Simulations of single grafted polyelectrolyte chains: ssDNA and dsDNA

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Abstract
The structure of a single, grafted polyelectrolyte, DNA, is investigated by molecular dynamics simulations. The polyelectrolyte is treated as a bead–spring model with explicit charges using parametrizations of both flexible (ssDNA) and stiff (dsDNA) polyelectrolytes. In this single chain limit with no added salt, the flexible ssDNA is always highly extended. Counterion condensation on both molecules is found to be chain length dependent. The counterion distribution is not localized to the chain volume as in related polyelectrolyte brush states. Even at large chain lengths, where the majority of counterions are condensed, a significant fraction of counterions reside far from the chain. The distributions of positions of the nongrafted end monomer for ssDNA and dsDNA differ significantly, indicating a possibility for distinguishing the two states in DNA array technologies.