“Can DNA-Nanoparticle Motors Compete with the Speed of Nature’s Motor Proteins?”

These nanoscopic motors are highly customizable and can be engineered for applications in molecular computation, diagnostics, and transport. Despite their brilliance, DNA-nanoparticle motors lack the velocity of their biological equivalents, the motor proteins, which presents a challenge. Researchers engage in efforts to examine, refine, and reconstruct a swifter artificial motor utilizing single-particle tracking experiments and geometry-based kinetic simulations.

“Natural motor proteins are crucial in biological functions, with speeds of 10-1000 nm/s. So far, artificial molecular motors have encountered difficulty in reaching these speeds, as most traditional designs attain less than 1 nm/s,” explained Takanori Harashima, researcher and principal author of the study.

The researchers shared their findings in Nature Communications on January 16th, 2025, proposing a solution to the most significant concern of speed: modifying the bottleneck.

The experiment and simulation indicated that the binding of RNase H is the bottleneck that slows down the entire process. RNase H is an enzyme that plays a role in genome maintenance and degrades RNA within RNA/DNA hybrids in the motor. The slower the binding of RNase H occurs, the longer the pauses in motion, which ultimately results in a longer overall processing time. By elevating the concentration of RNase H, there was a significant enhancement in speed, resulting in a reduction of pause durations from 70 seconds to approximately 0.2 seconds.

Nonetheless, the increase in motor speed came at the expense of processivity (the number of steps before separation) and run-length (the distance the motor travels before separation). Researchers discovered that this exchange between speed and processivity/run-length could be enhanced by increasing the DNA/RNA hybridization rate, bringing the simulated performance nearer to that of a motor protein.

The engineered motor, featuring restructured DNA/RNA sequences and a 3.8-fold enhancement in hybridization rate, attained a speed of 30 nm/s, 200 processivity, and a 3 μm run-length. These findings indicate that the DNA-nanoparticle motor now matches a motor protein in its performance.

“Our ultimate goal is to invent artificial molecular motors that outperform natural motor proteins,” remarked Harashima. These synthetic motors can prove to be immensely beneficial in molecular computations based on the motor’s movement, as well as in diagnosing infections or disease-related molecules with excellent sensitivity.

The experiments and simulations conducted in this study provide an optimistic perspective for the future of DNA-nanoparticle and related artificial motors and their capacity to compete with motor proteins, along with their potential applications in nanotechnology.

Takanori Harashima, Akihiro Otomo, and Ryota Iino from the Institute for Molecular Science at National Institutes of Natural Sciences and the Graduate Institute for Advanced Studies at SOKENDAI played an integral role in this research.

This work received support from JSPS KAKENHI, Grants-in-Aid for Transformative Research Areas (A) (Publicly Offered Research) “Materials Science of Meso-Hierarchy” (24H01732) and “Molecular Cybernetics” (23H04434), Grant-in-Aid for Scientific Research on Innovative Areas “Molecular Engine” (18H05424), Grant-in-Aid for Early-Career Scientists (23K13645), JST ACT-X “Life and Information” (MJAX24LE), and Tsugawa foundation Research Grant for FY2023.