Living cells may be the most sophisticated example of functional machines operating on the nano- and microscale. But is it possible engineer synthetic analogues in the laboratory? In this fellowship, we propose a strategy to engineer cells de novo, by merging two precision technologies, microfluidics and DNA nanotechnology, to position and manipulate functional parts in space and time . In particular, we use DNA as a near-universal linker to functionalize microfluidic compartments. Using this DNA handle approach, we demonstrate the stimuli-responsive attachment of natural and synthetic subcellular components. We further employ DNA to construct functional parts, including ion channels or a pH-responsive DNA-based cytoskeleton mimic, which serves as a stabilizing cortex. Following passive encapsulation, we actuate DNA nanostructures in microfluidic or lipid-based compartments to assemble dynamic systems with structural reconfigurability. By the integration of plasmonic probes we achieve real-time optical feedback to monitor the dynamics upon external stimulation. These unique tools bridging the mico- and nanoscale will enable synthetic cellular systems, which are not merely copies of nature’s own example of life, but prescribe a direction towards synthetic cellular machines, ultimately applicable as active probes inside the human body.