This thesis investigates the use of engineered DNA to program fusion and aggregation behaviors of artificial cells, mimicking biological cells and their important functions. To achieve this goal, we construct synthetic cells from engineered lipids and DNA to recognize and process intercellular signals.<div><br></div><div>Cell fusion is regulated by snap receptor (SNARE) proteins in mammalian cells. The zippering of SNARE proteins exerts forces to the adjacent cell membrane and induces membrane fusion. The hybridization of membrane anchored DNA can induce fusion in a similar way. The advantage of using DNA as a fusion signal is that oligonucleotides are much easier to engineer and control. In this study, we construct two types of small vesicles decorated with DNA oligonucleotides and demonstrate their fusion using programmable DNA base-pairing. Fluorescent probes are used to measure fusion events. The experiment advances our understanding of the dynamic vesicle fusion behavior.<br></div><div><br></div><div>Cell aggregation is a complex behavior that is closely associated to the differentiation, migration, and viability of biological cells. An effort to create synthetic analogs could lead to considerable advances in cell physiology and biophysics. Rendering and modulating such a dynamic artificial cell system require mechanisms for receiving, transducing, and transmitting intercellular signals, yet effective tools are limited at present. Here we construct synthetic cells and show their programmable aggregation behaviors using DNA oligonucleotides as a signaling molecule. The synthetic cells have transmembrane DNA origami that are used to recognize and process intercellular signals. We demonstrate that multiple small vesicles aggregate onto a giant vesicle after a transduction of external DNA signals by an intracellular enzyme, and that the small vesicles dissociate when receiving ‘release’ signals.<br></div><div><br></div><div>We envision that this thesis will provide a new platform for building programmable synthetic protocells capable of chemical communication and coordination. <br></div>

Synthetic cells and tissues engineered from the bottom-up using non-living building blocks have many potential applications in medicine and biochemistry. Nonetheless, the applications of these synthetic cells and tissues remain limited by virtue of the challenging, costly, and uncontrollable methodologies available for their construction. Droplet microfluidic techniques, which are powerful analytical tools that can be used for the accurate and precise control over micro-sized droplets, offer potential solutions to these problems. The development of these droplet microfluidic platforms is a burgeoning and challenging field, with room for many impactful innovations. In the following dissertation, I first show the development of two different droplet microfluidic platform for the generation of two variations of synthetic cells: the first from polymeric-based building blocks and the second from biomimetic lipid-based building blocks. I then use the former of these platforms for the bottom-up generation of functional synthetic tissues (also known as prototissues). Using these techniques, I am able to elicit previously elusive structural and behavioral information. These methods contribute towards the creation of superior mimics of sophisticated life-like structures as well as a better understanding of how bespoke microfluidic platforms can be engineered to yield reliable and reproducible results. I have shown that microfluidic technologies are an invaluable tool for the creation and study of life-like systems and that these synthetic cells and tissues open up new avenues for research into multidisciplinary applications. / Graduate / 2023-06-07

Living cells are highly complex, making it an extremely challenging task to understand how they function. A possible solution is the bottom-up assembly of non-living components and building up life-like features from scratch, i.e., using synthetic cells as a tool to understand the basic characteristics of life. One such chassis for synthetic cells are liposomes, which, like the cell membrane of living cells, are made of phospholipids. As living cells grow, lipids are incorporated into their membrane in order to cope up with the volume increase of the cell. In a similar fashion, a variety of ways are currently being investigated to achieve growth of synthetic cells. Few examples include incorporation of fatty acids from the surrounding environment, reconstituting the enzymes for fatty acid or lipid biosynthesis in the liposome, or by carrying out the synthesis of artificial membrane components through the external addition of precursor molecules. Here, we demonstrate the membrane-tension mediated growth of giant unilamellar vesicles (GUVs) by fusing sub-micrometre-sized feeder vesicles to them. We use a recently developed microfluidic technique, octanol-assisted liposome assembly (OLA), to produce cell-sized (~10 μm) GUVs on-chip. Following the density-based separation of the liposomes from the waste product (1-octanol droplets), we supply small unilamellar vesicles (SUVs, ~30 nm in diameter) which act as a lipid reserve for growth by fusing with the GUVs. The lipids molecules, being very stable in bilayer conformation, require energy to reorient themselves and undergo membrane fusion. We show that increased membrane tension of GUVs can act as a sole driver to carry out multiple fusion events and cause significant growth. By placing a mass population (&gt;1000) of GUVs in a sufficiently hypotonic solution (delta c 3−5 mM), we build up the membrane tension (~10 mN/m) driving multiple SUV-GUV fusionevents, eventually doubling the volume of a part of the population. We probe a variety of lipid compositions, including hybrid (composed of lipids and fatty acids) GUVs and find the growth to be dependent on the lipid composition. Maximum growth is obtained when using a hybrid system, as compared to pure lipids. Our results show the possibility to use a protein-freeminimal system to induce growth in a minimalistic manner and the demonstrated highthroughput microfluidic approach may have useful implications towards realizing an autonomous entity capable of undergoing a continuous growth-division cycle.

