A platform for the formation of uniform DNA condensate droplets using vibration-induced local vortices

Abstract

DNA condensate droplets (hereafter referred to as DNA condensates), which arise from specific interactions between sticky ends embedded in multi-arm DNA nanostructures, hold significant promise as programmable smart materials. However, from an engineering standpoint, the controlled preparation of DNA condensates with uniform size and a well-defined structure remains a major challenge due to the stochastic nature of the condensation process. This study presents a novel approach that employs vibration-induced local vortices (VILV) within a microfluidic platform to achieve spatial control over DNA condensate dimensions and enable their parallel generation. A key advantage of this platform is its ability to support direct observation and real-time tracking of structural morphology and dynamics. Through flow-field analysis of the VILV system, we demonstrate that uniform microvortices serve as semi-closed compartments, wherein DNA molecules confined within each vortex space rapidly aggregate and relax into uniform spherical condensate droplets. By modulating parameters such as DNA concentration and micropillar dimensions, the VILV platform not only enables systematic control of condensate size but also facilitates the construction of complex, multicomponent “patchy” condensates with consistent morphology. This platform provides a robust and scalable tool for studying liquid–liquid phase separation (LLPS) and offers broad potential for applications in the bottom-up synthesis of condensed molecular systems.