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Nonmonotonic DNA-length-dependent mobility in pluronic gels

Seungyong You1, Ling Wei1, Sachin Shanbhag2, and David H. Van Winkle1,*

  • 1Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
  • 2Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306, USA

  • *rip@phy.fsu.edu
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Phys. Rev. E 95, 042602 – Published 7 April, 2017

DOI: https://doi.org/10.1103/PhysRevE.95.042602

Abstract

Two-dimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO100PO70EO100) and pluronic P123 (EO20PO70EO20). The 20–3500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly correlated with the diameter of the spherical micelles. Brownian dynamics (BD) simulations with short-ranged intra-DNA hydrodynamic interactions were performed to numerically calculate the length-dependent mobility in pluronic lattices. The rising and falling trends, as well as the oscillations of mobility, were captured by the coarse-grained BD simulations. Molecular dynamics simulations in pluronic F127, with explicitly modeled micelle coronas, justified that the hydrodynamic interactions mediated by the complex fluid of hydrated poly(ethylene oxide) are a possible reason for the initial rise of mobility with DNA length.

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Outline

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Phys. Rev. E 95, 042602– Published 7 April, 2017
  • Received 20 July 2016
  • Revised 28 February 2017
Article part of CHORUS

©2017 American Physical Society

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