Dynamic self-assembly of compartmentalized DNA nanotubes

Abstract

Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.

Bottom-Up Assembly of Synthetic Cells with a DNA Cytoskeleton

“…Toward this aim, DNA filaments as more versatile cytoskeleton mimics have only very recently been encapsulated into water-in-oil droplets. 22 However, the high surface tension compared to that in lipid vesicles and the lack of a surrounding aqueous environment prevents the implementation of downstream functions.…”

Amphiphilic DNA nanostructures for bottom-up synthetic biology

“…Thankfully, examples are emerging demonstrating the coupling of nucleic-acid molecular reaction networks and self-assembly to enzymatic processes, 187–191 also in the context of cytomimetic agents. 192 Given these encouraging results, we argue that a generalised enzymatic pathway for the sustained production of a nucleic acid “free energy currency” would be a welcome development for the community, and unlock the modular design of self-sustaining, DNA-based artificial cells.…”

Mechanochemical signal transduction in synthetic cells

“…However, apart from molecular substrate exchange, a mechanochemical connection to intracellular downstream functions within synthetic cellular compartments is missing. Concomitantly, DNA nanotubes as structural and functional mimics of cytoskeletons have been reconstituted within cell-sized water-in-oil droplets 17,18 and recently also in GUVs 5 . Here, we link filament disassembly and cytoskeletal remodeling within GUVs to transmembrane properties of DNA origami and chemical signalling from the outside of GUVs reminiscent of focal adhesions within natural cells 19 .…”