Self-Assembly of DNA Homopolymers by Pathway Dependence to Evade Metastable States

A pathway-dependent strategy is proposed to assist single-stranded DNA polyadenine (poly(dA)) in evading metastable states and to achieve morphological regulation from microcapsules to microbowls by fractional n-butanol addition and emulsification (shaking) in a soft emulsion template (water-in-n-butanol). The first stage is the formation of small microcapsules by a fourth solvent addition and shaking. The second stage is the expansion of the small microcapsules initiated by the fifth solvent addition and shaking, drawing them to a new pathway to evade metastable states. Osmotic re-equilibrium and shaking are two indispensable conditions for overcoming the energy barriers. The third stage is the buckling of the expanded microcapsules and the evolution into microbowls after the evaporation of n-butanol to reach a global free energy minimum stable state. Conversely, the conventional one-time solvent addition and shaking pathway do not obtain microbowls. This kinetics pathway-dependent strategy evades metastability and shapes DNA oligonucleotides into desired structures via self-assembly.

LLPS vs. LLCPS: analogies and differences

We compare the process of Liquid-Liquid Phase Separation (LLPS) of flexible macromolecular solutions, with the Liquid-Liquid Crystalline Phase Separation (LLCPS) of semiflexible polymers and rigid filamentous colloids, which involves the formation of a liquid phase that possesses a directional alignment. Although the observed phase separation follows a similar dynamic path, namely nucleation and growth or spinodal decomposition separating two phases of dilute and concentrated compositions, the underlying physics that defines the theoretical framework of LLCPS is completely different from the one of LLPS. We review the main theories that describe the phase separation processes and relying on thermodynamics and dynamical arguments, we highlight the differences and analogies between these two phase separation phenomena, attempting to clarify the inner mechanisms that regulate those two processes. A particular focus is given to metastable phases, as these intermediate states represent a key element in understanding how phase separation works.

A decade of innovation and progress in understanding the morphology and structure of heterogeneous polymers in rigid confinement

When confined in nanoscale domains, polymers generally encounter changes in their structural, thermodynamics and dynamics properties compared to those in the bulk, due to the high amount of polymer/wall interfaces and limited amount of matter. The present review specifically deals with the confinement of heterogeneous polymers (i.e. polymer blends and block copolymers) in rigid nanoscale domains (i.e. bearing non-deformable solid walls) where the processes of phase separation and self-assembly can be deeply affected. This review focuses on the innovative contributions of the last decade (2010-2020), giving a summary of the new insights and understanding gained in this period. We conclude this review by giving our view on the most thriving directions for this topic.

Mechanistic Inferences From Analysis of Measurements of Protein Phase Transitions in Live Cells

The combination of phase separation and disorder-to-order transitions can give rise to ordered, semi-crystalline fibrillar assemblies that underlie prion phenomena namely, the non-Mendelian transfer of information across cells. Recently, a method known as Distributed Amphifluoric Förster Resonance Energy Transfer (DAmFRET) was developed to study the convolution of phase separation and disorder-to-order transitions in live cells. In this assay, a protein of interest is expressed to a broad range of concentrations and the acquisition of local density and order, measured by changes in FRET, is used to map phase transitions for different proteins. The high-throughput nature of this assay affords the promise of uncovering sequence-to-phase behavior relationships in live cells. Here, we report the development of a supervised method to obtain automated and accurate classifications of phase transitions quantified using the DAmFRET assay. Systems that we classify as undergoing two-state discontinuous transitions are consistent with prion-like behaviors, although the converse is not always true. We uncover well-established and surprising new sequence features that contribute to two-state phase behavior of prion-like domains. Additionally, our method enables quantitative, comparative assessments of sequence-specific driving forces for phase transitions in live cells. Finally, we demonstrate that a modest augmentation of DAmFRET measurements, specifically time-dependent protein expression profiles, can allow one to apply classical nucleation theory to extract sequence-specific lower bounds on the probability of nucleating ordered assemblies. Taken together, our approaches lead to a useful analysis pipeline that enables the extraction of mechanistic inferences regarding phase transitions in live cells.

Crystal Memory near Discontinuous Triacylglycerol Phase Transitions: Models, Metastable Regimes, and Critical Points

It is proposed that "crystal memory", observed in a discontinuous solid-liquid phase transition of saturated triacylglycerol (TAG) molecules, is due to the coexistence of solid TAG crystalline phases and a liquid TAG phase, in a superheated metastable regime. Such a coexistence has been detected. Solid crystals can act as heterogeneous nuclei onto which molecules can condense as the temperature is lowered. We outlined a mathematical model, with a single phase transition, that shows how the time-temperature observations can be explained, makes predictions, and relates them to recent experimental data. A modified Vogel-Fulcher-Tammann (VFT) equation is used to predict time-temperature relations for the observation of "crystal memory" and to show boundaries beyond which "crystal memory" is not observed. A plot of the lifetime of a metastable state versus temperature, using the modified VFT equation, agrees with recent time-temperature data. The model can be falsified through its predictions: the model possesses a critical point and we outline a procedure describing how it could be observed by changing the hydrocarbon chain length. We make predictions about how thermodynamic functions will change as the critical point is reached and as the system enters a crossover regime. The model predicts that the phenomenon of "crystal memory" will not be observed unless the system is cooled from a superheated metastable regime associated with a discontinuous phase transition.

Pathway of orientational symmetry breaking in crystallization of short n-alkane droplets: A molecular dynamics study

We carry out molecular dynamics simulations by using an all-atom model to study the nucleation and crystallization of n-alkane droplets under three-dimensional and quasi-two-dimensional conditions. We focus on the development of orientational order of chains from a random state to a neatly ordered one. Two new methods, the map of symmetry breaking and the information entropy of chain orientations, are introduced to characterize the emerge and remelting phenomena of a primary nucleus at the early stage of crystallization. Stepwise nucleation, as well as the surface induced nucleation, of large droplets is observed. We elucidate the kinetic process of the formation of a primary nucleus and the rearrangement of every single molecule involved in a primary nucleus. We found that density fluctuation and orientational preordering are coupled together and occur simultaneously in nucleation. Our results show the pathway of orientational symmetry breaking in the crystallization of n-alkane droplets that are heuristic for the deeper understanding of the crystallization in more complex molecules such as polymers.

Influences of Structural Modification of S, N-Hexacenes on the Morphology and OFET Characteristics

Although chemical modifications on conjugated molecules are widely applied for the purpose of improving processability and device performances, the effect of the modification was far less investigated. Here, five S, N-hexacenes are studied to reveal the influences of (1) the lateral alkyl chain, (2) the terminal group (thiophene vs benzene), and (3) the end-capping phenyl group of the hexacenes on the morphology and organic field-effect transistor (OFET) performances. Crystal arrays of the hexacenes were prepared via polydimethylsiloxane (PDMS)-assisted crystallization (PAC) prior to morphological and OFET characterizations. The lattice structures and crystal quality of the hexacenes were evaluated by microscopy and diffraction techniques including single-crystal diffractometer, electron diffraction, and grazing incidence wide-angle X-ray scattering. The systematic analyses led to the following conclusions: (1) the bulkier alkyl side chain assists to form more densely packed crystals with less structural defects; (2) the terminal thiophene rings bring about higher-lying E_HOMO, more ordered phase, and crystal orientation, whereas the terminal benzene rings deteriorate the structural order of the active layer and result in the liquid crystal phase; and (3) the phenyl end caps ameliorate the morphological order, intermolecular overlapping, thermal stability and elevate E_HOMO. Thus, EH-DTPTt-Ph delivers the highest μ_h, contributing to high-lying E_HOMO, well-oriented crystal array with a longer correlation length, and suitable lattice orientation. This systematic research provides the aspects about the effects of the functionalized S, N-hexacenes on the morphology and OFET characteristics, which is anticipated to be useful for the molecular design of heteroacenes.

Phase Separation of Intrinsically Disordered Proteins

There is growing interest in the topic of intracellular phase transitions that lead to the formation of biologically regulated biomolecular condensates. These condensates are membraneless bodies formed by phase separation of key protein and nucleic acid molecules from the cytoplasmic or nucleoplasmic milieus. The drivers of phase separation are referred to as scaffolds whereas molecules that preferentially partition into condensates formed by scaffolds are known as clients. Recent advances have shown that it is possible to generate physical and functional facsimiles of many biomolecular condensates in vitro. This is achieved by titrating the concentration of key scaffold proteins and solution parameters such as salt concentration, pH, or temperature. The ability to reproduce phase separation in vitro allows one to compare the relationships between information encoded in the sequences of scaffold proteins and the driving forces for phase separation. Many scaffold proteins include intrinsically disordered regions whereas others are entirely disordered. Our focus is on comparative assessments of phase separation for different scaffold proteins, specifically intrinsically disordered linear multivalent proteins. We highlight the importance of coexistence curves known as binodals for quantifying phase behavior and comparing driving forces for sequence-specific phase separation. We describe the information accessible from full binodals and highlight different methods for-and challenges associated with-mapping binodals. In essence, we provide a wish list for in vitro characterization of phase separation of intrinsically disordered proteins. Fulfillment of this wish list through key advances in experiment, computation, and theory should bring us closer to being able to predict in vitro phase behavior for scaffold proteins and connect this to the functions and features of biomolecular condensates.

Study on the Thermodynamics of Polymer Crystallization Based on Twin-Lattice Model

Polymer crystallization is the most important part in determining the performance of polymeric materials. The twin-lattice model originally provided by Lennard-Jones and Devonshire, developed by Pople and Karasz and other researchers, is extended for describing the thermodynamics of polymer crystallization. The positional order of segments and the orientational order of bonds are considered in this model. The free energy of polymers is obtained by further introducing the conformational energy and entropy, and thus a new parameter is defined, which is the ratio of conformational energy and positional diffusion energy. We studied two kinds of processes in polymer crystallization, including the process with plastic crystal phase and without any mesophases. The choice of crystallizing process is determined by the magnitude of lattice energy and conformational energy. The solid-solid transition from crystal to plastic crystal shows a significant dependence on the conformational energy. Considering data reliability, n-paraffins are chosen as the representation of polymers to compare the predictions of the model with experimental observations. We predict the number of carbons beyond which the rotator phase disappears, which is quite in agreement with the experiments. These calculations and results show this model can provide a new understanding to the crystallization of polymers.

Potential of mean force and transient states in polyelectrolyte pair complexation

The pair association between two polyelectrolytes (PEs) of the same size but opposite charge is systematically studied in terms of the potential of mean force (PMF) along their center-of-mass reaction coordinate via coarse-grained, implicit-solvent, explicit-salt computer simulations. The focus is set on the onset and the intermediate transient stages of complexation. At conditions above the counterion-condensation threshold, the PE association process exhibits a distinct sliding-rod-like behavior where the polymer chains approach each other by first stretching out at a critical distance close to their contour length, then "shaking hand" and sliding along each other in a parallel fashion, before eventually folding into a neutral complex. The essential part of the PMF for highly charged PEs can be very well described by a simple theory based on sliding charged "Debye-Hückel" rods with renormalized charges in addition to an explicit entropy contribution owing to the release of condensed counterions. Interestingly, at the onset of complex formation, the mean force between the PE chains is found to be discontinuous, reflecting a bimodal structural behavior that arises from the coexistence of interconnected-rod and isolated-coil states. These two microstates of the PE complex are balanced by subtle counterion release effects and separated by a free-energy barrier due to unfavorable stretching entropy.

EMT: 2016

The significant parallels between cell plasticity during embryonic development and carcinoma progression have helped us understand the importance of the epithelial-mesenchymal transition (EMT) in human disease. Our expanding knowledge of EMT has led to a clarification of the EMT program as a set of multiple and dynamic transitional states between the epithelial and mesenchymal phenotypes, as opposed to a process involving a single binary decision. EMT and its intermediate states have recently been identified as crucial drivers of organ fibrosis and tumor progression, although there is some need for caution when interpreting its contribution to metastatic colonization. Here, we discuss the current state-of-the-art and latest findings regarding the concept of cellular plasticity and heterogeneity in EMT. We raise some of the questions pending and identify the challenges faced in this fast-moving field.

"Brill Transition" Shown by Green Material Poly(octamethylene carbonate)

Poly(octamethylene carbonate) (POMC), as the eighth member of the newly developed biodegradable aliphatic polycarbonate family, demonstrates a reversible crystal-crystal transition, which is highly similar to Brill transition extensively studied in the nylon family. With the dipole-dipole interaction in POMC much weaker than the hydrogen bonding, POMC exhibits its "Brill transition" temperature at around 42 °C, much lower than nylons. The two crystalline structures of POMC at below and above the transition temperature can be identified. The transition of POMC is largely associated with the reversible conformation change of methylene sequences from trans-dominated at low temperatures to trans/gauche coexistence at high temperatures.

