Biology subjects

Rubio-Sanchez, R. M.

Publications and source records attributed to Rubio-Sanchez, R. M..

3 recordsLinked to original sources

bioRxiv2025

Organization and triggered release of liposomes with DNA-based synthetic condensates

Cells use a combination of membrane-bound and membrane-less compartments to dynamically orchestrate internal biochemical processes and sustain intracellular communication. Recapitulating the hierarchical integration and interplay between these physically and chemically diverse structures is required to enhance the functionalities of synthetic cells and other advanced biomimetic systems. Here, we describe the use of synthetic DNA condensates to selectively uptake and spatially organize lipid vesicles, interacting with the condensates thanks to cholesterol-DNA anchors. By modulating anchor density, the liposomes can be programmably localized on the surface or interior of the condensates, while base-pairing selectivity can be leveraged to target individual internal domains in multi-phasic condensates. The embedded liposomes can be released by adding a nucleic acid trigger and captured by a second condensate population, thus imitating extracellular vesicles in their ability to support long-range cellular communication. This modular platform demonstrates the potential of DNA-based condensates to program the spatial distribution of membranous subcompartments and to support dynamic cargo-handling capabilities. These features are valuable for engineering cell mimics, microreactors, and delivery systems.

synthetic biology↗

bioRxiv2025

Expression of nano-engineered RNA organelles in bacteria

Designing synthetic biomolecular condensates, or membrane-less organelles, offers insights on the functions of their natural counterparts, and is equally valuable for cellular and metabolic engineering. Choosing E. coli for its biotechnological relevance, we deploy RNA nanotechnology to design and express non-natural membrane-less organelles in vivo. The designer condensates assemble co-transcriptionally from branched RNA motifs interacting via base-pairing. Exploiting binding selectivity we express orthogonal, non-mixing condensates, and by embedding a protein-binding aptamer we achieve selective protein recruitment. Condensates can be made to dissolve and re-assemble upon thermal cycling, thereby reversibly releasing and re-capturing protein clients. The synthetic organelles are expressed robustly across the cell population and remain stable despite enzymatic RNA processing. Compared with existing solutions based on peptide building blocks or repetitive RNA sequences, these nanostructured RNA motifs enable algorithmic control over interactions, affinity for clients, and condensate microstructure, opening new directions in synthetic biology and biotechnology.

synthetic biology↗

bioRxiv2025

Internal phase separation in synthetic DNA condensates

Biomolecular condensates regulate cellular biochemistry by organizing enzymes, substrates and metabolites, and often acquire partially de-mixed states whereby distinct internal domains play functional roles. Despite their physiological relevance, questions remain about the principles underpinning the emergence of multi-phase condensates. Here, we present a model system of synthetic DNA nanostructures able to form monophasic or biphasic condensates. Key condensate features, including the degree of interphase mixing and the relative size and spatial arrangement of domains, can be controlled by altering nanostructure stoichiometries. The modular nature of the system facilitates an intuitive understanding of phase behavior, and enables mapping of the experimental phenomenology onto a predictive Flory-Huggins model. The experimental and theoretical framework we introduce will help address open questions on multiphase condensation in biology and aid the design of functional biomolecular condensates in vitro, in synthetic cells, and in living cells.

biophysics↗