Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1999 Mar;76(3):1598–1605. doi: 10.1016/S0006-3495(99)77319-4

Quantitative study of polymer conformation and dynamics by single-particle tracking.

H Qian 1, E L Elson 1
PMCID: PMC1300136  PMID: 10049340

Abstract

We present a new method for analyzing the dynamics of conformational fluctuations of individual flexible polymer molecules. In single-particle tracking (SPT), one end of the polymer molecule is tethered to an immobile substratum. A microsphere attached to the other end serves as an optical marker. The conformational fluctuations of the polymer molecule can be measured by optical microscopy via the motion of the microsphere. The bead-and-spring theory for polymer dynamics is further developed to account for the microsphere, and together the measurement and the theory yield quantitative information about molecular conformations and dynamics under nonperturbing conditions. Applying the method to measurements carried out on DNA molecules provides information complementary to recent studies of single DNA molecules under extensional force. Combining high precision measurements with the theoretical analysis presented here creates a powerful tool for studying conformational dynamics of biological and synthetic macromolecules at the single-molecule level.

Full Text

The Full Text of this article is available as a PDF (83.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bustamante C., Marko J. F., Siggia E. D., Smith S. Entropic elasticity of lambda-phage DNA. Science. 1994 Sep 9;265(5178):1599–1600. doi: 10.1126/science.8079175. [DOI] [PubMed] [Google Scholar]
  2. Cluzel P., Lebrun A., Heller C., Lavery R., Viovy J. L., Chatenay D., Caron F. DNA: an extensible molecule. Science. 1996 Feb 9;271(5250):792–794. doi: 10.1126/science.271.5250.792. [DOI] [PubMed] [Google Scholar]
  3. Elson E. L. Simple sequential model for the kinetics of conformational transitions of oligomeric helices and proteins. Biopolymers. 1972;11(7):1499–1520. doi: 10.1002/bip.1972.360110713. [DOI] [PubMed] [Google Scholar]
  4. Elson E. L., Webb W. W. Concentration correlation spectroscopy: a new biophysical probe based on occupation number fluctuations. Annu Rev Biophys Bioeng. 1975;4(00):311–334. doi: 10.1146/annurev.bb.04.060175.001523. [DOI] [PubMed] [Google Scholar]
  5. Erickson H. P. Reversible unfolding of fibronectin type III and immunoglobulin domains provides the structural basis for stretch and elasticity of titin and fibronectin. Proc Natl Acad Sci U S A. 1994 Oct 11;91(21):10114–10118. doi: 10.1073/pnas.91.21.10114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Finzi L., Gelles J. Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science. 1995 Jan 20;267(5196):378–380. doi: 10.1126/science.7824935. [DOI] [PubMed] [Google Scholar]
  7. Gelles J., Schnapp B. J., Sheetz M. P. Tracking kinesin-driven movements with nanometre-scale precision. Nature. 1988 Feb 4;331(6155):450–453. doi: 10.1038/331450a0. [DOI] [PubMed] [Google Scholar]
  8. Horowitz D. S., Wang J. C. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol. 1984 Feb 15;173(1):75–91. doi: 10.1016/0022-2836(84)90404-2. [DOI] [PubMed] [Google Scholar]
  9. Kellermayer M. S., Smith S. B., Granzier H. L., Bustamante C. Folding-unfolding transitions in single titin molecules characterized with laser tweezers. Science. 1997 May 16;276(5315):1112–1116. doi: 10.1126/science.276.5315.1112. [DOI] [PubMed] [Google Scholar]
