Researchers combine two nanomachines to build lifelike DNA networks

Drawing inspiration from the dynamic architecture of living systems, researchers from Institute of Science Tokyo and Kyoto University have harnessed two chemically fueled biomolecular nanomachines, DNA polymerase and kinesin, to synthesize and actively assemble complex, hierarchical DNA networks. The work opens a route toward programmable, lifelike synthetic materials built from the nanoscale up.

Biomolecular nanomachines, such as enzymes and molecular motors, are the workhorses behind the synthesis and organization of complex materials in life. Powered by chemical energy, they build, transport, and organize biomolecules, allowing living systems to create and maintain highly ordered structures far from thermodynamic equilibrium.

In living systems, the synergy of multiple nanomachines performing sequential, energy-consuming steps is crucial for building ordered structures. Mimicking such bottom-up chemical and mechanical assembly of matter by artificial means, however, remains a challenge. Individual components have advanced in molecular robotics, including protein-based molecular motors that provide active transport to overcome diffusion limits, yet linking the work of multiple nanomachines in a stepwise process, where one hands off to the next, has proven far harder. In particular, two goals remain unexplored: achieving energy-dissipative self-assembly through dynamic processes and replicating the multistep coordination of different enzymatic and motor functions seen in life.

In a recent study, a research team led by Assistant Professor Shogo Hamada (tenure-track) from the Department of Computer Science, School of Computing, Institute of Science Tokyo (Science Tokyo), Japan, co-led by Professor Akira Kakugo from Kyoto University, Japan, developed a system that dynamically forms deoxyribonucleic acid (DNA) network materials through a bottom-up process driven by two types of biomolecular nanomachines, DNA polymerase and molecular motors. The international team included Dr. Farhana Afroze (Hokkaido University, Japan), Dr. Richard Archer (Science Tokyo), and Prof. Tetsuya Hiraiwa (Institute of Physics, Academia Sinica, Taiwan). Made available online on June 11, 2026, and published in Volume 22, Issue 36 of the journal Small on June 26, 2026, the work marks a key step toward constructing non-equilibrium materials that mimic how living systems organize themselves.

Taking inspiration from the synergy of cooperating molecular systems of life, the team designed a two-step process for synthesizing and assembling materials from the nanoscale up. First, DNA polymerase amplified DNA templates attached to microtubules through rolling circle amplification (RCA), growing long DNA strands directly on the microtubules. Kinesin motor proteins fixed to a substrate then consumed adenosine triphosphate (ATP) to propel these DNA-carrying microtubules across the surface. When the gliding microtubules collided, the DNA strands riding on them came into contact and connected. As the microtubules moved, they mechanically stretched and pulled the joined DNA strands, resulting in a growing network of organized, fiber-like architectures. In short, DNA polymerase generated the molecular material and ATP-powered kinesin motors physically assembled it into interconnected structures.

Further experiments confirmed that motor activity is essential to the process. No DNA networks were formed when kinesin was absent or when ATP was depleted, since the motors depend on ATP to function. The team also identified conditions that control network formation. Increasing microtubule density and the DNA synthesis time yielded networks with higher connectivity and structural complexity.  

The experimental findings were further supported by simulation studies. Without active force, the model chains mimicking DNA folded into compact states; however, with motor-like propulsion, multiple chains actively unfolded and connected, qualitatively reproducing the network architectures observed in the experiments.

More broadly, the study offers a framework for investigating how multiple active biomolecular processes can cooperate to build higher-order structures. Although the study does not yet quantify the chemical energy consumed and dissipated during assembly, the findings show that active molecular motion is a key driver of network formation, a step toward materials that assemble and organize themselves as living systems do.

By coupling molecular synthesis with mechanical force generation, we have taken a crucial step toward creating synthetic materials that mimic the dynamic construction strategies of living systems. We envision this bottom-up framework paving the way for dynamic, programmable, and lifelike materials with self-repairing, self-sustaining, and self-evolving characteristics that could find real-world applications, including molecular computing and molecular robotics."

Shogo Hamada (tenure-track), Assistant Professor, Department of Computer Science, School of Computing, Institute of Science Tokyo