Institute of Science Tokyo researchers have demonstrated that macromolecular crowding can control synthetic DNA droplet formation and organization, establishing a design strategy for programmable artificial cell systems and molecular computing networks.
Living cells operate in an interior where up to 40 percent of the volume is packed with macromolecules at concentrations reaching 300 milligrams per milliliter. This dense molecular environment directly influences how biological structures form and function.
Scientists have long studied how these crowded conditions affect cellular processes. Recent work shows the same principles can be engineered from the ground up.
Tokyo Researchers Use DNA Nanostars to Mimic Cellular Crowding
A research team led by Professor Masahiro Takinoue investigated how crowded environments shape synthetic structures. They used Y-shaped branched DNA nanostructures known as DNA nanostars.
These nanostars connect through short complementary sequences called sticky ends. This allows them to self-assemble into liquid-like DNA droplets via liquid-liquid phase separation.
Graduate student Naoki C. Yoshida at Science Tokyo, Dr. Mayu Shono at The University of Tokyo, and Professor Kenichi Yoshikawa of Doshisha University conducted the study.
The findings were made available online on July 27, 2026. They appear in Volume 6, Issue 8 of the journal JACS Au on August 24, 2026.
We provide a new design strategy for constructing sophisticated artificial cell architectures and molecular networks based on programmable self-organization.
Takinoue, Institute of Science Tokyo
Polymeric Agents Raise Droplet Formation Temperatures and Control Structure
Without crowding agents, the team observed droplet formation only below 63 °C when cooling solutions from 85 °C. Adding polymeric crowding agents promoted droplet formation at higher temperatures.
Polyethylene glycol (PEG) raised the formation threshold. This proved that molecular crowding stabilizes the condensates and helps them form more easily.
The experiments revealed that PEG cannot operate in isolation. When added to nanostars lacking sticky ends, PEG produced no condensates at all, demonstrating that crowding requires complementary base interactions to drive assembly.
Polyethylene Glycol Concentration Directs Multi-Droplet Patterning
By introducing two types of nanostars whose sticky ends did not bind to each other, the researchers tested whether crowding could organize separate phases.
Under normal conditions, these distinct nanostar types formed independent droplets that refused to mix. Adding PEG brought the droplets into physical contact without causing them to fuse.
Adjusting the PEG concentration, salt levels, and nanostar ratios allowed the team to dictate how the droplets interacted. This control generated specific spatial patterns ranging from alternating, network-like structures to complex arrangements containing up to three distinct types of DNA nanostars.
These findings reveal that macromolecular crowding is not merely a feature of the cellular environment but also serves as a powerful design parameter for engineering artificial DNA condensates.
Takinoue, Institute of Science Tokyo
Implications for Programmable Micromachines and Artificial Cell Tissues
As explored in separate microbiological literature, macromolecular crowding can directly modulate biochemical reactions and help cells sense physical stresses and osmotic changes without a sensor
by altering reaction rates and triggering phase separation.
In bacterial systems like Vibrio cholerae, macromolecular crowding links ribosomal protein gene dosage to growth rate.
For engineered systems, the team emphasizes that harnessing these physical principles opens concrete pathways for future technology.
The resulting design principles are expected to contribute to the development of artificial cell tissues, molecular communication networks, molecular computing systems, and programmable micromachines, where function emerges through controlled self-organization of biomolecular components.
Takinoue, Institute of Science Tokyo
Takinoue of the Institute of Science Tokyo believes these advancements will enable more precise control over the self-organization of these complex biomolecular systems.