  10. Klapper I., Qian H. Remarks on discrete and continuous large-scale models of DNA dynamics. Biophys J. 1998 May;74(5):2504–2514. doi: 10.1016/S0006-3495(98)77959-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Neher E., Stevens C. F. Conductance fluctuations and ionic pores in membranes. Annu Rev Biophys Bioeng. 1977;6:345–381. doi: 10.1146/annurev.bb.06.060177.002021. [DOI] [PubMed] [Google Scholar]
  12. Perkins T. T., Quake S. R., Smith D. E., Chu S. Relaxation of a single DNA molecule observed by optical microscopy. Science. 1994 May 6;264(5160):822–826. doi: 10.1126/science.8171336. [DOI] [PubMed] [Google Scholar]
  13. Perkins T. T., Smith D. E., Larson R. G., Chu S. Stretching of a single tethered polymer in a uniform flow. Science. 1995 Apr 7;268(5207):83–87. doi: 10.1126/science.7701345. [DOI] [PubMed] [Google Scholar]
  14. Qian H., Sheetz M. P., Elson E. L. Single particle tracking. Analysis of diffusion and flow in two-dimensional systems. Biophys J. 1991 Oct;60(4):910–921. doi: 10.1016/S0006-3495(91)82125-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Rief M., Gautel M., Oesterhelt F., Fernandez J. M., Gaub H. E. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science. 1997 May 16;276(5315):1109–1112. doi: 10.1126/science.276.5315.1109. [DOI] [PubMed] [Google Scholar]
  16. Rippe K., von Hippel P. H., Langowski J. Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci. 1995 Dec;20(12):500–506. doi: 10.1016/s0968-0004(00)89117-3. [DOI] [PubMed] [Google Scholar]
  17. Schellman J. A., Harvey S. C. Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys Chem. 1995 Jun-Jul;55(1-2):95–114. doi: 10.1016/0301-4622(94)00144-9. [DOI] [PubMed] [Google Scholar]
  18. Shapiro B. E., Qian H. A quantitative analysis of single protein-ligand complex separation with the atomic force microscope. Biophys Chem. 1997 Sep 1;67(1-3):211–219. doi: 10.1016/s0301-4622(97)00045-8. [DOI] [PubMed] [Google Scholar]
  19. Shapiro B. E., Qian H. Hysteresis in force probe measurements: a dynamical systems perspective. J Theor Biol. 1998 Oct 21;194(4):551–559. doi: 10.1006/jtbi.1998.0774. [DOI] [PubMed] [Google Scholar]
  20. Shore D., Langowski J., Baldwin R. L. DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4833–4837. doi: 10.1073/pnas.78.8.4833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Smith S. B., Cui Y., Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 1996 Feb 9;271(5250):795–799. doi: 10.1126/science.271.5250.795. [DOI] [PubMed] [Google Scholar]
  22. Smith S. B., Finzi L., Bustamante C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 1992 Nov 13;258(5085):1122–1126. doi: 10.1126/science.1439819. [DOI] [PubMed] [Google Scholar]
  23. Strick T. R., Allemand J. F., Bensimon D., Bensimon A., Croquette V. The elasticity of a single supercoiled DNA molecule. Science. 1996 Mar 29;271(5257):1835–1837. doi: 10.1126/science.271.5257.1835. [DOI] [PubMed] [Google Scholar]
  24. Tskhovrebova L., Trinick J., Sleep J. A., Simmons R. M. Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature. 1997 May 15;387(6630):308–312. doi: 10.1038/387308a0. [DOI] [PubMed] [Google Scholar]
  25. Tsong T. Y., Baldwin R. L., Elson E. L. The sequential unfolding of ribonuclease A: detection of a fast initial phase in the kinetics of unfolding. Proc Natl Acad Sci U S A. 1971 Nov;68(11):2712–2715. doi: 10.1073/pnas.68.11.2712. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Wang J. C., Giaever G. N. Action at a distance along a DNA. Science. 1988 Apr 15;240(4850):300–304. doi: 10.1126/science.3281259. [DOI] [PubMed] [Google Scholar]
  27. Yin H., Landick R., Gelles J. Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule. Biophys J. 1994 Dec;67(6):2468–2478. doi: 10.1016/S0006-3495(94)80735-0. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES