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Structural equilibrium of DNA represented with different force fields

M Feig1, B M Pettitt

  • 1Department of Chemistry, University of Houston, Houston, Texas 77204-5641 USA.

Biophysical Journal
|July 2, 1998
PubMed
Summary
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Molecular dynamics simulations reveal CHARMM and AMBER force fields yield different DNA structures. CHARMM favors A-DNA, while AMBER shows intermediate A-/B-DNA, highlighting force field impact on DNA conformation.

Area of Science:

  • Computational Biology
  • Molecular Biophysics
  • Biochemistry

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding DNA structure and dynamics.
  • Different molecular mechanics force fields can produce varied simulation outcomes.
  • Previous studies suggested discrepancies between CHARMM and AMBER force fields in DNA simulations.

Purpose of the Study:

  • To conduct a detailed comparison of DNA structure and dynamics using CHARMM and AMBER force fields.
  • To evaluate the accuracy of these force fields against experimental data for the DNA duplex d(C5T5)·d(A5G5).
  • To assess the convergence and dynamical behavior of DNA structures over extended simulation times.

Main Methods:

  • Explicit solvent molecular dynamics simulations of the DNA duplex d(C5T5)·d(A5G5).

Related Experiment Videos

  • Extended simulation times of 10 nanoseconds for both CHARMM and AMBER force fields.
  • Analysis of average structures, base geometry, backbone conformation, and dynamical fluctuations.

    • Main Results:

    • CHARMM force field resulted in an A-DNA base geometry and heterogeneous backbone structures (A-form purine, A/B-form pyrimidine).
    • AMBER force field produced an intermediate A-/B-DNA base geometry and B-form backbone.
    • Both force fields showed fluctuations between A and B conformations, with AMBER exhibiting more pronounced dynamics.

    Conclusions:

    • CHARMM and AMBER force fields yield distinct DNA structural ensembles, impacting conformation predictions.
    • Simulation results partially agree with experimental data, particularly for the C/G tract, but struggle with the T/A tract B-conformation.
    • Nanosecond-scale simulations are necessary for achieving dynamical equilibrium in DNA structural properties.