Summary Compartmentalization in cells is central to the spatial and temporal control of biochemistry. In addition to membrane-bound organelles, membrane-less compartments form partitions in cells. Increasing evidence suggests that these compartments assemble through liquid-liquid phase separation. However the spatiotemporal control of their assembly, and how they maintain distinct functional and physical identities is poorly understood. We have previously shown an RNA-binding protein with a polyQ-expansion called Whi3 is essential for the spatial patterning of cyclin and formin transcripts in cytosol. Here, we show that specific mRNAs that are known physiological targets of Whi3 drive phase separation. mRNA can alter the viscosity of droplets, their propensity to fuse, and the exchange rates of components with bulk solution. Different mRNAs impart distinct biophysical properties of droplets indicating mRNA can bring individuality to assemblies. Our findings suggest that mRNAs can encode not only genetic information, but also the biophysical properties of phase-separated compartments.

Cells contain numerous membraneless organelles that assemble by intracellular liquid-liquid phase separation. The viscous properties and associated biomolecular mobility within these condensed phase droplets, or condensates, are increasingly recognized as important for cellular function and also dysfunction, for example, in protein aggregation pathologies. Fluorescence recovery after photobleaching (FRAP) is widely used to assess condensate fluidity and to estimate protein diffusion coefficients. However, the models and assumptions utilized in FRAP analysis of protein condensates are often not carefully considered. Here, we combine FRAP experiments on both in vitro reconstituted droplets and intracellular condensates with systematic examination of different models that can be used to fit the data and evaluate the impact of model choice on measured values. A key finding is that model boundary conditions can give rise to widely divergent measured values. This has important implications, for example, in experiments that bleach subregions versus the entire condensate, two commonly employed experimental approaches. We suggest guidelines for determining the appropriate modeling framework and highlight emerging questions about the molecular dynamics at the droplet interface. The ability to accurately determine biomolecular mobility both in the condensate interior and at the interface is important for obtaining quantitative insights into condensate function, a key area for future research.

Using two-photon confocal microscopy, equilibrium partition coefficients, k, were measured for aqueous Na-fluorescein, fluorescently labeled dextrans with molecular masses ranging from 4 to 20 kDa, two fluorescently labeled proteins with opposite charges, anionic bovine serum albumin (BSA), and cationic avidin in anionic 70 wt % hydroxyethyl methacrylate (HEMA)/30 wt % methacrylic acid (MAA) gels saturated with aqueous phosphate buffer solution. Cross-linking density with ethylene glycol–dimethacrylate (EGDMA) ranged from 0 to 1 wt %. All partition coefficients, except for avidin, were considerably less than unity and diminished strongly with increasing Stokes–Einstein diameter of the free aqueous solute. The average mesh size of the wet gels, obtained from the zero-frequency oscillatory shear-storage gel modulus, ranged from 3.6 to 8.3 nm over the cross-link ratios studied. Except for Na-fluorescein, solute hydrodynamic diameters were larger than the smallest average gel mesh size. Yet, all solutes permeated the gels but with small partition coefficients less than about 0.001 for the largest diameter solutes in the small mesh size gels. To express deviation from ideal partitioning, we define an enhancement (or exclusion) factor, E ≡ k/(1 – φ), where φ is the polymer volume fraction in the gel and E is unity for point solutes. A hard-sphere excluded-volume Ogston mesh size distribution is adopted to predict a priori the measured enhancement factors as a function of average gel mesh size for those solutes that do not interact specifically with the anionic gel (i.e., for solutes with E < 1). Agreement between the extended Ogston distribution and experiment is qualitative for both enhancement factors and water content of the gels. The cationic protein, Fl-avidin, exhibits a large enhancement factor in the anionic gels due to strong specific interaction with the charged carboxylate groups of MAA. In this case, consideration must be given to both hard-sphere size exclusion and specific complexation with the polymer strands.

Transient solute absorption and desorption concentration profiles were measured in a 70 wt % hydroxyethyl methacrylate (HEMA)/30 wt % methacrylic acid (MAA) anionic hydrogel using two-photon confocal microscopy. Dilute aqueous solutes included fluorescently labeled dextrans with molecular masses of 4, 10, and 20 kDa, and fluorescently labeled cationic avidin protein. Cross-linking densities with ethylene glycol dimethacrylate (EGDMA) varied from 0 to 1 wt % with polymer volume fractions increasing from 0.15 to 0.25. Average gel mesh sizes, determined from zero-frequency oscillatory shear storage moduli, ranged from about 3.6 to 8.4 nm over the cross-link ratios studied. All solutes exhibit Stokes−Einstein hydrodynamic radii obtained from measured free diffusion coefficients, D o , comparable to or larger than the average gel mesh size. In spite of considerable size exclusion, the studied solutes penetrate the gels indicating a range of mesh sizes available for transport. Transient uptake and release concentration profiles for FITC-dextrans follow simple diffusion theory with diffusion coefficients, D, essentially independent of loading or release characteristic of reversible absorption. Although strongly sizeexcluded, these solutes do not interact specifically with the polymer network. Diffusivities are accordingly predicted from a largepore effective-medium (LPEM) model developed to account for solute size, hydrodynamic drag, and distribution of mesh sizes available for transport in the polymer network. For this class of solute, and using no adjustable parameters, diffusivities predicted from the new effective-medium model demonstrate good agreement with experiment. For the specific-interacting cationic protein, avidin, gel loading is 3 orders of magnitude slower than that of dextran of similar hydrodynamic radius. Desorption of avidin is not complete even after 2 weeks of extraction. On the basis of size alone, avidin is strongly size-excluded, yet it exhibits a partition coefficient of over 20. For the positively charged protein, we observed specific ion binding on the negatively charged carboxylate groups of MAA-decorated polymer strands in the larger mesh spaces. Simple linear sorption kinetics gives an adsorption time constant of 5 min and a desorption time constant of about 20 days, suggesting nearly irreversible uptake of cationic avidin on the anionic gel matrix.

