Control of DNA Structure and Topology: DNA Branches, Polyhedra and Knots

Nadrian Seeman
Department of Chemistry, New York University

Artistic rendering by Ken Eward of a DNA truncated
octahedron constructed in Seeman's laboratory.

The control of structure on the nanometer scale is a key goal of molecular biophysics, materials science and nanotechnology. We use the specificity of DNA complementary to direct the assembly of discrete DNA structures; for example, we have assembled catenated molecules whose helix axes have the connectivities of a cube and of a truncated octahedron. The topological control afforded by this system has stimulated us to make DNA knots. Trefoil knots of both signs and a figure-8 knot have been constructed, and an RNA knot has been used to demonstrate the existence of an RNA topoisomerase. We have suggested that periodic arrays (crystals) of DNA objects could be used to direct the assembly of biochips. In order to exploit DNA assembly to construct periodic matter, it is necessary to identify rigid DNA motifs. We have found that the antiparallel DNA double crossover molecule behaves as a rigid unit. These molecules have been adopted by Erik Winfree as the components used in his approach to DNA computing by cellular automata.