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

Biophysical Journal

Volumn 76, Issue 3, 1999, Pages 1598-1605

  Qian, Hong ^a   Elson, Elliot L ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICROSPHERE; POLYMER;

ARTICLE; CONFORMATION; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MICROSCOPY; MOLECULAR DYNAMICS; MOLECULE; OPTICS; THEORY;

EID: 0032983017     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77319-4     Document Type: Article

References (43)

1. Barkley, M. D., and B. H. Zimm. 1979. Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70:2991-3007.
2. Bird, R. B., C. F. Curtiss, R. C. Armstrong, and O. Hassager. 1987. Dynamics of Polymeric Liquids, Vol. 2, Kinetic Theory, 2nd Ed., John Wiley and Sons, New York.
3. Bustamante, C., J. F. Marko, E. D. Siggia, and S. Smith. 1994 Entropic elasticity of λ-phage DNA. Science. 265:1599-1600.
4. Cluzel, P., A. Lebrun, C. Heller, R. Lavery, J.-L. Viovy, D. Chatenay, and F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794.
5. Doi, M. and S. F. Edwards. 1986. The Theory of Polymer Dynamics. Clarendon Press, Oxford.
6. Einstein, A. 1956. Investigations on the Theory of the Brownian Movement. Dover, New York.
7. Elson, E. L. 1972. Simple sequential model for the kinetics of conformational transitions of oligomeric helices and proteins. Biopolymers. 11: 1499-1520.
8. Elson, E. L., and H. Qian. 1994. Measurements of molecular transport in small systems. Lect. Math. Life Sci. 24:37-49.
9. Elson, E. L., and W. W. Webb. 1975. Concentration correlation spectroscopy: a new biophysical probe based on occupation number fluctuations. Annu. Rev. Biophys. Bioeng. 4:311-334.
10. Erickson, H. P. 1994. 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. USA. 91: 10114-10118.
11. Finzi, L., and J. Gelles. 1995. Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science. 267:378-380.
12. Flory, P. J. 1969. Statistical Mechanics of Chain Molecules. Hanser Publisher, Munich.
13. Gelles, J., B. J. Schnapp, and M. P. Sheetz. 1988. Tracking kinesin-driven movements with nanometer-scale precision. Nature. 331:450-453.
14. Gittes, F., B. Schnurr, P. D. Olmsled, F. C. MacKintosh, and C. F. Schmidt. 1997. Microscopic viscoelasticity: shear moduli of soft materials determined from thermal fluctuations. Phys. Rev. Lett. 79: 3286-3289.
15. Horowitz, D. S., and J. C. Wang. 1984. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173:75-94.
16. Keizer, J. 1987. Statistical Thermodynamics of Nonequilibrium Processes. Springer-Verlag, New York.
17. Kellermayer, M. S. Z., S. B. Smith, H. L. Granzier, and C. Bustamante. 1997. Folding-unfolding transitions in single titin molecules characterized with laser tweezers. Science. 276:1112-1116.
18. Klapper, I., and H. Qian. 1998. Remarks on discrete and continuous large-scale models of DNA dynamics. Biophys. J. 74:2504-2514.
19. Larson, R. G., T. T. Perkins, D. E. Smith, and S. Chu. 1997. Hydrodynamics of a DNA molecule in a flow field. Phys. Rev. E. 55:1794-1797.
20. Lin, S.-C., and J. M. Schurr. 1978. Dynamic light-scattering studies of internal motions in DNA. I. Applicability of the Rouse-Zimm model. Biopolymers. 17:425-461.
21. Mason, T. G., K. Ganesan, J. H. van Zanten, D. Wirtz, and S. C. Kuo. 1997. Particle tracking microrheology of complex fluids. Phys. Rev. Lett. 79:3282-3285.
22. Neher, E., and C. F. Stevens. 1977. Conductance fluctuations and ionic pores in membranes. Annu. Rev. Biophys. Bioeng. 6:345-381.
23. Ninham, B., R. Nossal, and R. Zwanzig. 1969. Kinetics of a sequence of first-order reactions. J. Chem. Phys. 51:5028-5033.
24. Perkins, T. T., S. R. Quake, D. E. Smith, and S. Chu. 1994. Relaxation of a single DNA molecule observed by optical microscopy. Science. 264: 822-826.
25. Perkins, T. T., D. E. Smith, R. G. Larson, and S. Chu. 1995. Direct observation of tube-like motion of a single polymer chain. Science. 268: 83-87.
26. Qian, H., M. P. Sheetz, and E. L. Elson. 1991. Single-particle tracking: analysis of diffusion and flow in two-dimensional systems. Biophys. J. 60:910-921.
27. Reif, M., M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub. 1997. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science. 276:1109-1112.
28. Rippe, K., P. H. von Hippel, and J. Langowski. 1995. Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20: 500-506.
29. Rouse, P. 1953. A theory of the linear viscoelastic properties of dilute solutions of coiling polymers. J. Chem. Phys. 21:1272-1280.
30. Schellman, J. A., and S. C. Harvey. 1995. Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys. Chem. 55:95-114.
31. Shapiro, B. E., and H. Qian. 1997. A quantitative analysis of single protein-ligand complex separation with the atomic force microscope. Biophys. Chem. 67:211-219.
32. Shapiro, B. E., and H. Qian. 1998. Hysteresis in force probe measurements: a dynamical systems perspective. J. Theor. Biol. 194:551-559.
33. Shore, D., J. Langowski, and R. L. Baldwin. 1981. DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. USA. 78:4833-4837.
34. Smith, S. B., Y. J. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
35. Smith, S. B., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 258:1122-1126.
36. Strick, T. R., J.-F. Allemand, D. Bensimon, A. Bensimon, and V. Croquette. 1996. The elasticity of a single supercoiled DNA molecule. Science. 271:1835-1837.
37. Tskhovrebova, L., J. Trinick, J. A. Sleep, and R. M. Simmons. 1997. Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature. 387:308-312.
38. Tsong, T. Y., R. L. Baldwin, and E. L. Elson. 1971. The sequential unfolding of ribonuclease A: detection of a fast initial phase in the kinetics of unfolding. Proc. Natl. Acad. Sci. USA. 68:2712-2715.
39. Van Kampen, N. G. 1992. Stochastic Processes in Physics and Chemistry: Elsevier Science, North-Holland, Amsterdam.
40. Wang, J. C., and G. N. Giaever. 1988. Action at a distance along a DNA. Science. 240:300-304.
41. Wax, N. 1954. Selected Papers on Noise and Stochastic Processes. Dover, New York.
42. Yin, H., R. Landick, and J. Gelles. 1994. Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule. Biophys. J. 67:2468-2478.
43. Zimm, B. H. 1956. Dynamics of polymer molecules in dilute solution: viscoelasticity, flow birefringence and dielectric loss. J. Chem. Phys. 24:269-278.