An investigation into the role of polymeric carriers on crystal growth within amorphous solid dispersion systems

Using phase diagrams derived from Flory-Huggins theory, we defined the thermodynamic state of amorphous felodipine within three different polymeric carriers. Variation in the solubility and miscibility of felodipine within different polymeric materials (using F-H theory) has been identified and used to select the most suitable polymeric carriers for the production of amorphous drug-polymer solid dispersions. With this information, amorphous felodipine solid dispersions were manufactured using three different polymeric materials (HPMCAS-HF, Soluplus, and PVPK15) at predefined drug loadings, and the crystal growth rates of felodipine from these solid dispersions were investigated. Crystallization of amorphous felodipine was studied using Raman spectral imaging and polarized light microscopy. Using this data, we examined the correlation among several characteristics of solid dispersions to the crystal growth rate of felodipine. An exponential relationship was found to exist between drug loading and crystal growth rate. Moreover, crystal growth within all selected amorphous drug-polymer solid dispersion systems were viscosity dependent (η(-ξ)). The exponent, ξ, was estimated to be 1.36 at a temperature of 80 °C. Values of ξ exceeding 1 may indicate strong viscosity dependent crystal growth in the amorphous drug-polymer solid dispersion systems. We argue that the elevated exponent value (ξ > 1) is a result of drug-polymer mixing which leads to a less fragile amorphous drug-polymer solid dispersion system. All systems investigated displayed an upper critical solution temperature, and the solid-liquid boundary was always higher than the spinodal decomposition curve. Furthermore, for PVP-FD amorphous dispersions at drug loadings exceeding 0.6 volume ratio, the mechanism of phase separation within the metastable zone was found to be driven by nucleation and growth rather than liquid-liquid separation.

Unmasking the roles of N- and C-terminal flanking sequences from exon 1 of huntingtin as modulators of polyglutamine aggregation

Huntington disease is caused by mutational expansion of the CAG trinucleotide within exon 1 of the huntingtin (Htt) gene. Exon 1 spanning N-terminal fragments (NTFs) of the Htt protein result from aberrant splicing of transcripts of mutant Htt. NTFs typically encompass a polyglutamine tract flanked by an N-terminal 17-residue amphipathic stretch (N17) and a C-terminal 38-residue proline-rich stretch (C38). We present results from in vitro biophysical studies that quantify the driving forces for and mechanisms of polyglutamine aggregation as modulated by N17 and C38. Although N17 is highly soluble by itself, it lowers the saturation concentration of soluble NTFs and increases the driving force, vis-à-vis homopolymeric polyglutamine, for forming insoluble aggregates. Kinetically, N17 accelerates fibril formation and destabilizes nonfibrillar intermediates. C38 is also highly soluble by itself, and it lends its high intrinsic solubility to lower the driving force for forming insoluble aggregates by increasing the saturation concentration of soluble NTFs. In NTFs with both modules, N17 and C38 act synergistically to destabilize nonfibrillar intermediates (N17 effect) and lower the driving force for forming insoluble aggregates (C38 effect). Morphological studies show that N17 and C38 promote the formation of ordered fibrils by NTFs. Homopolymeric polyglutamine forms a mixture of amorphous aggregates and fibrils, and its aggregation mechanisms involve early formation of heterogeneous distributions of nonfibrillar species. We propose that N17 and C38 act as gatekeepers that control the intrinsic heterogeneities of polyglutamine aggregation. This provides a biophysical explanation for the modulation of in vivo NTF toxicities by N17 and C38.

