Roger Rubio Sánchez

Using DNA nanostructures for lipid membrane biophysics and bioengineering in synthetic cell science

Keywords: artificial cells, synthetic membranes, DNA nanotechnology, nano-scaled DNA structures, cell surface.

Artificial cells are human-made objects that replicate behaviours typically observed in living organisms. Replicas of living cells constitute a simplified platform to study biological processes isolated from cellular complexity, and they have also allowed to investigate pathways for life to emerge and evolve. Given their versatility, artificial cells could revolutionise various industries. For instance, they could travel the body, recognise diseased sites, and deliver therapeutic cargoes. Similarly, artificial cells could detect, capture, and degrade pollutants in the environment.

Biological membranes host numerous key pathways facilitated by membrane proteins, from signal transduction to motility and cell division. Much like their biological counterparts, artificial cells are often built using synthetic lipid membranes to achieve the compartmentalisation needed to induce and exploit chemical gradients. However, reconstituting membrane proteins in synthetic membranes has proven challenging, and artificial-cell membranes typically lack the sophisticated responses of biological membranes.

Imparting synthetic membranes with functionality is therefore crucial for artificial cells to fulfil their exciting technological potential. To that end, the tools of DNA nanotechnology are particularly promising, as they exploit the physical and chemical properties of DNA molecules to precisely control structure and dynamics at the nano-scale, offering a unique toolkit to replicate the action of membrane nano-machines.

My research uses nano-scaled DNA structures to study the biophysical principles governing the activity of cell-surface machinery, which I apply to engineer functionality in artificial-cell membranes. Thanks to highly collaborative approaches, my contributions reveal important interactions between DNA and synthetic lipid bilayers, introducing strategies to coordinate bio-inspired responses in artificial-cell membranes.

By unravelling key electrostatic properties, we outlined principles to guide the adhesion of DNA to lipid membranes. With our strategy, we regulate DNA-lipid attachment with independent physical and chemical parameters like temperature, membrane composition, and medium ionic composition, unlocking, for instance, avenues for next-generation mRNA- lipid vaccine technologies.

Using hydrophobic modifications on the DNA, we anchored nanostructures to the surface of membranes and investigated their ability to preferentially localise in specific regions, dubbed lipid domains, of the membrane. Exploiting different hydrophobic “anchors”, we introduced a platform to spatially organise and transport cargoes across the membrane- surface of artificial cells. We then expanded our strategy to develop DNA nano-machines that localise at domain boundaries, stabilising lipid domains and enabling domain fission when triggered by chemical stimuli. Our approach affords previously unachieved control over the two- and three-dimensional membrane morphology, paving the way for division in artificial cells.

Finally, we showed that pH changes, driven by temperature fluctuations, induce disassembly and re-assembly of lipid membranes. We thus proposed temperature cycling as a mechanism to generate functional artificial cells from non-functional “parent” cells, where membrane disassembly/re-assembly enables cell-content mixing and re-uptake. Our content reshuffling pathway is a plausible avenue for “primitive” cells to exchange material in the absence of highly-evolved biological machinery, furthering our knowledge of how life could have emerged in early Earth.

Altogether, my contributions deepen our understanding of fundamental biophysical processes in lipid membranes and expand our toolkit to construct artificial cells with increasingly sophisticated behaviours and applications.

My research sits at the interface between DNA nanotechnology, biological physics, and synthetic biology. My work draws inspiration from biological processes to engineer synthetic models using tools and concepts from soft matter and membrane biophysics, statistical mechanics, and chemical nanotechnology. Their experimental realisation is heavily informed and supported by (analytical and numerical) theoretical models as well as coarse-grained simulations, thus providing comprehensive insights on important biophysical phenomena. Owing to their cross-disciplinary nature, my contributions are readily inspiring discussions across communities in the broader biological, physical, and mathematical sciences.

Roger's publications

Department of Chemical Engineering and Biotechnology

Lorenzo Di Michele Lab

Figure legend: With my research, I have developed several biomimetic membrane-hosted responses in artificial cells, underpinned by a refined understanding of the interactions between (modified and unmodified) nucleic acids and synthetic lipid membranes.