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Deterministic model of DNA gel electrophoresis Deterministic model of DNA gel electrophoresis in strong electric fields

Publication ,  Journal Article
Lee, N; Obukhov, S; Rubinstein, M
Published in: Electrophoresis
1996

We present a new model for the motion of a megabase-long DNA molecule undergoing gel electrophoresis. We assume that the dynamics of large seg-ments of DNA is almost deterministic and can be described by a set of simple mechanical equations. This allows the numerical study of g,el electrophoresis of ultra-high molecular weight DNA. A strong electric field’ forces DNA in a gel into a tree-like structure with branches -loops of different sizes. We deter-mined the loop-size distribution function. This distribution has a power law form, confirming the hypothesis of the statistical self-similarity of a moving polymer. We find periodic configuration changes in the motion of a circular polymer, with the average period proportional to the molecular weight. During the period, a polymer goes through three distinct phases: a simple V-shape configuration, a growing tree, and a decaying tree. For a linear polymer this periodicity is much less pronounced because of additional perturbations to the dynamics caused by free ends. A circular polymer stays in a simple V-shaped configuration about 30 O/ o of the time, independent of molecular weight (10% for a linear polymer).

Duke Scholars

Published In

Electrophoresis

Publication Date

1996

Volume

17

Start / End Page

1011 / 1017

Related Subject Headings

  • Analytical Chemistry
  • 0904 Chemical Engineering
  • 0601 Biochemistry and Cell Biology
  • 0301 Analytical Chemistry
 

Citation

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MLA
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Lee, N., Obukhov, S., & Rubinstein, M. (1996). Deterministic model of DNA gel electrophoresis Deterministic model of DNA gel electrophoresis in strong electric fields. Electrophoresis, 17, 1011–1017.
Lee, Namkyoung, Sergei Obukhov, and Michael Rubinstein. “Deterministic model of DNA gel electrophoresis Deterministic model of DNA gel electrophoresis in strong electric fields.” Electrophoresis 17 (1996): 1011–17.

Published In

Electrophoresis

Publication Date

1996

Volume

17

Start / End Page

1011 / 1017

Related Subject Headings

  • Analytical Chemistry
  • 0904 Chemical Engineering
  • 0601 Biochemistry and Cell Biology
  • 0301 Analytical Chemistry