Much recent interest has focused on DNA as a material for the construction of two- and three-dimensional objects on the nanometer to micrometer scale. Such constructions have made use of the recognition of "complementary" nucleotide sequence by single-stranded stretches of DNA and the formation of double helices (duplexes) via the formation of Watson-Crick base pairs. Recently, we have described a quite distinct paradigm for the side-by-side binding ("synapsis") by two intact DNA duplexes modified by the inclusion of short elements of eight guanine-guanine mismatch base pairs (a "G-G domain") within them. Here, we demonstrate that it is possible to design nonidentical G-G domains, which have the property of synapsing exclusively to "self " as opposed to "non-self ". Two modes of synapsis are observed in this versatile system: that in which two distinct species of duplex in a mixture concertedly undergo "self "-synapsis and that in which one designated species out of the two "self "-synapses specifically. Incorporation of these novel methodologies for "self "-synapsis and site-specific synapsis by DNA duplexes into current methods for constructing DNA nanostructures and mesostructures may facilitate the assembly of more complex DNA-based materials and arrays.