Many packages exist and which is best depends on the size and purpose for your design. For DNA "origami" designs you have the choice of several great packages, including caDNAno (http://cadnano.org/) and SARSE-DNA (http://www.cdna.dk/default.asp?getreq=%2Findex.php%2Fsoftware.html).

Lower density tile designs usually start from SEQUIN (possibly still available?) and/or custom scripts using Turner model thermodynamics (nearest-neighbor, e.g., MFOLD, MELTING4, etc.) or other newer models (e.g., NUPACK). These techniques also work for high density tiles (e.g., "origami") but the options above for origami are very well tuned for that process.

If you're looking for a commercial turn-key solution, Parabon NanoLabs (PNL) (http://www.parabon-nanolabs.com) can help with, among other things, custom design, synthesis, and validation work for low- or high-density systems. [FULL DISCLOSURE: I am affiliated with PNL]

Thank you Chris,

I am mostly interested in constructing 2D and 3D structures using single stranded oligonucleotides. I have found the available software in the net not so straightforward to use.

It would be interesting to evaluate the "inSēquio™ Sequence Design Studio" which I guess is a possible software to what I aim at. Is this possible?

You might find suitable designs already in the literature that you can tweak for your research purposes... this requires less work than figuring out the various packages but can possibly help you reach your goal.

inSēquio™ runs on Parabon grid resources... so, unless you have the need for many, many designs (and a hardware cluster) it's not likely that this would be a feasible option. I suggest that you contact PNL and ask about design services that might fit your project.

Hi, i use NUPARM/NUCGEN and "nanoengineer" to device small DNA designs like tetra, icoshedron cages, as well bundles of DNA tubes. i can let you know the details if this what u r looking for