Publications

Phase separation of nucleic acids and proteins is a ubiquitous phenomenon regulating subcellular compartment structure and function. While complex coacervation of flexible single-stranded nucleic acids is broadly investigated, coacervation of double-stranded DNA (dsDNA) is less studied because of its propensity to generate solid precipitates. Here, we reverse this perspective by showing that short dsDNA and poly-l-lysine coacervates can escape precipitation while displaying a surprisingly complex phase diagram, including the full set of liquid crystal (LC) mesophases observed to date in bulk dsDNA. Short dsDNA supramolecular aggregation and packing in the dense coacervate phase are the main parameters regulating the global LC-coacervate phase behavior. LC-coacervate structure was characterized upon variations in temperature and monovalent salt, DNA, and peptide concentrations, which allow continuous reversible transitions between all accessible phases. A deeper understanding of LC-coacervates can gain insights to decipher structures and phase transition mechanisms within biomolecular condensates, to design stimuli-responsive multiphase synthetic compartments with different degrees of order and to exploit self-assembly driven cooperative prebiotic evolution of nucleic acids and peptides.

Concentrated solutions of blunt-ended DNA oligomer duplexes self-assemble in living polymers and order into lyotropic nematic liquid crystal phase. Using the optical torque provided by three distinct illumination geometries, we induce independent splay, twist, and bend deformations of the DNA nematic and measure the corresponding elastic coefficients K1, K2, and K3, and viscosities ηsplay, ηtwist, and ηbend. We find the viscoelasticity of the system to be remarkably soft, as the viscoelastic coefficients are smaller than in other lyotropic liquid crystals. We find K1 > K3 > K2, in agreement with the elasticity of the nematic phase of flexible polymers, and ηbend > ηsplay > ηtwist a behavior that is nonconventional in the context of chromonic, polymeric, and thermotropic liquid crystals, indicating a possible role of the weakness and reversibility of the DNA aggregates.

The onset of liquid crystal (LC) phases in concentrated aqueous solutions of DNA oligomers crucially depends on the end-to-end interaction between the DNA duplexes, which can be provided by the aromatic stacking of the terminal base-pairs or by the pairing of complementary dangling-ends. Here we investigated the LC behavior of three blunt-end 12-base-long DNA duplexes synthesized with hydroxyl, phosphate and triphosphate 5’-termini. We experimentally characterized the concentration-temperature phase diagrams and we quantitatively estimated the end-to-end stacking free energy, by comparing the empirical data with the predictions of coarse-grained linear aggregation models. The preservation of LC ordering, even in presence of the bulky and highly charged triphosphate group, indicates that attractive stacking interactions are still present and capable of induce linear aggregation of the DNA duplexes. This finding strengthens the potential role of chromonic like self-assembly for the prebiotic formation of linear polymeric nucleic acids.

Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth

The transport of bio-particles in viscous flows exhibits a rich variety of dynamical behaviour, such as
morphological transitions, complex orientation dynamics or deformations. Characterising such complex
behaviour under well controlled flows is key to understanding the microscopic mechanical properties of
biological particles as well as the rheological properties of their suspensions. While generating regions of
simple shear flow in microfluidic devices is relatively straightforward, generating straining flows in which
the strain rate is maintained constant for a sufficiently long time to observe the objects’ morphologic
evolution is far from trivial. In this work, we propose an innovative approach based on optimised design
of microfluidic converging–diverging channels coupled with a microscope-based tracking method to
characterise the dynamic behaviour of individual bio-particles under homogeneous straining flow.
The tracking algorithm, combining a motorised stage and a microscopy imaging system controlled by
external signals, allows us to follow individual bio-particles transported over long-distances with highquality
images. We demonstrate experimentally the ability of the numerically optimised microchannels
to provide linear velocity streamwise gradients along the centreline of the device, allowing for extended
consecutive regions of homogeneous elongation and compression. We selected three test cases (DNA,
actin filaments and protein aggregates) to highlight the ability of our approach for investigating dynamics
of objects with a wide range of sizes, characteristics and behaviours of relevance in the biological world

Understanding confined flows of complex fluids requires simultaneous access to the mechanical behaviour of the liquid and the boundary condition at the interfaces. Here, we use evanescent wave microscopy to investigate near-surface flows of semi-dilute, unentangled polyacrylamide solutions. By using both neutral and anionic polymers, we show that monomer charge plays a key role in confined polymer dynamics. For solutions in contact with glass, the neutral polymers display chain-sized adsorbed layers, while a shear-rate-dependent apparent slip length is observed for anionic polymer solutions. The slip lengths measured at all concentrations collapse onto a master curve when scaled using a simple two-layer depletion model with non-Newtonian viscosity. A transition from an apparent slip boundary condition to a chain-sized adsorption layer is moreover highlighted by screening the charge with additional salt in the anionic polymer solutions. We anticipate that our study will be a starting point for more complex studies relating the polymer dynamics at interfaces to their chemical and physical composition.

