Using MD simulations we investigated the dynamics of DNA mononucleotides moving through hydrophobic nanoslits driven by electric fields. The nucleotides adsorbed and desorbed from the slit walls multiple times and the mechanism(s) of absorption/ desorption events were studied by monitoring the angle of the nucleotide bases with the walls. Various nucleotide properties such as their velocity, their angle with the walls, and their association with sodium ions are a function of whether the nucleotide is adsorbed or not and of the electric field strength.  The association of sodium ions with the phosphate group of the nucleotides has a great influence on nucleotide velocity along the direction of applied field. The mean nucleotide velocity increases with increasing field strength, but is not linearly with the field strength. Work supported by NSF-EPSCoR LA-SiGMA Grant #EPS-1003897, and by LONI and HPC@LSU.

MD simulation study of the effect of electric field on the dynamics of DNA nucleotides in hydrophobic nanoslits

243rd National Meeting (2012)

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