A nanomechanical device based on the B–Z transition of DNA

Abstract

The assembly of synthetic, controllable molecular mechanical systems^{1,2,3,4,5,6,7} is one of the goals of nanotechnology. Protein-based molecular machines, often driven by an energy source such as ATP, are abundant in biology⁸,⁹. It has been shown previously that branched motifs of DNA can provide components for the assembly of nanoscale objects¹⁰, links¹¹ and arrays¹². Here we show that such structures can also provide the basis for dynamic assemblies: switchable molecular machines. We have constructed a supramolecular device consisting of two rigid DNA ‘double-crossover’ (DX) molecules connected by 4.5 double-helical turns. One domain of each DX molecule is attached to the connecting helix. To effect switchable motion in this assembly, we use the transition between the B and Z¹³,¹⁴ forms of DNA. In conditions that favour B-DNA, the two unconnected domains of the DX molecules lie on the same side of the central helix. In Z-DNA-promoting conditions, however, these domains switch to opposite sides of the helix. This relative repositioning is detected by means of fluorescence resonance energy transfer spectroscopy, which measures the relative proximity of two dye molecules attached to the free ends of the DX molecules. The switching event induces atomic displacements of 20–60 Å.