Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins

Takanori Harashima (harashima@ims.ac.jp), Akihiro Otomo and Ryota Iino (iino@ims.ac.jp)
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Takanori Harashima: National Institutes of Natural Sciences
Akihiro Otomo: National Institutes of Natural Sciences
Ryota Iino: National Institutes of Natural Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract DNA-nanoparticle motor is a burnt-bridge Brownian ratchet moving on RNA-modified surface driven by Ribonuclease H (RNase H), and one of the fastest nanoscale artificial motors. However, its speed is still much lower than those of motor proteins. Here we resolve elementary processes of motion and reveal long pauses caused by slow RNase H binding are the bottleneck. As RNase H concentration ([RNase H]) increases, pause lengths shorten from ~70 s to ~0.2 s, while step sizes (displacements between two consecutive pauses) are constant ( ~ 20 nm). At high [RNase H], speed reaches ~100 nm s−1, however, processivity (total number of steps before detachment), run-length, and unidirectionality largely decrease. A geometry-based kinetic simulation reveals switching of bottleneck from RNase H binding to DNA/RNA hybridization at high [RNase H], and trade-off mechanism between speed and other performances. An engineered motor with 3.8-times larger DNA/RNA hybridization rate simultaneously achieves 30 nm s−1 speed, 200 processivity, and 3 μm run-length comparable to motor proteins.

Date: 2025
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DOI: 10.1038/s41467-025-56036-0

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