DNA flipping as facile mechanism for transmembrane signaling in synthetic cells

Abstract

Transmembrane signaling is essential for cellular communication, yet reconstituting such mechanisms in synthetic systems remains challenging. Here, we report a simple and robust DNA-based mechanism for transmembrane signaling in synthetic cells using cholesterol-modified single-stranded DNA (Chol-ssDNA). We discovered that anchored Chol-ssDNA spontaneously flips across the membrane of giant unilamellar lipid vesicles (GUVs) in a nucleation-driven, defect-mediated process. This flipping enables internal signal processing through hybridization with encapsulated complementary DNA and activation of downstream processes such as RNA transcription. The phenomenon shows a high transduction efficiency, is generic across DNA sequences and lipid compositions, and can be enhanced by glycerol, which modulates membrane dynamics. Mechanistic insights using fluorescence microscopy, nuclease degradation assays, and membrane permeability assays reveal that flipping is dominated by transient membrane pores. Leveraging this facile translocation process, we demonstrate selective transcriptional activation inside synthetic cells, underscoring the potential of Chol-ssDNA flipping as a programmable tool for synthetic biology and bottom-up synthetic cell design.