As an alternative to the tile-based approach, two-dimensional DNA structures can be made from a single, long DNA strand of arbitrary sequence.........

As an alternative to the tile-based approach, two-dimensional DNA structures can be made from a single, long DNA strand of arbitrary sequence which is folded into the desired shape by using shorter, "staple" strands. This allows the creation of two-dimensional shapes at the nanoscale using DNA. Demonstrated designs have included the smiley face and a coarse map of North America. DNA origami was the cover story of Nature on March 15, 2006.


DNA polyhedra
A number of three-dimensional DNA molecules have been made which have the connectivity of a polyhedron such as an octahedron or cube. In other words, the DNA duplexes trace the edges of a polyhedron with a DNA junction at each vertex. The earliest demonstrations of DNA polyhedra involved multiple ligations and solid-phase synthesis steps to create catenated polyhedra. More recently, there have been demonstrations of a DNA truncated octahedron made from a long single strand designed to fold into the correct conformation, as well as a tetrahedron which can be produced from four DNA strands in a single step.


DNA nanomechanical devices
Main article: DNA machine
DNA complexes have been made which change their conformation upon some stimulus. These are intended to have applications in nanorobotics. One of the first such devices, called "molecular tweezers," changes from an open to a closed state based upon the presence of control strands.

DNA machines have also been made which show a twisting motion. One of these makes use of the transition between the B-DNA and Z-DNA forms to respond to a change in buffer conditions. Another relies on the presence of control strands to switch from a paranemic-crossover (PX) conformation to a double-junction (JX2) conformation.


Stem Loop Controllers
A design called a stem loop, consisting of a single strand of DNA which has a loop at an end, are a dynamic structure that opens and closes when a piece of DNA bonds to the loop part. This effect has been exploited to create several logic gates. These logic gates have been used to create the computers MAYA I and MAYA II which can play tick-tac-toe to some extent