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DNA Lattice-Encoded Information for Genotype-to-Phenotype Evolution of Self-Replicating Synthetic Cells

Periodic Reporting for period 1 - DNA-ENC SYNCELLS (DNA Lattice-Encoded Information for Genotype-to-Phenotype Evolution of Self-Replicating Synthetic Cells)

Reporting period: 2018-03-01 to 2020-02-29

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 [1]. 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.
First, I established a new method to form giant unilamellar vesicles as cell-like compartments in a simple one-pot reaction. This technique will directly benefit laboratories around the world (ACS Synth. Biol.). Second, I invented a near-universal method to functionalize microfluidic droplets via DNA handles – now filed to the European Patent Office. Having guided my Master student through the attachment of various functional groups and components, I am the co-corresponding author on the manuscript in Adv. Funct. Mater. I then employed proteorhodopsin-expressing bacteria in synthetic cells to trigger the reversible assembly and disassembly of a pH-responsive DNA-based cytoskeleton upon illumination. For the first time, bacteria are used as organelles in synthetic cells (to be submitted). Remarkably, I then demonstrated autonomous division of synthetic cells. I further established a small group with independent collaborations and laid out my view on engineering synthetic cells in a review featured on the cover of Trends in Biotechnology.
We combined DNA nanotechnology and droplet-based microfluidics. Thereby, we established a new direction in synthetic biology, paving the way towards truely synthetic cells assembled de novo. Tangible applications were realized with a new technique to functionalize microfluidic droplets (patent pending).
Functionalization of microfluidic droplets with DNA