Single-polymer dynamics in steady shear flow

Science

Volumn 283, Issue 5408, 1999, Pages 1724-1727

  Smith, Douglas E ^a   Babcock, Hazen P ^a   Chu, Steven ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE DNA; POLYMER;

ARTICLE; BACTERIOPHAGE LAMBDA; CONFORMATION; FLOW KINETICS; FLUID FLOW; FLUORESCENCE MICROSCOPY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; SHEAR RATE;

BACTERIOPHAGE LAMBDA; BIOPOLYMERS; BIREFRINGENCE; CHEMISTRY, PHYSICAL; DNA, VIRAL; LIGHT; MICROSCOPY, FLUORESCENCE; MICROSCOPY, VIDEO; NEUTRONS; NUCLEIC ACID CONFORMATION; RHEOLOGY; SCATTERING, RADIATION; STRESS, MECHANICAL; VISCOSITY;

EID: 0033548494     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.283.5408.1724     Document Type: Article

References (42)

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26. A 1.3 cm by 2.5 cm glass slide glued to a piece of Plexiglass (acrylic plastic) was positioned above a 2.5 cm by 5.7 cm by 1.5 cm channel by three micrometer screws. The plate was held against the screws by a stiff spring, allowing one to level the plates and to adjust the size of the gap between them (with <5% variation). The bottom plate, which acted as an optical window, was a 1.5 cm by 5.7 cm, no. 2 glass coverslip. The top plate was connected to the channel by a translation stage that was leveled relative to the bottom plate by a fourth micrometer screw. The translation stage was driven by an optically encoded dc motor moving at speeds of 10 to 200 μm/s with ∼2% root mean square variation over 2.4 cm of travel.
27. λ-DNA (Gibco BRL, Gaithersburg, MD) was labeled with YOYO-1 (Molecular Probes, Eugene, OR) at a dye/base pair ratio of 1:4 for >1 hour. The persistence length of native DNA is ∼53 nm [C. Bustamante, J. Marko, E. Siggia, S. Smith, Science 265, 1599 (1994)] and its hydrodynamic diameter is ∼2 nm [R. Pecora, ibid. 251, 893 (1991)]. When labeled with YOYO, the contour length increases to ∼22 μm [T. T. Perkins, D. E. Smith, R. G. Larson, S. Chu, ibid. 268, 83 (1995)]. Experiments were performed at ∼20°C in a pH 8 buffer consisting of 10 mM tris-HCl, 2 mM EDTA, 10 mM NaCl, 4% β-mercaptoethanol, glucose oxidase (∼50 μg/ml) and catalase (∼10 μg/ml), ∼10 to 18% (w/w) glucose, and 40 to 55% (w/w) sucrose. In this solution, where the free oxygen has been minimized, the photobleaching of the molecules during the measurements was found to be negligible. The viscosity of each solution was measured and adjusted by varying the sugar concentrations.
28. λ-DNA (Gibco BRL, Gaithersburg, MD) was labeled with YOYO-1 (Molecular Probes, Eugene, OR) at a dye/base pair ratio of 1:4 for >1 hour. The persistence length of native DNA is ∼53 nm [C. Bustamante, J. Marko, E. Siggia, S. Smith, Science 265, 1599 (1994)] and its hydrodynamic diameter is ∼2 nm [R. Pecora, ibid. 251, 893 (1991)]. When labeled with YOYO, the contour length increases to ∼22 μm [T. T. Perkins, D. E. Smith, R. G. Larson, S. Chu, ibid. 268, 83 (1995)]. Experiments were performed at ∼20°C in a pH 8 buffer consisting of 10 mM tris-HCl, 2 mM EDTA, 10 mM NaCl, 4% β-mercaptoethanol, glucose oxidase (∼50 μg/ml) and catalase (∼10 μg/ml), ∼10 to 18% (w/w) glucose, and 40 to 55% (w/w) sucrose. In this solution, where the free oxygen has been minimized, the photobleaching of the molecules during the measurements was found to be negligible. The viscosity of each solution was measured and adjusted by varying the sugar concentrations.
29. λ-DNA (Gibco BRL, Gaithersburg, MD) was labeled with YOYO-1 (Molecular Probes, Eugene, OR) at a dye/base pair ratio of 1:4 for >1 hour. The persistence length of native DNA is ∼53 nm [C. Bustamante, J. Marko, E. Siggia, S. Smith, Science 265, 1599 (1994)] and its hydrodynamic diameter is ∼2 nm [R. Pecora, ibid. 251, 893 (1991)]. When labeled with YOYO, the contour length increases to ∼22 μm [T. T. Perkins, D. E. Smith, R. G. Larson, S. Chu, ibid. 268, 83 (1995)]. Experiments were performed at ∼20°C in a pH 8 buffer consisting of 10 mM tris-HCl, 2 mM EDTA, 10 mM NaCl, 4% β-mercaptoethanol, glucose oxidase (∼50 μg/ml) and catalase (∼10 μg/ml), ∼10 to 18% (w/w) glucose, and 40 to 55% (w/w) sucrose. In this solution, where the free oxygen has been minimized, the photobleaching of the molecules during the measurements was found to be negligible. The viscosity of each solution was measured and adjusted by varying the sugar concentrations.
30. Molecules were epi-illuminated by a 100 W mercury arc lamp (Zeiss) with a 470 ± 32 nm bandpass excitation filter and a 500-nm long-pass dichroic mirror and imaged with a X60, 1.2 numerical aperture water immersion objective (Nikon), a 160-mm-to-infinity-corrected conversion lens (Zeiss), a 40-cm tube lens, a 515-nm long-pass emission filter, a microchannel plate intensifier (Hamamatsu), and a video camera (Phillips CCD).
31. 5 times lower than the concentration (c*) at which coiled molecules begin to overlap.
32. G were free parameters.
33. E. Atkins and M. Taylor, Biopolymers 32, 911 (1992).
34. Also, the birefringence does not directly correspond to the extension but rather the ordering of portions of the chain along the polarization axis.
35. D. E. Smith, T. T. Perkins, S. Chu, Macromolecules 29, 1372 (1996).
36. The FFT was calculated after subtracting the mean extension from all of the data points and multiplying the data by a Welch window function [W. H. Press et al., Numerical Recipes in C (Cambridge Univ. Press, Cambridge, 1988), p. 442]. The PSD for all of the data sets at the same γ̇ and η were averaged together and normalized according to Parseval's theorem.
37. G. Jeffery, Proc. R. Soc. Lond. Ser. A 102, 161 (1922).
38. The maximum frequency that can be resolved is determined by the sampling rate, typically 0.1 s. The minimum frequency is determined by the length of the run, typically 150 s for γ̇ > 2 and as long as 800 s for γ̇ = 0.2.
39. The ratio of the values determined experimentally (16) were close to, but not exactly equal to, the ratio of the solvent viscosities. The deviation from a strict linear proportionality may be due to slight differences in the solvent arising from the differing fractions of water in the two solutions.
40. M. Wang and G. Uhlenbeck, Rev. Mod. Phys. 17, 323 (1945).
41. E. Shaqfeh and J. Hur, personal communication.
42. We acknowledge assistance from T. Perkins with an earlier version of this experiment and helpful comments from J. Hur, R. Larson, T. Perkins, E. Shaqfeh, and B. Zimm. This work was supported in part by the AFOSR and the NSF. D.E.S received support from a fellowship from the NSF Program in Mathematics and Molecular Biology. H.P.B. was supported in part by an NIH biophysics training grant.