The readers of this volume are all aware that DNA is the molecule that nature uses as genetic material. The iconic antiparallel double helical structure assumed by its two strands facilitates high fidelity recognition between the nucleotides of complementary molecules. Although every base can pair with every other base, including itself (1
), the Watson-Crick pairing (2
) of adenine (A) with thymine (T) and guanine (G) with cytosine (C) appears to be the favored type of interaction between polynucleotides if the sequences of the molecules permit it. Biology clearly exploits this form of interaction in the replication of genetic information and in its expression. Nevertheless, biology is no longer the only branch of science where DNA is finding a significant role: It is now possible to exploit DNA complementarity to control the structure of matter.
This article will review the history and current status of using DNA to construct novel nanomaterials and to control their structures over time. We shall see below that DNA is used today build specific objects, periodic lattices in two and three dimensions, and nanomechanical devices. The dimensions of DNA are inherently on the nanoscale: The diameter of the double helix is about 2 nm, and the helical pitch is about 3.5 nm; hence construction involving DNA is fundamentally an exercise in nanoscience and nanotechnology. Consequently, the area we are discussing is called ‘structural DNA nanotechnology’ and its goal is the finest possible level of control over the spatial and temporal structure of matter: Putting what you want where you want it in three dimensions (3D), when you want it there.
Structural DNA nanotechnology rests on three pillars:  Hybridization;  Stably branched DNA; and  Convenient synthesis of designed sequences.
 Hybridization. The self-association of complementary nucleic acid molecules or parts of molecules (3
), is implicit in all aspects of structural DNA nanotechnology. Individual motifs are formed by the hybridization of strands designed to produce particular topological species. A key aspect of hybridization is the use of sticky ended cohesion to combine pieces of linear duplex DNA; this has been a fundamental component of genetic engineering for over 35 years (4
). Sticky-ended cohesion is illustrated in , where two double helical molecules are shown to cohere by hydrogen bonding. Not only is hybridization critical to the formation of structure, but it is deeply involved in almost all the sequence-dependent nanomechanical devices that have been constructed, and it is central to many attempts to build structural motifs in a sequential fashion (5
). Among the various types of cohesion known between biological molecules, sticky ended cohesion is very special: Not only do we know that two sticky ends will cohere with each other in a specific and programmable fashion (affinity), but we also know the structure
that they form when they do cohere, a Watson-Crick double helix (6
). This key point is illustrated in . Thus, in contrast to other biologically-based affinity interactions (e.g., an antigen and an antibody), we know on a predictive basis the local product structure formed when sticky ends cohere, without the need to do a crystal structure first to establish the relative orientation of the two components.
Sticky-Ended Cohesion. (a) Cohesion Between Two Molecular Overhangs
 Stably Branched DNA. Although the DNA double helix is certainly the best-known structure in biology, little biology would occur if the DNA molecule were locked tightly into that structure with an unbranched helix axis. For example, triply branched replication forks occur during semi-conservative replication (7
), and four-arm branched Holliday junctions (8
) are intermediates in genetic recombination. Likewise, branched DNA molecules are central to DNA nanotechnology. It is the combination of in vitro
hybridization and synthetic branched DNA that leads to the ability to use DNA as a construction material (9
). The fundamental notion behind DNA nanotechnology is illustrated in , which shows the cohesion of four copies of a 4-arm branched DNA molecule tailed in sticky ends associating to form a quadrilateral. In the example shown, only the inner sticky ends are used in forming the quadrilateral. Consequently, the structure can be extended to form an infinite lattice (9
Self-Assembly of Branched DNA Molecules to Form Larger Arrangements
 Convenient Synthesis of Designed Sequences. Biologically derived branched DNA molecules, such as Holliday junctions, are inherently unstable, because they exhibit sequence symmetry; i.e., the four strands actually consist of two pairs of strands with the same sequence. This symmetry enables an isomerization known as branch migration that allows the branch point to relocate (10
). Branch migration can be eliminated if one chooses sequences that lack symmetry in the vicinity of the branch point. We will discuss below different approaches to the use of symmetry in DNA nanotechnology, but the first approaches to DNA nanotechnology entailed sequence design that attempted to minimize sequence symmetry in every way possible. Such sequences are not readily obtained from natural sources, which leads us to the third pillar supporting DNA nanotechnology, the synthesis of DNA molecules of arbitrary sequence (11
). Fortunately, this is a capability that has existed for about as long as needed by this enterprise: Synthesis within laboratories or centralized facilities has been around since the 1980s; today it is possible to order all the DNA components needed for DNA nanotechnology, so long as they lack complex modifications, i.e., so-called ‘vanilla’ DNA. In addition, the biotechnology enterprise has generated demand for many variants on the theme of DNA (e.g., biotinylated molecules), and these molecules are also readily synthesized or purchased.