Particle transport in fluids at micro-and nano-scales is important in many domains. As compared to the quiescent case, the time evolution of particle dispersion is enhanced by coupling: i) advection along the flow; and ii) diffusion along the associated velocity gradients. While there is a well-known, long-time limit for this advection-diffusion enhancement, understanding the short-time limit and corresponding crossover between these two asymptotic limits is less mature. We use evanescent-wave video microscopy for its spatio-temporal resolution. Specifically, we observe a near-surface zone of where the velocity gradients, and thus dispersion, are the largest within a simple microfluidic channel. Supported by a theoretical model and simulations based on overdamped Langevin dynamics, our experiments reveal the crossover of this so-called Taylor dispersion from short to long time scales. Studying a range of particle size, viscosity and applied pressure, we show that the initial spatial distribution of particles can strongly modify observed master curves for short-time dispersion and its crossover into the long-time regime.

Modern interfacial science is increasingly multidisciplinary. Unique insight into interfacial interactions requires new multimodal techniques for interrogating surfaces with simultaneous complementary physical and chemical measurements. Here, we describe the design and testing of a microscope that incorporates a miniature surface forces apparatus (μSFA) in sphere vs flat geometry for force–distance measurements, while simultaneously acquiring Raman spectra of the confined zone. The simple optical setup isolates independent optical paths for (i) the illumination and imaging of Newton’s rings and (ii) Raman scattering excitation and efficient signal collection. We benchmark the methodology by examining Teflon thin films in asymmetric (Teflon–water–glass) and symmetric (Teflon–water–Teflon) configurations. Water is observed near the Teflon–glass interface with nanometer-scale sensitivity in both the distance and Raman signals. We perform chemically resolved, label-free imaging of confined contact regions between Teflon and glass surfaces immersed in water. Remarkably, we estimate that the combined approach enables vibrational spectroscopy with single water monolayer sensitivity within minutes. Altogether, the Raman-μSFA allows exploration of molecular confinement between surfaces with chemical selectivity and correlation with interaction forces.

Advances in the research of intermolecular and surface interactions result from the development of new and improved measurement techniques and combinations of existing techniques. Here, we present a new miniature version of the surface forces apparatus—the μSFA—that has been designed for ease of use and multimodal capabilities with the retention of the capabilities of other SFA models including accurate measurements of the surface separation distance and physical characterization of dynamic and static physical forces (i.e., normal, shear, and friction) and interactions (e.g., van der Waals, electrostatic, hydrophobic, steric, and biospecific). The small physical size of the μSFA, compared to previous SFA models, makes it portable and suitable for integration into commercially available optical and fluorescence light microscopes, as demonstrated here. The large optical path entry and exit ports make it ideal for concurrent force measurements and spectroscopy studies. Examples of the use of the μSFA in combination with surface plasmon resonance (SPR) and Raman spectroscopy measurements are presented. Because of the short working distance constraints associated with Raman spectroscopy, an interferometric technique was developed and applied to calculate the intersurface separation distance based on Newton’s rings. The introduction of the μSFA will mark a transition in SFA usage from primarily physical characterization to concurrent physical characterization with in situ chemical and biological characterization to study interfacial phenomena, including (but not limited to) molecular adsorption, fluid flow dynamics, the determination of surface species and morphology, and (bio)molecular binding kinetics.

In capillary-driven fluid dynamics, simple departures from equilibrium offer the chance to quantitatively model the resulting relaxations. These dynamics in turn provide insight on both practical and fundamental aspects of thin-film hydrodynamics. In this work, we describe a model trilayer dewetting experiment elucidating the effect of solid, no-slip confining boundaries on the bursting of a liquid film in a viscous environment. This experiment was inspired by an industrial polymer processing technique, multilayer coextrusion, in which thousands of alternating layers are stacked atop one another. When pushed to the nanoscale limit, the individual layers are found to break up on time scales shorter than the processing time. To gain insight on this dynamic problem, we here directly observe the growth rate of holes in the middle layer of the trilayer films described above, wherein the distance between the inner film and solid boundary can be orders of magnitude larger than its thickness. Under otherwise identical experimental conditions, thinner films break up faster than thicker ones. This observation is found to agree with a scaling model that balances capillary driving power and viscous dissipation with a no-slip boundary condition at the solid substrate/viscous environment boundary. In particular, even for the thinnest middle-layers, no finite-size effect related to the middle film is needed to explain the data. The dynamics of hole growth is captured by a single master curve over four orders of magnitude in the dimensionless hole radius and time, and is found to agree well with predictions including analytical expressions for the dissipation.