In this study, we introduce novel, truly non-ionic hydrogen-bonded layer-by-layer (LbL) coatings for cell surface engineering capable of long-term support of cell function. Utilizing the LbL technique imparts the ability to tailor membrane permeability, which is of particular importance for encapsulation of living cells as cell viability critically depends on the diffusion of nutrients through the artificial polymer membrane. Ultrathin, permeable polymer membranes are constructed on living cells without a cationic pre-layer, which is usually employed to increase the stability of LbL coatings. In the absence of the cytotoxic PEI pre-layer, viability of encapsulated cells drastically increases to 94%, as compared to 20-50% in electrostatically-bonded shells. Engineering surfaces of living cells with natural or synthetic compounds can mediate intercellular communication, render the cells less sensitive to environmental changes, and provide a protective barrier from hostile agents. Surface engineered cells show great potential for biomedical applications, including biomimetics, biosensing, enhancing biocompatibility of implantable materials, and may represent an important step toward construction of an artificial cell.

Recently, there has been a growing drive towards the bottom-up development of synthetic cells that mimic key cellular features. A cellular feature ubiquitous amongst cells is that of compartmentalisation. Compartmentalisation enables the spatiotemporal control of biochemical reactions and is thus vital for the development of synthetic cells. To date, most synthetic cell models have utilised classical membrane bound containers as model compartments. However, recent advances in cell biology have highlighted the importance of membraneless compartments formed via liquid-liquid phase separation (LLPS) as organisation centres. It has been suggested that these organelles play a critical role in regulating cell biochemistry, yet very little is known about their interactions with enzymatic reactions. Thus, aiming to develop novel synthetic capabilities, the work presented in this thesis designs and characterises synthetic cells which include features of membraneless compartmentalisation. These systems utilise complex coacervates, a specific type of LLPS that is driven by the electrostatic attraction of oppositely charged polymers, as model membraneless compartments. These low complexity systems subsequently provide ideal platforms for systematic investigations of the interaction of membraneless coacervate compartments with enzymatic reactions. In Chapter 3 and 4, I focus on developing a responsive synthetic cell system that recapitulates features of membrane-bound and membraneless compartmentalisation. I generate a pH-responsive system by exploiting the intrinsic pKa of cationic polylysine to trigger coacervation within a liposome. This synthetic cell is then functionalised with the enzyme formate dehydrogenase (FDH). I show that coacervate properties can be utilized to locally concentrate and activate the FDH reaction at low enzyme concentrations, thus demonstrating that membraneless compartments can activate reactions via sequestration into coacervate reaction centres. In Chapter 5, I then proceed to characterise whether the diffusive exchange of molecules across a droplet phase boundary effects enzyme dynamics. Synthetic cells constructed from emulsion droplets with coacervate sub-compartments were used as model systems with diffusive exchange, while bulk coacervate and supernatant phases were used as uncoupled model systems without exchange. I studied the FDH reaction in both models and I conclude that coupling of the phases increases reaction