Liquid crystals of self-assembled DNA bottlebrushes

Brownian dynamics simulations of bottlebrush polymers in dilute solution under simple shear and uniaxial extensional flows

We study the dynamics of bottlebrush polymer molecules in dilute solutions subjected to shear and uniaxial extensional flows using Brownian dynamics simulations with hydrodynamic interaction (HI). Bottlebrush polymers are modeled using a coarse-grained representation, consisting of a set of beads interacting pairwise via a purely repulsive potential and connected by finitely extensible nonlinear springs. We present the results for molecular stretching, stress, and solution viscosity during the startup of flow as well as under steady state as a function of side chain length while keeping the backbone length fixed. In extensional flow, the backbone fractional extension and the first normal stress difference decrease with an increase in side chain length at a fixed Weissenberg number (Wi). Using simulation results both in the presence of and in the absence of HI, we show that this is primarily a consequence of steric interaction resulting from the dense grafting of side chains. In shear flow, we observe a shear-thinning behavior in all cases, although it becomes less pronounced with increasing side chain length. Furthermore, nonmonotonicity in the backbone fractional extension is observed under shear, particularly at high Wi. We contextualize our simulation results for bottlebrush polymers with respect to existing studies in the literature for linear polymers and show that the unique dynamical features characterizing bottlebrush polymers arise on account of their additional molecular thickness due to the presence of densely grafted side chains.

Self-Assembly of Elastin-like Polypeptide Brushes on Silica Surfaces and Nanoparticles

Control over the placement and activity of biomolecules on solid surfaces is a key challenge in bionanotechnology. While covalent approaches excel in performance, physical attachment approaches excel in ease of processing, which is equally important in many applications. We show how the precision of recombinant protein engineering can be harnessed to design and produce protein-based diblock polymers with a silica-binding and highly hydrophilic elastin-like domain that self-assembles on silica surfaces and nanoparticles to form stable polypeptide brushes that can be used as a scaffold for later biofunctionalization. From atomic force microscopy-based single-molecule force spectroscopy, we find that individual silica-binding peptides have high unbinding rates. Nevertheless, from quartz crystal microbalance measurements, we find that the self-assembled polypeptide brushes cannot easily be rinsed off. From atomic force microscopy imaging and bulk dynamic light scattering, we find that the binding to silica induces fibrillar self-assembly of the peptides. Hence, we conclude that the unexpected stability of these self-assembled polypeptide brushes is at least in part due to peptide-peptide interactions of the silica-binding blocks at the silica surface.

Novel Trends in Lyotropic Liquid Crystals

We introduce and shortly summarize a variety of more recent aspects of lyotropic liquid crystals (LLCs), which have drawn the attention of the liquid crystal and soft matter community and have recently led to an increasing number of groups studying this fascinating class of materials, alongside their normal activities in thermotopic LCs. The diversity of topics ranges from amphiphilic to inorganic liquid crystals, clays and biological liquid crystals, such as viruses, cellulose or DNA, to strongly anisotropic materials such as nanotubes, nanowires or graphene oxide dispersed in isotropic solvents. We conclude our admittedly somewhat subjective overview with materials exhibiting some fascinating properties, such as chromonics, ferroelectric lyotropics and active liquid crystals and living lyotropics, before we point out some possible and emerging applications of a class of materials that has long been standing in the shadow of the well-known applications of thermotropic liquid crystals, namely displays and electro-optic devices.

Theoretical prediction of an isotropic to nematic phase transition in bottlebrush homopolymer melts

Bottlebrushes are an emerging class of polymers, characterized by a high density of side chains grafted to a linear backbone that offer promise in creating materials with unusual combinations of mechanical, chemical, and optoelectronic properties. Understanding the role of molecular architecture in the organization and assembly of bottlebrushes is of fundamental importance in polymer physics, but also enabling in applications. Here, we apply field-theoretic simulations to study the effect of grafting density, backbone length, and side-chain (SC) length on the structure and thermodynamics of bottlebrush homopolymer melts. Our results provide evidence for a phase transition from an isotropic to a nematic state with increasing grafting density and side-chain length. Variation in the backbone length is also observed to influence the location of the transition, primarily for short polymers just above the star to bottlebrush transition.

