A robust DNA mechanical device controlled by hybridization topology

Abstract

Controlled mechanical movement in molecular-scale devices has been realized in a variety of systems—catenanes and rotaxanes^1,2,3, chiroptical molecular switches⁴, molecular ratchets⁵ and DNA⁶—by exploiting conformational changes triggered by changes in redox potential or temperature, reversible binding of small molecules or ions, or irradiation. The incorporation of such devices into arrays^7,8 could in principle lead to complex structural states suitable for nanorobotic applications, provided that individual devices can be addressed separately. But because the triggers commonly used tend to act equally on all the devices that are present, they will need to be localized very tightly. This could be readily achieved with devices that are controlled individually by separate and device-specific reagents. A trigger mechanism that allows such specific control is the reversible binding of DNA strands, thereby ‘fuelling’ conformational changes in a DNA machine⁹. Here we improve upon the initial prototype system that uses this mechanism but generates by-products⁹, by demonstrating a robust sequence-dependent rotary DNA device operating in a four-step cycle. We show that DNA strands control and fuel our device cycle by inducing the interconversion between two robust topological motifs, paranemic crossover (PX) DNA^10,11 and its topoisomer JX₂ DNA, in which one strand end is rotated relative to the other by 180°. We expect that a wide range of analogous yet distinct rotary devices can be created by changing the control strands and the device sequences to which they bind.