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Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair
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Relationship between frequency and deflection angle in the DNA prism.

Zhen Chen1, Kevin D Dorfman

  • 1Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|February 16, 2013
PubMed
Summary

DNA prism electrophoresis separates DNA by molecular weight. Simulations reveal deflection angle maxima due to DNA reorientation time and high-frequency decay from inadequate stretching, explaining experimental observations.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Pulsed-field electrophoresis is a standard technique for separating large DNA molecules.
  • The DNA prism is a modification offering continuous DNA separation based on molecular weight.
  • Existing models predict a monotonic increase in deflection angle with field-switching frequency.

Purpose of the Study:

  • To investigate discrepancies between experimental DNA prism results and current theoretical models.
  • To elucidate the biophysical mechanisms governing DNA deflection angles in pulsed-field electrophoresis.
  • To explain the observed maximum deflection angle and high-frequency decay phenomena.

Main Methods:

  • Utilized Brownian dynamics simulations to model DNA behavior within the DNA prism.
  • Analyzed the dependence of DNA deflection angle on molecular weight, switching frequency, and electric field strength.
  • Investigated DNA reorientation times and stretching dynamics during the separation process.

Main Results:

  • Simulations confirm experimental observations of a maximum deflection angle before decay at high frequencies.
  • The maximum deflection angle is linked to the DNA molecule's reorientation time.
  • High-frequency decay is attributed to insufficient DNA stretching during the electric field switching cycles.

Conclusions:

  • Brownian dynamics simulations accurately reproduce key experimental features of DNA prism separation.
  • The study clarifies the roles of DNA reorientation and stretching in determining deflection angles.
  • Findings provide a more comprehensive understanding of DNA behavior in pulsed-field electrophoresis.