A well-directional three-dimensional DNA walking nanomachine that runs in an orderly manner

Abstract

Herein, we report a three-dimensional (3D) DNA walking nanomachine innovatively constructed from a functionalized 3D DNA track, which runs in an orderly manner with favorable directionality to allow for programming certain pathways of information transduction for some target tasks. The nanomachine was constructed using a departure station of walker (U^B + W) and a functionalized 3D track, which was made up of a rolling circle amplification (RCA)-generated backbone chain and numerous triangular rung units with stators (U^A + S) assembled into a repeating array along the backbone. A specific domain (SD) was designed at the 5′-end of the backbone to capture the U^B + W, and stators with specific RNA substrates were immobilized at the three U^A corners for the DNA walker to travel on. Powered by 10–23 DNAzyme, the DNA walker started moving from the SD end to the other end of the track by the autonomous cleavage of RNA substrates. Significantly, the homogeneous distribution of stators in the longitudinal and horizontal extensions paved a specific path for each walker to move along the 3D track. This resulted in random and inactive self-avoiding walking; thus, the nanomachine exhibited good executive ability. These properties allowed the DNA walking nanomachine to program the certain pathways of information transduction for the stepwise and programmed execution of some target tasks, such as the synthesis of specific polyorganics and cargo delivery. We believe that such a 3D DNA walking nanomachine could enrich the concept in the field of dynamic DNA nanotechnology, and may improve the development of novel DNA nanomachines in cargo delivery and composite product synthesis.