. Spudich, D. A. Smith, and R. M. Simmons, Science 283, 1689 (1999).
  12. J. Gelles, B. J. Schnapp, and M. P. Sheetz, Nature (London) 331, 450 (1988).
  13. A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin, Science 300, 2061 (2003).
  14. B. S. Swartzentruber, Phys. Rev. Lett. 76, 459 (1996).
  15. M. Schunack, T. R. Linderoth, F. Rosei, E. Laegsgaard, I. Stensgaard, and F. Besenbacher, Phys. Rev. Lett. 88, 156102 (2002).
  16. T. T. Tsong, Prog. Surf. Sci. 67, 235 (2001).
  17. Y. Shirai, A. J. Osgood, Y. M. Zhao, K. F. Kelly, and J. M. Tour, Nano Lett. 5, 2330 (2005).
  18. S. Bonneau, M. Dahan, and L. D. Cohen, IEEE Trans. Image Process. 14, 1384 (2005).
  19. K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, S. L. Schmid, and G. Danuser, Nat. Methods 5, 695 (2008).
  20. A. Serge, N. Bertaux, H. Rigneault, and D. Marguet, Nat. Methods 5, 687 (2008).
  21. J. Enderlein, I. Gregor, D. Patra, and J. Fitter, J. Fluoresc. 15, 415 (2005).
  22. E. Haustein and P. Schwille, Annu. Rev. Biophys. Biomol. Struct. 36, 151 (2007).
  23. S. Khatua, J. M. Guerrero, K. Claytor, G. Vives, A. B. Kolomeisky, J. M. Tour, and S. Link, ACS Nano 3, 351 (2009).
  24. M. Kuno, D. P. Fromm, H. F. Hamann, A. Gallagher, and D. J. Nesbitt, J. Chem. Phys. 115, 1028 (2001).
  25. C. E. Aitken, R. A. Marshall, and J. D. Pulglisi, Biophys. J. 94, 1826 (2008).
  26. R. E. Thompson, D. R. Larson, and W. W. Webb, Biophys. J. 82, 2775 (2002).
  27. X. Qu, D. Wu, L. Mets, and N. F. Scherer, Proc. Natl. Acad. Sci. U.S.A. 101, 11298 (2004).
  28. A. Yildiz and P. R. Selvin, Acc. Chem. Res. 38, 574 (2005).
  29. M. J. Rust, M. Bates, and X. W. Zhuang, Nat. Methods 3, 793 (2006).
  30. J. S. Biteen, M. A. Thompson, N. K. Tselentis, G. R. Bowman, L. Shapiro, and W. E. Moerner, Nat. Methods 5, 947 (2008).
  31. E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, Science 313, 1642 (2006).
  32. M. K. Cheezum, W. F. Walker, and W. H. Guilford, Biophys. J. 81, 2378 (2001).
  33. D. B. Reid, IEEE Trans. Autom. Control 24, 843 (1979).
  34. J. C. Crocker and D. G. Grier, J. Colloid Interface Sci. 179, 298 (1996).
  35. A. Genovesio, T. Liedl, V. Emiliani, W. J. Parak, M. Coppey-Moisan, and J. C. Olivo-Marin, IEEE Trans. Image Process. 15, 1062 (2006).
  36. J. W. Yoon, A. Bruckbauer, W. J. Fitzgerald, and D. Klenerman, Biophys. J. 94, 4932 (2008).
  37. Y. Shirai, J. F. Morin, T. Sasaki, J. M. Guerrero, and J. M. Tour, Chem. Soc. Rev. 35, 1043 (2006).
  38. J. -F. Morin, T. Sasaki, Y. Shirai, J. M. Guerrero, and J. M. Tour, J. Org. Chem. 72, 9481 (2007).

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