rates compared to an uncoupled system. When coupled, the supernatant acts as a ’sink’ removing the product NADH from the coacervate droplets. This increases the apparent reaction rate in the supernatant, while the reduction of NADH concentration in the coacervate reduces product inhibition. This demonstrated that the open phase boundary tightly couples membraneless droplets to their surroundings, which can ultimately lead to increased reaction rates both inside and outside the compartments. Finally in Chapter 6, I scrutinize enzyme kinetics of the enzymes FDH and β -galactosidase in the unique coacervate physicochemical environment using Michaelis-Menten assays in CM-Dex/PDDA bulk phase. Results show that the KM and Vmax of FDH significantly increased compared to buffer, while those of β-galactosidase do not. I hypothesise that the negatively charged formate substrate of the FDH reaction interacts strongly with the positively charged PDDA, decreasing its affinity for the enzyme. Furthermore, I suggest that the coacervate environment facilitates the rate limiting hydride transfer of the reaction, thereby increasing the maximum rate. This data demonstrates that the coacervate environment itself can tune and control enzyme dynamics. In conclusion, my work establishes responsive, tunable and enzymatically active syn- thetic cellular systems with features of membraneless compartmentalisation. My results indicate that membraneless compartments can have significant impact on the dynamics of enzymatic reactions, opening up possible ways to control reaction rates in synthetic systems and suggesting plausible functions for membraneless organelles in vivo. Overall, I demonstrate that rationally designed synthetic cells provide biomimetic experimental platforms that offer insights into the influence of membraneless compartmentalisation on enzymatic reactions. Parts of the presented work have been published as two first author publications in peer-reviewed journals. / ‘Bottom-up'’ Modelle synthetischer Zellen, die Schlüsselmerkmale zellbasierten Lebens imitieren, rücken immer mehr in den Fokus. Von zentraler Bedeutung ist hier die Kompartmentbildung. Sie erst ermöglicht die räumliche und zeitliche Kontrolle biochemischer Abläufe und ist daher entscheidend bei der Entwicklung synthetischer Zellen. Bisher wurden in der Mehrzahl der synthetischen Zellmodelle klassische, membrangebundene Reaktionsräume als Modellkompartimente verwendet. Jüngste Fortschritte in der Zellbiologie belegen jedoch die Bedeutung von membranlosen Kompartimenten, die durch Flüssig-Flüssig-Phasentrennung (LLPS) gebildet werden. Es wird angenommen, dass diese membranlosen Kompartimente eine zentrale Rolle bei der Regulierung der Zellchemie spielen. Jedoch ist bisher nur sehr wenig über ihren Einfluss auf enzymatische Reaktionen bekannt und experimentell belegt. Mit dem Ziel, die Bandbreite und das Verständnis synthetischer Modelle zu erweitern, wurden in dieser Arbeit neue Methoden entwickelt und dargestellt, die membranlose Kompartmentbildung benutzen. Es wurden hierfür komplexe Koazervate eingesetzt, eine spezielle Art der LLPS, welche durch die elektrostatische Anziehung von entgegengesetzt geladenen Polymeren angetrieben wird. Diese verhältnismäßig einfachen Systeme bieten eine ideale Plattform für systematische Untersuchungen des Einflusses von membranlosen Koazervatkompartimenten auf enzymatische Reaktionen. In den Kapiteln 3 und 4 konzentrierte ich mich auf die Entwicklung eines reaktionsfähigen synthetischen Modellsystems, das die Phänomene sowohl membrangebundener als auch membranfreier Kompartmentbildung vereint. Zur Steuerung der Koazervierung innerhalb von Liposomen wurde ein pH-reaktives