Production of protein-based polymers in Pichia pastoris

Materials science and genetic engineering have joined forces over the last three decades in the development of so-called protein-based polymers. These are proteins, typically with repetitive amino acid sequences, that have such physical properties that they can be used as functional materials. Well-known natural examples are collagen, silk, and elastin, but also artificial sequences have been devised. These proteins can be produced in a suitable host via recombinant DNA technology, and it is this inherent control over monomer sequence and molecular size that renders this class of polymers of particular interest to the fields of nanomaterials and biomedical research. Traditionally, Escherichia coli has been the main workhorse for the production of these polymers, but the methylotrophic yeast Pichia pastoris is finding increased use in view of the often high yields and potential bioprocessing benefits. We here provide an overview of protein-based polymers produced in P. pastoris. We summarize their physicochemical properties, briefly note possible applications, and detail their biosynthesis. Some challenges that may be faced when using P. pastoris for polymer production are identified: (i) low yields and poor process control in shake flask cultures; i.e., the need for bioreactors, (ii) proteolytic degradation, and (iii) self-assembly in vivo. Strategies to overcome these challenges are discussed, which we anticipate will be of interest also to readers involved in protein expression in P. pastoris in general.

Dilute solution structure of bottlebrush polymers

Bottlebrush polymers are a class of macromolecules that have recently found use in a wide variety of materials, ranging from lubricating brushes and nanostructured coatings to elastomeric gels that exhibit structural colors. These polymers are characterized by dense branches extending from a central backbone and thus have properties distinct from linear polymers. It remains a challenge to specifically understand conformational properties of these molecules, due to the wide range of architectural parameters that can be present in a system, and thus there is a need to accurately characterize and model these molecules. In this paper, we use a combination of viscometry, light scattering, and computer simulations to gain insight into the conformational properties of dilute solution bottlebrush polymers. We focus on a series of model bottlebrushes consisting of a poly(norbornene) (PNB) backbone with poly(lactic acid) (PLA) side chains. We demonstrate that intrinsic viscosity and hydrodynamic radius are experimental observations sensitive to molecular architecture, exhibiting distinct differences with different choices of branches and backbone lengths. Informed by the atomistic structure of this PNB-PLA system, we rationalize a coarse-grained simulation model that we evaluate using a combination of Brownian dynamics and Monte Carlo simulations. We show that this exhibits quantitative matching to experimental results, enabling us to characterize the overall shape of the bottlebrush via a number of metrics that can be extended to more general bottlebrush architectures.

Electrostatic stiffening and induced persistence length for coassembled molecular bottlebrushes

A self-consistent field analysis for tunable contributions to the persistence length of isolated semiflexible polymer chains including electrostatically driven coassembled deoxyribonucleic acid (DNA) bottlebrushes is presented. When a chain is charged, i.e., for polyelectrolytes, there is, in addition to an intrinsic rigidity, an electrostatic stiffening effect, because the electric double layer resists bending. For molecular bottlebrushes, there is an induced contribution due to the grafts. We explore cases beyond the classical phantom main-chain approximation and elaborate molecularly more realistic models where the backbone has a finite volume, which is necessary for treating coassembled bottlebrushes. We find that the way in which the linear charge density or the grafting density is regulated is important. Typically, the stiffening effect is reduced when there is freedom for these quantities to adapt to the curvature stresses. Electrostatically driven coassembled bottlebrushes, however, are relatively stiff because the chains have a low tendency to escape from the compressed regions and the electrostatic binding force is largest in the convex part. For coassembled bottlebrushes, the induced persistence length is a nonmonotonic function of the polymer concentration: For low polymer concentrations, the stiffening grows quadratically with coverage; for semidilute polymer concentrations, the brush chains retract and regain their Gaussian size. When doing so, they lose their induced persistence length contribution. Our results correlate well with observed physical characteristics of electrostatically driven coassembled DNA-bioengineered protein-polymer bottlebrushes.

Force and Scale Dependence of the Elasticity of Self-Assembled DNA Bottle Brushes

As a model system to study the elasticity of bottle-brush polymers, we here introduce self-assembled DNA bottle brushes, consisting of a DNA main chain that can be very long and still of precisely defined length, and precisely monodisperse polypeptide side chains that are physically bound to the DNA main chains. Polypeptide side chains have a diblock architecture, where one block is a small archaeal nucleoid protein Sso7d that strongly binds to DNA. The other block is a net neutral, hydrophilic random coil polypeptide with a length of exactly 798 amino acids. Light scattering shows that for saturated brushes the grafting density is one side chain per 5.6 nm of DNA main chain. According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle brushes using AFM, we find that the effective persistence of the saturated DNA bottle brushes is P_eff = 95 nm, but from force–extension curves of single DNA bottle brushes measured using optical tweezers we find P_eff = 15 nm. The latter is equal to the value expected for DNA coated by the Sso7d binding block alone. The apparent discrepancy between the two measurements is rationalized in terms of the scale dependence of the bottle-brush elasticity using theory previously developed to analyze the scale-dependent electrostatic stiffening of DNA at low ionic strengths.

Reversible hierarchical structure induced by solvation and temperature modulation in an ionic liquid-based random bottlebrush copolymer

Discoidal bottlebrush poly(ionic liquid)s are reversibly stacked into 1-D rod like assembles by temperature changes.

