Autonomous stepping dynamics of a two-legged DNA walker on a nanopore track.

DNA walkers, a key component of nanorobots, require precise movement control for applications in nanoscale transport and sensing. While biological tracks are widely used in experiments, recent proof-of-principle studies suggest that nanopore-based tracks offer a promising alternative for stepwise motion of the walkers. This study employs Langevin dynamics simulations to investigate the autonomous walking mechanism of a two-legged DNA walker on a track with positively charged nanopores. In addition to the forward motion of the stepping leg from one nanopore to another, a complete step also includes an additional stage, in which the walker is required to adjust to a suitable conformation for the next step. However, due to the confinement effects of the nanopores on the DNA legs, the walker often undergoes multiple failed adjustment attempts. As the salt concentration increases, the enhanced ion screening can reduce the nanopore confinement, favoring conformational adjustment of the walker but hindering the forward motion of the stepping leg. Consequently, the duration for the walker to complete a step exhibits a non-monotonic dependence on the salt concentration. This work elucidates the fundamental principles enabling two-legged autonomous walking on the nanopore track, providing important insights for the design of future DNA nanodevices.