DNA is typically not thought of forming much in the way of complicated structures by itself – at least not in comparison to RNA. Is there some indication that your DNA molecule is doing something other than forming a standard double helix, or being an unstructured polymer? Are you trying to model the DNA by itself, or in complex with something else (like a binding protein)?
If you do expect non-trivial structure for just the DNA, you may be able to repurpose the RNA structure prediction machinery. I don’t have any experience with nucleic acid modeling myself, but we just released version 3.4 which has a number of new applications specifically for RNA modeling, so looking though the documentation and demos there should give you a hint of what’s possible with Rosetta.
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