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Effect of confinement on DNA dynamics in microfluidic devices

J. Chem. Phys. 119, 1165 (2003); doi:10.1063/1.1575200

Issue Date: 8 July 2003

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Richard M. Jendrejack
Department of Chemical Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706

David C. Schwartz
Laboratory for Molecular and Computational Genomics, Department of Chemistry and Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin 53706

Michael D. Graham and Juan J. de Pablo
Department of Chemical Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706
The dynamics of dissolved long-chain macromolecules are different in highly confined environments than in bulk solution. A computational method is presented here for detailed prediction of these dynamics, and applied to the behavior of ~1–100 µm DNA in micron-scale channels. The method is comprised of a self-consistent coarse-grained Langevin description of the polymer dynamics and a numerical solution of the flow generated by the motion of polymer segments. Diffusivity and longest relaxation time show a broad crossover from free-solution to confined behavior centered about the point H[approximate]10Sb, where H is the channel width and Sb is the free-solution chain radius of gyration. In large channels, the diffusivity is similar to that of a sphere diffusing along the centerline of a pore. For highly confined chains (H/Sb<<1), Rouse-type molecular weight scaling is observed for both translational diffusivity and longest relaxation time. In the highly confined region, the scaling of equilibrium length and relaxation time with H/Sb are in good agreement with scaling theories. In agreement with the results of Harden and Doi [J. Phys. Chem. 96, 4046 (1992)], we find that the diffusivity of highly confined chains does not follow the scaling relation predicted by Brochard and de Gennes [J. Chem. Phys. 67, 52 (1977)]; that relationship does not account for the interaction between chain and wall. ©2003 American Institute of Physics.
History: Received 21 October 2002; accepted 17 March 2003
Permalink: http://link.aip.org/link/?JCPSA6/119/1165/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.14.Gg
    DNA, RNA
  • 87.15.He
    Biomolecular dynamics and conformational changes
  • 61.25.Hq
    Structure of macromolecular and polymer solutions, and polymer melts; swelling
  • 05.60.-k
    Transport processes
  • YEAR: 2003

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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