Simulations reveal design rules for high-performance DNA particle motors

A 3D-printed model of a DNA-modified particle moving on an RNA-modified surface. DNA strands on the particle bind to RNA footholds, which are subsequently hydrolyzed as the motor moves. DNA, intact RNA and hydrolyzed RNA are shown in blue, pink and red, respectively. Credit: Takanori Harashima, Ryota Iino

DNA-nano/microparticle motors are among the fastest artificial molecular motors reported to date, moving at approximately 30 nm per second. However, they are still slower than natural motor proteins (approximately 100–1,000 nm per second), and further improvements in design and performance are required.

Researchers at the Institute for Molecular Science (IMS) and the Graduate University for Advanced Studies, Sokendai, performed geometry-based kinetic simulations that reproduce the motion of DNA-nano/microparticle motors with particle diameters of 100–5,000 nm and identified conditions for improving their speed, run length and unidirectionality.

The work was published in Biophysical Journal.

Particle size shapes motor performance

DNA-nano/microparticle motors operate through a "burnt-bridge Brownian ratchet" mechanism. Single-stranded DNAs on the particle hybridize with RNAs on a surface, and the enzyme RNase H hydrolyzes the RNA bound to DNA. Because hydrolyzed RNA can no longer serve as a foothold, backward motion is suppressed and the random Brownian motion of the particle is biased toward intact RNA in the forward direction.

Previous experiments showed a puzzling size dependence. Motors ranging from 100 to 5,000 nm in particle diameter—a 50-fold difference in size—were found to move at a characteristic speed of about 30 nm/s, while large particles travel long distances.

To understand this behavior, the researchers simulated motors with diameters of 100, 500, 1,000 and 5,000 nm and investigated factors governing these performance metrics. The analysis of elementary stepping motion showed that large particles take large steps but also undergo long pauses before each step. These two effects compensate for each other, explaining why motor speed changes only weakly with particle size.

Particle size had different effects on the other performance metrics. Large particles can form many DNA/RNA duplexes with the surface, suppressing detachment from the substrate and thereby increasing run length.

Large particles can also hydrolyze RNA more efficiently along their trajectories and form many DNA/RNA duplexes whose collective effect biases the next step toward the forward direction, resulting in high unidirectionality. These results show that particle size affects different motor properties in different ways.

Faster reactions unlock higher speeds

The simulations further showed that, while particle size has only a limited effect on speed, the biochemical reaction kinetics strongly influence speed. When the rates of DNA/RNA hybridization, RNase H binding and RNA hydrolysis were each increased 10-fold in the model, predicted motor speeds exceeded 200 nm/s across the entire particle-size range.

Under these fast-reaction conditions, the slow rotational diffusion of large particles increasingly reduced their speed. This indicates that small DNA-particle motors retain more room for further acceleration toward the speeds of fast natural motor proteins.

The findings provide design principles for engineering high-performance artificial molecular motors that could be applied as power sources for molecular machines and in sensing and computation technologies.

Publication details

Takanori Harashima et al., Artificial DNA-nano/microparticle motors: Factors governing speed, run length, and unidirectionality revealed by geometry-based kinetic simulations, Biophysical Journal (2026). DOI: 10.1016/j.bpj.2026.09.041

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Citation: Simulations reveal design rules for high-performance DNA particle motors (2026, October 26) retrieved 26 October 2026 from https://phys.org/news/2026-10-simulations-reveal-high-dna-particle.html

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