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We review molecular dynamics simulations of nucleic acids, including those
completed from 1995 to 2000, with a focus on the applications and results
rather than the methods. After the introduction, which discusses recent
advances in the simulation of nucleic acids in solution, we describe force
fields for nucleic acids and then provide a detailed summary of the published
literature. We emphasize simulations of small nucleic acids (∼6 to 24 mer)
in explicit solvent with counterions, using reliable force fields and modern
simulation protocols that properly represent the long-range electrostatic
interactions. We also provide some limited discussion of simulation in the
absence of explicit solvent. Absent from this discussion are results from
simulations of protein-nucleic acid complexes and modified DNA analogs.
Highlights from the molecular dynamics simulation are the spontaneous
observation of A B transitions in duplex DNA in response to the environment, specific ion
binding and hydration, and reliable representation of protein-nucleic acid
interactions. We close by examining major issues and the future promise for
these methods.
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