Long-Range Surface-Directed Polymerization-Induced Phase Separation: A Computational Study

The presence of a surface preferably attracting one component of a polymer mixture by the long-range van der Waals surface potential while the mixture undergoes phase separation by spinodal decomposition is called long-range surface-directed spinodal decomposition (SDSD). The morphology achieved under SDSD is an enrichment layer(s) close to the wall surface and a droplet-type structure in the bulk. In the current study of the long-range surface-directed polymerization-induced phase separation, the surface-directed spinodal decomposition of a monomer–solvent mixture undergoing self-condensation polymerization was theoretically simulated. The nonlinear Cahn–Hilliard and Flory–Huggins free energy theories were applied to investigate the phase separation phenomenon. The long-range surface potential led to the formation of a wetting layer on the surface. The thickness of the wetting layer was found proportional to time t*1/5 and surface potential parameter h11/5. A larger diffusion coefficient led to the formation of smaller droplets in the bulk and a thinner depletion layer, while it did not affect the thickness of the enrichment layer close to the wall. A temperature gradient imposed in the same direction of long-range surface potential led to the formation of a stripe morphology near the wall, while imposing it in the opposite direction of surface potential led to the formation of large particles at the high-temperature side, the opposite side of the interacting wall.

Optimal synthesis of polyelectrolyte nanogels by electrostatic assembly directed polymerization for dye loading and release

We fully address the process parameters of EADP regarding optimal and controlled preparation of PE nanogels. The response behaviour of the nanogels, and their take-up and release of charged dye molecule upon varying pH and salt are also investigated.

Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization

The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3′-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.

Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization

ABSTRACTThe prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3’-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer ten-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.

Critical events of the origins of life

We discuss some critical events of the origins of life using a mathematical model and simulation studies. We find that for a replicating population of RNA molecules participating in template-directed polymerization, the hitting and establishment of a high-fidelity replicator depends critically on the polymerase fitness and sequence specificity landscapes and on genome dimension. Probability of hitting is dominated by polymerase landscape curvature, whereas hitting time is dominated by genome dimension. Surface chemistries, compartmentalization, and decay increase hitting times. These results suggest replication to be the first ‘privileged function’ marking the start of Darwinian evolution, possibly in conjunction with clay minerals or preceded by metabolism, whose dynamics evolved mostly during the final period of the search.

Capping protein is dispensable for polarized actin network growth and actin-based motility

Heterodimeric capping protein (CP) binds the rapidly growing barbed ends of actin filaments and prevents the addition (or loss) of subunits. Capping activity is generally considered to be essential for actin-based motility induced by Arp2/3 complex nucleation. By stopping barbed end growth, CP favors nucleation of daughter filaments at the functionalized surface where the Arp2/3 complex is activated, thus creating polarized network growth, which is necessary for movement. However, here using an in vitro assay where Arp2/3 complex-based actin polymerization is induced on bead surfaces in the absence of CP, we produce robust polarized actin growth and motility. This is achieved either by adding the actin polymerase Ena/VASP or by boosting Arp2/3 complex activity at the surface. Another actin polymerase, the formin FMNL2, cannot substitute for CP, showing that polymerase activity alone is not enough to override the need for CP. Interfering with the polymerase activity of Ena/VASP, its surface recruitment or its bundling activity all reduce Ena/VASP's ability to maintain polarized network growth in the absence of CP. Taken together, our findings show that CP is dispensable for polarized actin growth and motility in situations where surface-directed polymerization is favored by whatever means over the growth of barbed ends in the network.

Gastrointestinal synthetic epithelial linings

Epithelial tissues line the organs of the body, providing an initial protective barrier as well as a surface for nutrient and drug absorption. Here, we identified enzymatic components present in the gastrointestinal epithelium that can serve as selective means for tissue-directed polymerization. We focused on the small intestine, given its role in drug and nutrient absorption and identified catalase as an essential enzyme with the potential to catalyze polymerization and growth of synthetic biomaterial layers. We demonstrated that the polymerization of dopamine by catalase yields strong tissue adhesion. We characterized the mechanism and specificity of the polymerization in segments of the gastrointestinal tracts of pigs and humans ex vivo. Moreover, we demonstrated proof of concept for application of these gastrointestinal synthetic epithelial linings for drug delivery, enzymatic immobilization for digestive supplementation, and nutritional modulation through transient barrier formation in pigs. This catalase-based approach to in situ biomaterial generation may have broad indications for gastrointestinal applications.