Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets

Abstract

Higher-order structures that originate from the specific and reversible DNA-directed self-assembly of microscopic building blocks hold great promise for future technologies. Here, we functionalized biotinylated soft colloid oil-in-water emulsion droplets with biotinylated single-stranded DNA oligonucleotides using streptavidin as an intermediary linker. We show the components of this modular linking system to be stable and to induce sequencespecific aggregation of binary mixtures of emulsion droplets. Three length scales were thereby involved: nanoscale DNA base pairing linking microscopic building blocks resulted in macroscopic aggregates visible to the naked eye. The aggregation process was reversible by changing the temperature and electrolyte concentration and by the addition of competing oligonucleotides. The system was reset and reused by subsequent refunctionalization of the emulsion droplets. DNA-directed self-assembly of oil-in-water emulsion droplets, therefore, offers a solid basis for programmable and recyclable soft materials that undergo structural rearrangements on demand and that range in application from information technology to medicine.C omplex higher-order structures that spontaneously arise from the specific and reversible self-assembly of simple building blocks hold great promise to become the foundation of tomorrow's technology (1). In the context of DNA-directed self-assembly of hard colloids and artificial vesicles, linear DNA oligonucleotides were shown to be adhesive elements that allowed the self-assembly process not only to be specific but also to be reversible by a variety of external stimuli such as temperature (2-4), changes in the electrolyte concentration (4, 5), addition of competing oligonucleotides (6), and exploitation of the secondary structure of DNA oligonucleotides (7).Oil-in-water (o/w) emulsion droplets (EDs) offer a robust, configurable, and recyclable soft-colloid system with interesting properties for the fabrication of new delivery systems and advanced synthetic materials with adaptable properties (8). By exploiting the well-characterized ligand-receptor pair biotin-streptavidin, EDs were immobilized on glass surfaces (9) and actively transported along microtubules (10). In the context of self-assembly, both polymer-mediated (11-13) and biotin-streptavidin-mediated aggregation of EDs was shown (14). Despite the advantages a combination of EDs as building blocks and DNA oligonucleotides as linking agent offers, a protocol for DNA-directed self-assembly of EDs is currently missing.To close this gap, here we prepared an o/w emulsion composed of heavier-than-water diethyl phthalate (DEP) dispersed in an aqueous medium, stabilized by phospholipids, and functionalized with single-stranded DNA (ssDNA) oligonucleotides. Palmitoyloleoyl phosphatidylcholine (POPC) and distearoylphosphatidyl ethanolamine (DSPE) in a 9:1 molar ratio were used to stabilize the EDs. The DSPE was grafted with flexible poly(ethylene glycol) (PEG) tethers with a molecular weight of 2,000 (DSPE-PEG...

Application of nucleic acid–lipid conjugates for the programmable organisation of liposomal modules

“…Biotinylated DNA has been attached to biotinylated lipids within liposomes and lipid-coated emulsions using streptavidin cross-linkers (Fig. 3d) [67][68][69]. The challenge here is that streptavidin can directly cross-link biotinylated particles [26].…”

“…DNA functionalities have been used to form multicompartment assemblies between other soft nanostructures, these include attaching liposomes to gas microbubbles for medical theranostics [75], linking liposomes to layer-by-layer capsules [76] and assembly of lipid-coated oil-in-water microemulsions [67], which would allow extension to compartmentalisation of hydrophobic chemistries.…”

Formalizing Modularization and Data Hiding in Synthetic Biology

“…In the context of guiding the assembly of supramolecular compartments, the ssDNA oligonucleotides anchored to the surface of the compartments were shown to act as biomolecular combination locks, linking exclusively compartments that display complementary sequences. Using ssDNA oligonucleotides as 'smart glue' therefore allowed the programmable linkage of both hard [5,6,23,51,68,78,85] and soft colloids [3,19,29,31,32,50,71,72]. As demonstrated in Magnusson et al [48] even the entire compartment (in this case a small micelle) can be assembled and disassembled via DNA strand displacement.…”

pH-Driven Reversible Self-Assembly of Micron-Scale DNA Scaffolds

“…Because DNA nanostructures can serve as scaffolds for a variety of ligands, the proposed framework could be used to modularly control the organization of heterogeneous nanomaterials with a variety of functions. 38,39 We also speculate that the capacity to reversibly modulate nanostructure size may promote the development of smart devices for catalysis or drug delivery. For instance, tiles could permeate, diffuse, and assemble into a variety of environments otherwise inaccessible to large scaffolds, such as inside cells or cellular organelles, where they could spatially organize components and modulate efficiency of metabolic pathways.…”