Chuo University and Institute of Science Tokyo develop microscale vibration method for creating uniform biomolecular condensate

A joint research group comprising Professor Hiroaki Suzuki, Professor Takeshi Hayakawa, Graduate Student Zhitai Huang, Graduate Student Kanji Kaneko (at the time of research), and Graduate Student Ryotaro Yoneyama (at the time) from the Faculty of Science and Engineering, Chuo University, Appointed Assistant Professor Tomoya Maruyama and Professor Masahiro Takinoue from the Institute of Integrated Research, Institute of Science Tokyo, and their colleagues has successfully developed a new, simple method to efficiently produce uniform biomolecular condensates at the microscale. This method is based on vibration-induced flow technology developed by Hayakawa and enables precise control of condensate formation in a single aqueous phase similar to the cellular environment. It utilizes only simple mechanical vibration without requiring expensive equipment or complex microchannel designs. The research was published in Materials Horizons.

Worldwide, research is advancing on the bottom-up construction of artificial cell models by combining molecules such as lipids, DNA, and proteins. In this field, intensive analysis is being conducted to mimic the formation of biomolecular condensates, "membraneless organelles" formed through liquid-liquid phase separation. Among these, DNA nanostructure condensates are attracting attention as novel information processing materials because they can be created with various structures and functions through base sequence design.

If these condensate structures can be manufactured and controlled with high reliability, they are anticipated to contribute substantially to the advancement of cell-replacement biotechnology. However, the formation process of biomolecular condensates is a random process, similar to water droplet condensation on a window in winter; there has been no effective method for forming uniform condensates.

The research group solved this challenge using their proprietary fluid control technology, the Vibration-Induced Local Vortex (VILV) platform.

In this method, a DNA nanostar solution is placed on a chip with an array of micropillars (fine columns approximately 0.1 millimeters in diameter). Horizontal rotational vibration is then applied at a specific frequency. This generates uniform and stable microvortices around the pillars. These VILVs function as virtual micro-chambers without physical walls. Hydrodynamic effects within these virtual chambers concentrate small aggregates of dispersed DNA nanostars toward the center of the vortices. This results in the formation of uniform-sized DNA condensates in an array pattern.

Furthermore, the researchers achieved positional control over formed condensates. Under normal conditions, condensates in liquid drift and fuse with each other when left alone. However, by applying a maintenance mode that switches the vibration to a low frequency (200 Hz), the team succeeded in gently holding the condensates at the vortex centers and suppressing fusion between droplets for extended periods. They also demonstrated the construction of "patchy" condensates with smaller, different nanostructures attached to the center. This was performed by introducing DNA nanostructures with different sticky ends or DNA nanostructures serving as linkers. Given these composite structures can be used for applications such as molecular detection, uniform structural control leads to improved reproducibility.

The VILV platform established in this research is a groundbreaking technology that enables precise control of the formation position and size of uniform biomolecular condensates within a single aqueous phase. In the future, these uniform condensates are expected to serve as model artificial cell condensates in bottom-up synthetic biology, as well as applications such as molecular detection elements in disease diagnosis.

Journal Information
Publication: Materials Horizons
Title: A platform for the formation of uniform DNA condensate droplets using vibration-induced local vortices
DOI: 10.1039/d5mh01304f