A Modular, Dynamic, DNA-Based Platform for Regulating Cargo Distribution and Transport between Lipid Domains

Abstract

Cell membranes regulate the distribution of biological machinery between phase-separated lipid domains to facilitate key processes including signaling and transport, which are among the life-like functionalities that bottom-up synthetic biology aims to replicate in artificial-cellular systems. Here, we introduce a modular approach to program partitioning of amphiphilic DNA nanostructures in coexisting lipid domains. Exploiting the tendency of different hydrophobic “anchors” to enrich different phases, we modulate the lateral distribution of our devices by rationally combining hydrophobes and by changing nanostructure size and topology. We demonstrate the functionality of our strategy with a bioinspired DNA architecture, which dynamically undergoes ligand-induced reconfiguration to mediate cargo transport between domains via lateral redistribution. Our findings pave the way to next-generation biomimetic platforms for sensing, transduction, and communication in synthetic cellular systems.

Amphiphilic DNA nanostructures for bottom-up synthetic biology

“…The latter enabled the DNA receptors to reversibly transport the fluorescent cargoes across the surface of the vesicles by attaining programmed partitioned states. Importantly, the re-shuffling action of the DNA receptors, which evokes the recruitment of cell-surface entities, was observed to have characteristic re-distribution times of ∼ 5 min 83 , which are comparable to that of biological machinery involved in T-cell activation 136 and clathrin-mediated endocytosis 103,137 , with equilibration timescales in the order of tens to hundreds of seconds.…”

“…Combining amphiphilic DNA nanostructures with multi-component synthetic membranes displaying a rich phase behaviour 133 , enables biomimetic regulation of the lateral distribution, and consequently the functionality, of membrane inclusions. Key for achieving this objective is the ability of amphiphilic DNA nanostructures to selectively enrich different (coexisting) lipid phases, depending on the chemical identity of the anchoring motifs 134,135 , the lipid composition of the membrane 80 , and the size of the nanostructures 83,107 . Indeed, harnessing the preferential affinity that cholesterol and tocopherol moieties have for liquid-ordered (L o ) and liquid-disordered (L d ) lipid phases, respectively, Rubio-Sánchez et al showed that the lateral distribution of membrane-tethered DNA nanostructures can be statically and dynamically programmed 83 .…”

“…Key for achieving this objective is the ability of amphiphilic DNA nanostructures to selectively enrich different (coexisting) lipid phases, depending on the chemical identity of the anchoring motifs 134,135 , the lipid composition of the membrane 80 , and the size of the nanostructures 83,107 . Indeed, harnessing the preferential affinity that cholesterol and tocopherol moieties have for liquid-ordered (L o ) and liquid-disordered (L d ) lipid phases, respectively, Rubio-Sánchez et al showed that the lateral distribution of membrane-tethered DNA nanostructures can be statically and dynamically programmed 83 . In this contribution, DNA receptors were interfaced with GUVs displaying coexistence of L o and L d phases, each occupying a hemispherical domain and resulting in a Janus-like geometry, as shown in Fig.…”

“…In this feature article we delve into several examples of synthetic DNA nanostructures designed to replicate the structure and functionality of biological molecular machinery in the context of cell mimicry, focusing in particular on bilayer-anchored devices acting as synthetic receptors mediating adhesion [74][75][76][77][78][79][80] , tissue formation 74,81 , communication 82 and membrane sculpting [83][84][85][86][87] . Attachment of the DNA nanostructures to lipid bilayers often requires their modification with hydrophobic moieties, such as cholesterol, tocopherol or lipids, giving the nanostructures an amphiphilic character 88 .…”

“…Panels (a. ), (c.), (d.) are adapted with permission from ref 83 ,. and (e.), (f.) are adapted with permission from ref 84.…”