NUPACK (nupack.org) is a software suite for the analysis and design of nucleic acid systems.
CANDNANO (cadnano.org) is a popular DNA origami design software.
CANDO (cando-dna-origami.org) is a MIT-developed software providing computational predictions of solution shape and flexibility of DNA structures.
Some nucleic acid nanotech groups
Ned Seeman at NYU
William Shih at Harvard Medical School
LaBean Research Group at NCSU
Peng Yin at Harvard
Hao Yan at ASU
Andrew Turberfield at Oxford
Chengde Mao at Purdue
Kurt Gothelf at Aarhus
Erik Winfree at CIT
John Reif at Duke
Tim Liedl at LMU Munich
Hendrik Dietz at TUM
Chunhai Fan at Shanghai Institute of Applied Physics
Shawn Douglas at UCSF
Horoshi Sugiyama at Kyoto University
Dave Zhang at Rice University
Lulu Qian at CIT
Dongsheng Liu at Tsinghua University
Qiangbing Wang at Suzhou Institute of Nanotech and Nanobionics
Chenxiang Lin at Yale University