DNA-nanoparticle motors are precisely what the name suggests: they are tiny artificial motors that utilize DNA and RNA structures to generate movement through the breakdown of RNA by enzymes. In simpler terms, they convert chemical energy into mechanical movement by influencing Brownian motion. These motors operate using the ‘burnt-bridge’ Brownian ratchet method. In this mechanism, the motor moves forward by degrading (or ‘burning’) the connections (or ‘bridges’) it traverses on a surface, giving it a directional push.
DNA-nanoparticle motors are precisely what their name implies: tiny artificial motors that employ DNA and RNA structures to facilitate motion through enzymatic degradation of RNA. In essence, they transform chemical energy into mechanical movement by altering Brownian motion. This type of motor operates using the “burnt-bridge” Brownian ratchet mechanism, propelling itself by degrading (or “burning”) the bonds (or “bridges”) it encounters on the substrate, effectively directing its movement forward.
These minute motors can be programmed in various ways and have potential applications in molecular computing, diagnostics, and transportation tasks. However, despite their advanced design, DNA-nanoparticle motors fall short in speed compared to their biological equivalents, the motor proteins. This gap presents a challenge that researchers are eager to tackle, aiming to analyze, enhance, and reconstruct a faster artificial motor through single-particle tracking experiments and simulations based on geometry.
“Natural motor proteins are crucial for various biological functions and can move at speeds ranging from 10 to 1000 nanometers per second. In contrast, traditional artificial molecular motors have struggled to match these speeds, with many only operating below 1 nm/s,” stated Takanori Harashima, a researcher and primary author of the study.
The findings of the research were published in Nature Communications on January 16, 2025, highlighting a proposed strategy to address the crucial speed issue by overcoming the bottleneck.
The experiments and simulations identified that the binding of RNase H acts as a bottleneck, slowing down the entire motor process. RNase H is an enzyme crucial for maintaining the genome, which degrades RNA within RNA/DNA hybrids in the motor. A slower binding pace of RNase H leads to extended pauses in motion, contributing to a reduced overall processing time. By raising the concentration of RNase H, the speed improved significantly, reducing pause durations from 70 seconds to about 0.2 seconds.
However, while increasing speed improved performance, it negatively impacted processivity (the number of steps taken before detachment) and run-length (the distance traveled before separation). Researchers discovered that enhancing the DNA/RNA hybridization rate could balance this trade-off, bringing the motor’s simulated performance closer to that of natural motor proteins.
The modified motor, featuring redesigned DNA/RNA sequences and an increased hybridization rate by 3.8 times, managed to reach a speed of 30 nm/s, a processivity of 200, and a run-length of 3 μm. These results indicate that the DNA-nanoparticle motor’s performance is now on par with that of motor proteins.
“Our ultimate goal is to create artificial molecular motors that perform better than natural motor proteins,” Harashima remarked. These artificial designs hold promise for molecular computations based on motor kinetics and are also beneficial for sensitive diagnosis of infections or disease-related substances.
The studies conducted in this research offer a promising outlook for the future capabilities of DNA-nanoparticle motors and their potential to rival motor proteins, alongside their application prospects in nanotechnology.
This research was conducted by Takanori Harashima, Akihiro Otomo, and Ryota Iino from the Institute for Molecular Science at the National Institutes of Natural Sciences and the Graduate Institute for Advanced Studies at SOKENDAI.
This work was funded through various grants, including JSPS KAKENHI, Grants-in-Aid for Transformative Research Areas (A) focusing on “Materials Science of Meso-Hierarchy” (24H01732) and “Molecular Cybernetics” (23H04434), as well as other research support programs.