Phosphorylation-Induced Mechanical Regulation of Intrinsically Disordered Neurofilament Proteins

The biological function of protein assemblies has been conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it has been found that some assemblies contain long flexible regions that adopt multiple structural conformations. These include neurofilament proteins that constitute the stress-responsive supportive network of neurons. Herein, we show that the macroscopic properties of neurofilament networks are tuned by enzymatic regulation of the charge found on the flexible protein regions. The results reveal an enzymatic (phosphorylation) regulation of macroscopic properties such as orientation, stress response, and expansion in flexible protein assemblies. Using a model that explains the attractive electrostatic interactions induced by enzymatically added charges, we demonstrate that phosphorylation regulation is far richer and versatile than previously considered.

Structural Effects of Single Mutations in a Filamentous Viral Capsid Across Multiple Length Scales

Filamentous bacteriophage (phage) are single-stranded DNA viruses that infect bacteria. Single-site mutants of fd phage have been studied by magic-angle spinning nuclear magnetic resonance and by small-angle X-ray scattering. Detailed analysis has been performed that provides insight into structural variations on three length scales. The results, analyzed in conjunction with existing literature data, suggest that a single charge mutation on the capsid surface affects direct interviral interactions but not the structure of individual particles or the macroscale organization. On the other hand, a single hydrophobic mutation located at the hydrophobic interface that stabilizes capsid assembly alters the atomic structure of the phage, mainly affecting intersubunit interactions, affects its macroscale organization, that is, the pitch of the cholesteric liquid crystal formed by the particles, but skips the nanoscale hence does not affect direct interparticle interactions. An X-ray scattering under osmotic pressure assay provides the effective linear charge density of the phage and we obtain values of 0.6 Å^-1 and 0.4 Å^-1 for fd and M13 phage, respectively. These values agree with a simple consideration of a single cylinder with protein and DNA charges spread according to the most recent atomic-resolution models of the phage.

Domed Silica Microcylinders Coated with Oleophilic Polypeptides and Their Behavior in Lyotropic Cholesteric Liquid Crystals of the Same Polypeptide

Liquid crystals can organize dispersed particles into useful and exotic structures. In the case of lyotropic cholesteric polypeptide liquid crystals, polypeptide-coated particles are appealing because the surface chemistry matches that of the polymeric mesogen, which permits a tighter focus on factors such as extended particle shape. The colloidal particles developed here consist of a magnetic and fluorescent cylindrically symmetric silica core with one rounded, almost hemispherical end. Functionalized with helical poly(γ-stearyl-l-glutamate) (PSLG), the particles were dispersed at different concentrations in cholesteric liquid crystals (ChLC) of the same polymer in tetrahydrofuran (THF). Defects introduced by the particles to the director field of the bulk PSLG/THF host led to a variety of phases. In fresh mixtures, the cholesteric mesophase of the PSLG matrix was distorted, as reflected in the absence of the characteristic fingerprint pattern. Over time, the fingerprint pattern returned, more quickly when the concentration of the PSLG-coated particles was low. At low particle concentration the particles were "guided" by the PSLG liquid crystal to organize into patterns similar to that of the re-formed bulk chiral nematic phase. When their concentration increased, the well-dispersed PSLG-coated particles seemed to map onto the distortions in the bulk host's local director field. The particles located near the glass vial-ChLC interfaces were stacked lengthwise into architectures with apparent two-dimensional hexagonal symmetry. The size of these "crystalline" structures increased with particle concentration. They displayed remarkable stability toward an external magnetic field; hydrophobic interactions between the PSLG polymers in the shell and those in the bulk LC matrix may be responsible. The results show that bio-inspired LCs can assemble suitable colloidal particles into soft crystalline structures.

Loss of bottlebrush stiffness due to free polymers

A recently introduced DNA-bottlebrush system, which is formed by the co-assembly of DNA with a genetically engineered cationic polymer-like protein, is subjected to osmotic stress conditions. We measured the inter-DNA distances by X-ray scattering. Our co-assembled DNA-bottlebrush system is one of the few bottlebrushes known to date that shows liquid crystalline behaviour. The alignment of the DNA bottlebrushes was expected to increase with imposed pressure, but interestingly this did not always happen. Molecularly detailed self-consistent field calculations targeted to complement the experiments, focused on the role of molecular crowding on the induced persistence length lp due to the side chains and the cross-sectional width D of the molecular bottlebrushes. Both the thickness as well as the backbone persistence length drop with increasing protein-polymer bulk concentrations and dramatic effects are found above the overlap threshold. The flexibilisation is more significant and therefore the bottlebrush aspect ratio, lp/D, decreases with protein-polymer concentration. This loss in aspect ratio is yet another argument why molecular bottlebrushes rarely order in anisotropic phases and may explain why bottlebrushes are excellent lubricants.