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DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
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Nonmonotonic DNA-length-dependent mobility in pluronic gels.

Seungyong You1, Ling Wei1, Sachin Shanbhag2

  • 1Department of Physics, Florida State University, Tallahassee, Florida 32306, USA.

Physical Review. E
|May 17, 2017
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Summary

DNA fragment mobility in pluronic gels shows non-monotonic behavior, unlike traditional agarose gels. Brownian dynamics simulations explain these complex DNA size-dependent mobility patterns in micellar solutions.

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Area of Science:

  • Polymer Science
  • Biophysics
  • Physical Chemistry

Background:

  • Traditional gel electrophoresis separates DNA fragments based on size, with mobility decreasing monotonically with length.
  • Pluronic block copolymers form micellar gels with unique properties that can influence molecular transport.
  • Understanding DNA mobility in complex fluids is crucial for developing advanced separation techniques.

Purpose of the Study:

  • To investigate the size-dependent mobility of DNA fragments in pluronic F127 and P123 micellar gels.
  • To elucidate the mechanisms governing DNA migration in these non-traditional gel matrices.
  • To compare DNA mobility in pluronic gels with that in conventional agarose gels.

Main Methods:

  • Two-dimensional electrophoresis was employed to separate DNA fragments (20-3500 base pairs) in both agarose and pluronic gels.
  • Brownian dynamics simulations were utilized to model DNA mobility and hydrodynamic interactions within pluronic lattices.
  • Molecular dynamics simulations with explicit micelle coronas were performed for pluronic F127 to investigate interaction details.

Main Results:

  • DNA mobility in pluronic gels exhibited non-monotonic behavior with fragment length, contrasting with the monotonic decrease in agarose gels.
  • The observed mobility variations correlated strongly with the diameter of the spherical micelles in the pluronic gels.
  • Brownian dynamics simulations successfully reproduced the rising, falling, and oscillatory trends in DNA mobility.

Conclusions:

  • The complex, non-monotonic DNA mobility in pluronic gels is influenced by micellar structures and hydrodynamic interactions.
  • Hydrodynamic interactions mediated by the hydrated poly(ethylene oxide) corona of micelles likely contribute to the initial rise in mobility with DNA length.
  • These findings offer insights into DNA behavior in complex fluids and potential applications in separation science.