Peculiarities of Emulsions Stabilized by Stimuli-Responsive Interpenetrating Polymeric Network Microgels.

Emulsions have become a crucial product form in various industries in modern times. Expanding the class of substances used to stabilize emulsions can improve their stability or introduce new properties. Particularly, the use of stimuli-responsive microgels makes it possible to create "smart" emulsions whose stability can be controlled by changing any of the specified stimuli. Thus, finding new ways to stabilize emulsions may broaden their application. In this work, for the first time, we applied microgels based on interpenetrating polymeric networks (IPNs) of poly(N-isopropylacrylamide) (PNIPAM) and poly(acrylic acid) (PAA) as stabilizing agents for "oil-in-water" emulsions. We have demonstrated that emulsions stabilized by such soft particles can remain colloidally stable for an extended period, even after being heated up to 40 °C, which is above the lower critical solution temperature (LCST) of PNIPAM. On the contrary, the emulsions stabilized by PNIPAM homopolymer microgels were broken upon heating. To understand the stabilization mechanism of the emulsions, mesoscopic computer simulations were performed to study the IPN microgels at the liquid-liquid interface. The simulations demonstrated that when the first subnetwork (PNIPAM) collapses, the particle adopts a flattened core-shell morphology with a highly swollen PAA-rich shell and a collapsed PNIPAM-rich core. Unlike its PNIPAM homopolymer counterpart, the IPN microgel maintains its three-dimensional shape, which provides stability to the microgel-based emulsions over a wide range of temperatures. Our combined findings could be useful in developing new approaches to emulsions' storage, biphasic catalysis, and lubrication of mechanisms in various operating and climatic conditions.

Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study.

In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide-nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability.

Antiseptic Materials on the Base of Polymer Interpenetrating Networks Microgels and Benzalkonium Chloride.

Polymer microgels, including those based on interpenetrating networks (IPNs), are currently vastly studied, and their practical applications are a matter of thriving research. In this work, we show the perspective for the use of polyelectrolyte IPN microgels either as scavengers or carriers of antiseptic substances. Here, we report that poly-N-isopropylacrylamide/polyacrylic acid IPN microgels can efficiently absorb the common bactericidal and virucidal compound benzalkonium chloride. The particles can form a stable aqueous colloidal suspension or be used as building blocks for soft free-standing films. Both materials showed antiseptic efficacy on the examples of Bacillus subtilis and S. aureus, which was approximately equal to the commercial antibiotic. Such polymer biocides can be used as liquid disinfectants, stable surface coatings, or parts of biomedical devices and can enhance the versatility of the possible practical applications of polymer microgels.

Behavior of PNIPAM Microgels in Different Organic Solvents.

In this research, we studied, in detail, the behavior of common PNIPAM microgels, obtained through surfactant-free precipitation polymerization, in a number of organic solvents. We showed that many of the selected solvents serve as good solvents for the PNIPAM microgels and that the size and architecture of the microgels depend on the solvent chosen. Expanding the range of solvents used for PNIPAM microgel incubation greatly enhances the possible routes for microparticle functionalization and modification, as well as the encapsulation of water-insoluble species. In this demonstration, we successfully encapsulated water-insoluble Sudan III dye in PNIPAM microgels and prepared the aqueous dispersions of such composite-colored microparticles.

Swift Janitor: Efficient Absorption of a Minor Component from the Mixtures of Immiscible Liquids by Thermoresponsive Macroscopic and Microscopic Hydrogels.

Polymer hydrogels are known to be efficient absorbents of various aqueous solutions. Along with the hydrophilicity of the polymer network, the presence of specific functional groups is required for the absorption of respective solutes. Alternatively, a selective uptake can be realized without any specific attraction of solutes to the network, which is shown in this paper. By combining experimental and simulation approaches, we demonstrated that thermoresponsive poly(N-isopropylacrylamide) gels and microgels in compositionally strongly asymmetric water/1-octanol mixtures selectively uptake the minor (1-octanol) component. Initially swollen in water, the gels substitute water by the organic solvent upon the addition of its small fraction into aqueous solution. In turn, for microgels, it was shown that the single particles could absorb the amount of the organic liquid more than two times higher than their mass while preserving the colloidal stability. At the same time, the accumulation of 1-octanol in the networks "switches off" the temperature response. The mesoscopic computer simulations revealed a physical reason and molecular picture of the phenomenon. Absorption of the minor component by the gels is caused by the decrease in water/1-octanol interfacial tension due to the formation of the dense polymer layer at the interface. The simulations allowed tracking the evolution of the size and the internal structure of the single microgels with changing 1-octanol concentration.

