Conformational Entropy Mechanism for Periodic Motion of DNA under Constant-Field Gel Electrophoresis(Cross-disciplinary physics and related areas of science and technology)

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Entropic elasticity of a single charged polymer undergoing gel electrophoresis is a fundamental theme of polymer statistical physics since the discovery of "periodic" behavior in constant field gel electrophoresis (CFGE). In the present work we address the problem numerically by two steps. In the first step, we carry out Brownian dynamics (BD) simulations on CFGE by solving semi-microscopic Langevin equations of a polymer consisting of beads separated by a mean distance much smaller than the Kuhn length. Results are analyzed based on coarse-graining over the Kuhn length scale. We show the averaged elongation-contraction motion involves asymmetric V-shaped configurations whose shorter arm length depends on the field and the temperature consistently with what is expected when the BD chain is described by the freely-jointed chain (FJC) model with a suitable Kuhn length. To our knowledge, this is the first numerical confirmation of the FJC model itself from a submicroscopic description of polymer motion. The saturation of chain mobility in high fields agrees well with the nonlinear dependence of this shorter arm length on the field. In the second step, we discuss the periodic elongation-contraction motion of the coarse-grained chain by such a simplified model as a onedimensional chain consisting of beads, elastic strings, and obstacles. The results from these two chain models indicate that the periodic elongation-contraction motion of DNA under CFGE is self-organized by a balance between the field force and the conformational entropic force.
社団法人日本物理学会の論文
2006-06-15

Conformational Entropy Mechanism for Periodic Motion of DNA under Constant-Field Gel Electrophoresis(Cross-disciplinary physics and related areas of science and technology)

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