System verwendet, welches sich den intrinsischen pKa von kationischen Polylysin zunutze macht. Diese synthetis- che Zelle wurde im folgenden Schritt mit dem Enzym Formiat-Dehydrogenase (FDH) funktionalisiert. Ich konnte damit zeigen, dass es die Eigenschaften von Koazervaten ermöglichen, die FDH-Reaktion bei global sehr niedrigen Enzymkonzentrationen zu aktivieren. Hierbei wirken die membranlosen Koazervate in Folge einer lokal er- höhten Enzymkonzentration als Zentren gesteigerter Reaktivität. Dies geschieht durch die lokale Konzentrationserhöhung in Koazervaten, was bei LLPS auch durch den Verteilungskoeffizient beschrieben wird. Mit anderen Worten agieren diese membran- losen Kompartimente durch Sequestrierung als Reaktionszentren. Im Kapitel 5 charakterisierte ich den Einfluss von diffusivem Molekülaustausch auf die Enzymkinetik über die Koazervat-Phasengrenze hinweg. Hierbei wurden zwei Systeme miteinander verglichen. Einerseits wurde ein synthetisches Zellmodell, beste- hend aus mikrofluidisch hergestellten Wasser-in-Öl Emulsionstropfen, die Koazervate enthalten, als Modellsystem mit diffusivem Austausch zwischen den Phasen verwendet. Andererseits wurden separate, reine Koazervatphasen und reine Überstandsphasen als Modellsysteme ohne Austausch verwendet. Ich habe die FDH-Reaktion in beiden Modellsystemen untersucht und kam zu dem Schluss, dass die Kopplung der Phasen die Reaktionsgeschwindigkeiten im Vergleich zu den ungekoppelten Systemen erhöht. Bei der Kopplung wirkt die Überstandsphase als Senke, die das Produkt NADH aus den Koazervaten aufnimmt. Dies erhöht die scheinbare Reaktionsgeschwindigkeit im Überstand, während die Verringerung der NADH-Konzentration im Koazervat die Produkthemmung verringert. Dies zeigt, dass die offene Phasengrenze membranloser Kompartimente eng mit ihrer Umgebung gekoppelt ist, was als erhöhte Reaktionsraten sowohl innerhalb als auch außerhalb der Kompartimente gemessen werden kann. Schließlich untersuchte ich in Kapitel 6 die Enzymkinetik der Enzyme FDH und β- Galaktosidase in der physikalisch-chemischen Umgebung des Koazervats. Mit Hilfe von Michaelis-Menten-Experimenten in der CM-Dextran/PDDA-Bulkphase konnte gezeigt werden, dass KM und Vmax von FDH im Vergleich zum Überstand signifikant erhöht sind, wohingegen jene von β-Galaktosidase ein solches Verhalten nicht zeigen. Das führte mich zu der Hypothese, dass das negativ geladene Formiatsubstrat der FDH- Reaktion stark mit dem positiv geladenen PDDA interagiert, wodurch seine Affinität für das Enzym abnimmt. Darüber hinaus wird der ratenbegrenzende Hydridtransfer in der Umgebung des Koazervats erleichtert und es kann eine Erhöhung der Reaktionsrate beobachtet werden. Die Daten zeigen, dass abhängig vom Koazervat-Milieu die Enzymdynamik in verschiedene Richtungen gesteuert werden kann. Zusammenfassend lässt sich sagen, dass meine Arbeit reaktionsfähige, steuerbare und enzymatisch aktive synthetische Zellsysteme mit Eigenschaften membranloser Kompartmentbildung etabliert. Meine Ergebnisse deuten darauf hin, dass membranlose Kompartimente einen signifikanten Einfluss auf die Dynamik enzymatischer Reaktio- nen haben. Meine Untersuchungen eröffnen damit neuartige Wege zur Kontrolle der Reaktionsgeschwindigkeit in synthetischen Systemen und erweitern das Verständnis möglicher Funktionen membranloser Organellen in vivo. Insgesamt zeige ich, dass über- legt entworfene synthetische Zellen eine hervorragende biomimetische Plattform bieten, um Einblicke in den Einfluss von membranloser Kompartimentierung auf enzymatische Reaktionen zu gewinnen. Teile der vorgestellten Arbeit wurden als wissenschaftliche Beiträge in zwei begutachteten Journalen als Erstautor veröffentlicht.