Directing the structure of matter through DNA nanotechnology

The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of B-DNA, whose structure is well known. The use of stable branched DNA molecules permits one to make stick-figures. We have used this strategy to construct a covalently closed DNA molecule whose helix axes have the connectivity of a cube, and a second molecule, whose helix axes have the connectivity of a truncated octahedron. In addition to branching topology, DNA also affords control of linking topology, because double helical half-turns of B-DNA or Z-DNA can be equated, respectively, with negative or positive crossings in topological objects. Consequently, we have been able to use DNA to make trefoil knots of both signs and figure-8 knobs. DNA-based topological control has also led to the construction of Borromean rings. The key feature previously lacking in DNA construction has been a rigid molecule. We have discovered that antiparallel DNA double crossover molecules can provide this capability.