Sculpting DNA-based synthetic cells through phase separation and phase-targeted activity

Abstract

Synthetic cells, like their biological counterparts, require internal compartments with distinct chemical and physical properties where different functionalities can be localised. Inspired by membrane-less compartmentalisation in biological cells, here we demonstrate how micro-phase separation can be used to engineer heterogeneous cell-like architectures with programmable morphology and compartment-targeted activity. The synthetic cells self-assemble from amphiphilic DNA nanostructures, producing core-shell condensates due to size-induced de-mixing. Lipid deposition and phase-selective etching are then used to generate a porous pseudo-membrane, a cytoplasm analogue, and membrane-less organelles. The synthetic cells can sustain RNA synthesis via in vitro transcription, leading to cytoplasm and pseudo-membrane expansion caused by an accumulation of the transcript. Our approach exemplifies how architectural and functional complexity can emerge from a limited number of distinct building blocks, if molecular-scale programmability, emergent biophysical phenomena, and biochemical activity are coupled to mimic those observed in live cells.

Protein recruitment to dynamic DNA-RNA host condensates

“…This means that the local conditions of the dense phase could be optimized for specific guest molecules and reactions. Through sequence optimization, distinct coexisting DNA condensates can be spatially segregated, or made to interact to form compartments that include multiple subcompartments: this means DNA condensates could be used to host multi-step reactions and potentially enhance their yield 18,39,40 . Finally, the recruitment and release of guest molecules could be finely controlled through strand displacement reactions that could fold or disrupt the guest binding domains 41 .…”