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Keywords:

  • adaptive biasing force;
  • DNA structures;
  • ion transport;
  • molecular dynamics
Thumbnail image of graphical abstract

How easily can ions move in DNA channels? Three-dimensional free-energy landscapes for the movement of Na+, K+, and NH4+ ions through G-quadruplex DNA channels have been obtained by molecular dynamics simulations. The computed results are in qualitative agreement with the limited experimental data: large K+ and NH4+ ions squeeze through the G-quartets with some difficulty, while Na+ ions pass through with less impedance.