Macromolecular crowding helps organize synthetic DNA droplets

Researchers at the Institute of Science Tokyo have found that macromolecular crowding can be used as a tool to control how synthetic DNA droplets form and organize (710). By using DNA nanostars and polymeric agents, the team mimicked the crowded environment found within living cells (710).

The study utilized Y-shaped DNA nanostructures, known as nanostars, which self-assemble into liquid-like droplets via short complementary DNA sequences called sticky ends (710). In solutions without crowding agents, these droplets form when the temperature is cooled below 63°C (710). Introducing crowding agents at a 10% concentration allows droplets to form at higher temperatures: 76°C with polyethylene glycol (PEG), 65°C with dextran, and 67°C with Ficoll (710). PEG with a high molecular weight of 7.5 kDa had the strongest effect, though it requires the presence of sticky ends to function (710).

Beyond formation, crowding agents can be used to organize different types of DNA droplets into specific patterns without causing them to fuse (710). The researchers created two types of nanostars with incompatible sticky ends that would normally form separate, non-mixing droplets (710). When PEG was added, the crowding effect brought these droplets into contact to form structures like networks, without merging them (710). These patterns can be controlled by adjusting the salt concentration, the ratio of nanostars, or the concentration of PEG (710).

This approach offers a method for designing programmable artificial cell systems (710). Professor Masahiro Takinoue noted that the strategy could help build complex artificial cell architectures and molecular networks through programmable self-organization (710). Such principles could eventually support the development of molecular computing, programmable micromachines, and artificial cell tissues (710).