Wired turned me on to the 3-D nanoassembly work in Harvard's Shih Lab.
Wired: "DNA Nanotech Gains a Third Dimension"
Bjorn Hogberg posts the Nature (2009) preprint, "Self-assembly of DNA into nanoscale three-dimensional shapes."
Here is an illustration from the Wired piece:
Scale: the horizontal white bar is 20 nm long.
If you visit the Shih Lab site, hyperlinked above, you'll find a link to a nanoscale CAD program...