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Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel


  • This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada. All MD simulations were performed on the SHARCNET.


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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.