Role of inter-diffusion on the crystallization dynamics in polyethylene/poly(ethylene-alt-propylene) blend system

Influence of inter-diffusion on the crystallization dynamics in polyethylene/poly(ethylene-alt-propylene) (PE/PEP) blends was studied by a combination of optical microscopy (OM), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR). OM measurements showed that the crystal nuclei may be first generated at phase separated interface where concentration fluctuation is greatly enhanced in the temperature quench process. After the formation of crystal nuclei, the only crystallizable components, PE chains, are necessary to reach the nucleation site via inter-diffusion to continue the secondary nucleation and growth process. DSC showed that there is only one 96 °C crystallization peak when PE (M(W) = 52 kg/mol) is blended with low molecular weight PEP (M(W) = 32 kg/mol); while there are two crystallization peaks, which are 96 °C and 72 °C, respectively, when the same PE is blended with high molecular weight PEP (M(W) = 110 kg/mol). The origin of the 72 °C crystallization peak was studied by DSC isothermal crystallization and time resolved FTIR. It was proved that the 72 °C crystallization peak is resulted from the smaller inter-diffusion coefficient in the PEP-rich region. Both slow mode theory and fast mode/constraint release models of inter-diffusion can be used to explain the smaller inter-diffusion coefficient in the PEP-rich region, which dynamically results in the disappearance of the 72 °C crystallization peak after isothermal crystallization at 90 °C for 60 min. Therefore, inter-diffusion plays an important role on crystallization dynamics in multi-component and multi-phase polymeric blends.

Control of the fold surface conformation of the lamellae of an oligomer

Small-angle X-ray scattering revealed that a semirigid oligomer of bisphenol-A-co-ether-octane with a monodisperse chain length is capable of forming ciliated-folded, once-folded, ciliated-extended and fully extended lamellar structures. Isothermal crystallization studies suggested a sequence of structures with increasing crystallization temperature, from a ciliated-folded to a once-folded form and then to a ciliated-extended form as the degree of supercooling is decreased. The crystal surface thus changed from octane cilia to bisphenol A segments and then back to octane cilia as the lamellar structure changed. The results of time-of-flight secondary ion mass spectrometry analyses strongly supported the fold structural models.

Interplay between two phase transitions: crystallization and liquid-liquid phase separation in a polyolefin blend

The interplay between liquid-liquid phase separation (LLPS) and crystallization at several compositions in statistical copolymer blends of poly(ethyleneco-hexene) and poly(ethylene-cobutene) has been examined by optical microscopy (OM), atomic force microscopy (AFM), and differential scanning calorimetry (DSC). The phase contrast optical microscopy shows interconnected bicontinuous structures for deeply quenched LLPS, characteristic of spinodal decomposition. After a second quench to a temperature below the melting point, an overwhelming change in crystallization kinetics has been clearly observed, which is caused by the increase of the nucleation rate assisted by concentration fluctuations due to the spontaneous spinodal LLPS. We propose a new mechanism of "fluctuation assisted nucleation" in the crystallization process for such interactive process in a blend system. The experimental results from OM, AFM, and DSC measurements at various conditions are all consistent with the fluctuation assisted nucleation model.

Self-Assembly of Chemically Linked Rod−Disc Mesogenic Liquid Crystals

A series of new molecular discs (RDn, here n is the number of carbon atoms between the rod and disc mesogens) was synthesized via the chemical attachment of six cyanobiphenyl calamitic (rod) mesogens (R) linked to the triphenyl discotic (disc) mesogen (D) with a series of six alkyl chain linkages (n = 6-12). In this study, phase structures, transitions, and liquid crystalline (LC) behavior of the RD12 compound with 12 carbon atoms in each alkyl chain linkage between the rod and disc mesogens were investigated. Differential scanning calorimetry, polarized light microscopy, wide-angle X-ray diffraction (WAXD), and selected area electron diffraction (SAED) allowed us to identify three ordered phases below the isotropization temperature: nematic (N) LC and K1 and K2 crystalline phases. On the basis of the structural results obtained via 2D WAXD experiments on oriented samples and SAED experiments on single crystals, the K1 crystalline unit cell was determined to be triclinic with the dimensions of a = 1.36 nm, b = 1.45 nm, c = 2.11 nm, alpha = 85 degrees, beta = 100 degrees, and gamma = 50 degrees. The K2 phase was metastable with respect to the K1 phase. It also possessed a triclinic unit cell with a = 1.40 nm, b = 1.51 nm, c = 1.92 nm, alpha = 87 degrees, beta = 117 degrees, and gamma = 62 degrees. Molecular packing models for the crystalline phases were proposed on the basis of the diffraction results. In the whole range of ordered structures, it was found that RD12 molecular discs are intercalated. Both triphenyl discotic mesogens and cyanobiphenyl calamitic mesogens are completely interdigitated.