DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size

Abstract

We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions.

Stimuli‐Responsive DNA Self‐Assembly: From Principles to Applications

“…[49] They also conducted an experimental and theoretical study to investigate the influence of step size on the walking efficiency and stepping kinetics of the DNA bipedal motor. [50] Beyondw alking alongp rescribed tracks, Qian and co-workers built aD NA nanorobot capable of random walkinga nd smart cargo sorting on at wo-dimensional DNA origami land. [51] In addition to homogeneous solutions, toehold-mediated strand displacement could also be operatedi nv ery different environments.…”

Dynamic DNA Origami Devices<strong> </strong>

“…As another class of DNA-DNA interaction, a number of non-autonomous, autonomous and directed DNA walkers have been introduced and analyzed both experimentally and theoretically [58,59,67]. By taking advantage of the DNA origami addressability and programmability, the environment where the walker or robot is moving can be defined and precisely tuned.…”

Mechanisms, Methods of Tracking and Applications of DNA Walkers: A Review

“…[21] Coarse-grained simulations can further be employed to optimize the walker performance and efficiency, as well as to confirm the experimental findings, which is necessary for development of computational tools for designing DNA walkers. [22] Finally, in order to be suitable for application, DNA walkers need to be able to traverse required distances in as short time span as possible, while still being subjectable to receive distinct instructions to start, stop, or decide on the direction, even on complex tracks that include forks and junctions. It is also beneficial if the track is reusable, simplifying the construction of the system.…”