Two-photon confocal microscopy and back extraction with UV/Vis-absorption spectrophotometry quantify equilibrium partition coefficients, k, for six prototypical drugs in five soft-contact-lens-material hydrogels over a range of water contents from 40 to 92%. Partition coefficients were obtained for acetazolamide, caffeine, hydrocortisone, Oregon Green 488, sodium fluorescein, and theophylline in 2-hydroxyethyl methacrylate/methacrylic acid (HEMA/MAA, pKa≈5.2) copolymer hydrogels as functions of composition, aqueous pH (2 and 7.4), and salinity. At pH 2, the hydrogels are nonionic, whereas at pH 7.4, hydrogels are anionic due to MAA ionization. Solute adsorption on and nonspecific electrostatic interaction with the polymer matrix are pronounced. To express deviation from ideal partitioning, we define an enhancement or exclusion factor, E ≡ k/φ1, where φ1 is hydrogel water volume fraction. All solutes exhibit E > 1 in 100 wt % HEMA hydrogels owing to strong specific adsorption to HEMA strands. For all solutes, E significantly decreases upon incorporation of anionic MAA into the hydrogel due to lack of adsorption onto charged MAA moieties. For dianionic sodium fluorescein and Oregon Green 488, and partially ionized monoanionic acetazolamide at pH 7.4, however, the decrease in E is more severe than that for similar-sized nonionic solutes. Conversely, at pH 2, E generally increases with addition of the nonionic MAA copolymer due to strong preferential adsorption to the uncharged carboxylic-acid group of MAA. For all cases, we quantitatively predict enhancement factors for the six drugs using only independently obtained parameters. In dilute solution for solute i, Ei is conveniently expressed as a product of individual enhancement factors for size exclusion (Ei(ex)), electrostatic interaction (Ei(el)), and specific adsorption (Ei(ad)):Ei≡Ei(ex)Ei(el)Ei(ad). To obtain the individual enhancement factors, we employ an extended Ogston mesh-size distribution for Ei(ex); Donnan equilibrium for Ei(el); and Henry's law characterizing specific adsorption to the polymer chains for Ei(ad). Predicted enhancement factors are in excellent agreement with experiment.

Living cells contain numerous membrane-less RNA/protein (RNP) bodies that assemble by intracellular liquid-liquid phase separation. The properties of these condensed phase droplets are increasingly recognized as important in their physiological function within living cells, and also through the link to protein aggregation pathologies. However, techniques such as droplet coalescence analysis or standard microrheology do not always enable robust property measurements of model RNA/protein droplets in vitro. Here, we introduce a microfluidic platform that drives protein droplets into a single large phase, which facilitates viscosity measurements using passive microrheology and/or active two-phase flow analysis. We use this technique to study various phase separating proteins from structures including P granules, nucleoli, and Whi3 droplets. In each case, droplets exhibit simple liquid behavior, with shear rate-independent viscosities, over observed timescales. Interestingly, we find that a reported order of magnitude difference between the timescale of Whi3 and LAF-1 droplet coalescence is driven by large differences in surface tension rather than viscosity, with implications for droplet assembly and function. The ability to simultaneously perform active and passive microrheological measurements enables studying the impact of ATP-dependent biological activity on RNP droplets, which is a key area for future research.

We measure and, for the first time, theoretically predict four prototypical aqueous-drug diffusion coefficients in five soft-contact-lens material hydrogels where solute-specific adsorption is pronounced. Two-photon fluorescence confocal microscopy and UV/Vis-absorption spectrophotometry assess transient solute concentration profiles and concentration histories, respectively. Diffusion coefficients are obtained for acetazolamide, riboflavin, sodium fluorescein, and theophylline in 2-hydroxyethyl methacrylate/methacrylic acid (HEMA/MAA) copolymer hydrogels as functions of composition, equilibrium water content (30-90%), and aqueous pH (2 and 7.4). At pH2, MAA chains are nonionic, whereas at pH7.4, MAA chains are anionic (pKa≈5.2). All studied prototypical drugs specifically interact with HEMA and nonionic MAA (at pH2) moieties. Conversely, none of the prototypical drugs adsorb specifically to anionic MAA (at pH7.4) chains. As expected, diffusivities of adsorbing solutes are significantly diminished by specific interactions with hydrogel strands. Despite similar solute size, relative diffusion coefficients in the hydrogels span several orders of magnitude because of varying degrees of solute interactions with hydrogel-polymer chains. To provide a theoretical framework for the new diffusion data, we apply an effective-medium model extended for solute-specific interactions with hydrogel copolymer strands. Sorptive-diffusion kinetics is successfully described by local equilibrium and Henry's law. All necessary parameters are determined independently. Predicted diffusivities are in good agreement with experiment.

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