DNA self-assembled nanostructures as addressable vessels for functional chemical moieties

Complex function arises in biology from the proximity and relations amongst different functional units. Often, separate containers are employed in order to segregate specialized function within a cell, or in order to control reactions by facilitated substrates and products diffusion. DNA nanostructures have some exclusive advantages among nanostructures: they are relatively easy to design, fairly predictable in their geometric structures, and have been experimentally implemented in a growing number of labs around the world. [1] DNA has been utilized as a programmable building material to construct designer nanoscale architectures for a broad range of applications, such as organizing different functional units that can be stably attached at locations defined with nanometer accuracy. To date, a large variety of two- and three-dimensional (2D and 3D) DNA nanostructures have been successfully designed and assembled. In this communication, a few examples developed in our lab will be presented. The self-assembled DNA parallelogram, originally designed by Ned Seeman [2], can be used as a relatively rigid template for the assembly of different functional elements, such as oligonucleotides, fluorophores, proteins. As in the case of fluorophores, it can be shown that the rigidity and addressability of the parallelogram tile enables a high degree of control of the relation among the functional units: the measured FRET between two organic dyes is greater than in other less flexible structures where the dyes could in principle be located at the same distance one from the other. Alternatively, the rigid template can be employed to prevent interaction between functional units that are co-localized at distant sites on it. Three-dimensional (3D) construction by self-assembly requires rigid building blocks such as tetrahedra. The DNA tetrahedron is designed to be mechanically robust; it consists of rigid triangles of DNA helices covalently joined at the vertices. The four component oligonucleotides each run around one face and hybridize to form the double-helical edges[3]