Histone dynamics mediate DNA unwrapping and sliding in nucleosomes.

Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ∼147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucleosomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.

Linking chromatin composition and structural dynamics at the nucleosome level.

Nucleosomes are fundamental units of chromatin compaction, which organize ∼200 DNA base pairs using an octamer of histone proteins. Their ubiquitous presence in the cell nucleus since the first eukaryotes compelled the chromatin machinery to coevolve and learn how to exploit various modes of nucleosome dynamics and sense differences in nucleosome composition. Alterations to histone or DNA sequences, post-translational modifications (PTM) of histones, recruitment of chromatin proteins modulate nucleosome dyn amics and provide epigenetic regulation to the DNA processing pathways (transcription, replication, repair, etc.). Our understanding of this complex interplay between nucleosome composition, dynamics and functioning is constantly evolving through new insights and discoveries. In this review, we highlight recent contributions to the field while attempting to organize them in a unified framework.

Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.

Hydroxyl-radical footprinting (HRF) is a powerful method for probing structures of nucleic acid-protein complexes with single-nucleotide resolution in solution. To tap the full quantitative potential of HRF, we describe a protocol, hydroxyl-radical footprinting interpretation for DNA (HYDROID), to quantify HRF data and integrate them with atomistic structural models. The stages of the HYDROID protocol are extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at each nucleotide and theoretical estimation of the DNA cleavage frequency from atomistic structural models, followed by comparison of experimental and theoretical results. Example scripts for each step of HRF data analysis and interpretation are provided for several nucleosome systems; they can be easily adapted to analyze user data. As input, HYDROID requires polyacrylamide gel electrophoresis (PAGE) images of HRF products and optionally can use a molecular model of the DNA-protein complex. The HYDROID protocol can be used to quantify HRF over DNA regions of up to 100 nucleotides per gel image. In addition, it can be applied to the analysis of RNA-protein complexes and free RNA or DNA molecules in solution. Compared with other methods reported to date, HYDROID is unique in its ability to simultaneously integrate HRF data with the analysis of atomistic structural models. HYDROID is freely available. The complete protocol takes ~3 h. Users should be familiar with the command-line interface, the Python scripting language and Protein Data Bank (PDB) file formats. A graphical user interface (GUI) with basic functionality (HYDROID_GUI) is also available.

Investigation of physical-chemical properties of agarose hydrogels with embedded emulsions.

Composite agarose hydrogels with embedded tetradecane emulsions stabilized by cetylpyridinium chloride were studied. The absorption efficiency of 4-nitrophenyl ethers of carbonic acids by the composite agarose gels increases with the length of the hydrocarbon tail of the ester. The diffusion rate of amphiphilic substances in the composite gels was demonstrated to be much less that than in the standard agarose gels. The reaction kinetics between the esters and dodecylmercaptan dissolved in tetradecane droplets of composite hydrogel was studied. In the region of physiological pH, the reactivity of SH groups embedded in the composite agarose gel in the reaction with the esters is significantly higher than that in a homogeneous solution. Hydrogels with embedded emulsion droplets are of considerable practical importance as drug delivery systems, microreactors, and absorbers. Composite gels filled with emulsions incorporating lipophilic mercaptanes are effective absorbers of heavy metal ions.

Intelligent gels and cryogels with entrapped emulsions.

Smart thermoresponsive gels and cryogels with incorporated emulsions have been synthesized and studied. The gels were obtained by three-dimensional copolymerization of N-isopropylacrylamide and N,N'-methylene-bis-acrylamide or N,N'-bis(acryloyl)cystamine in the presence of dispersion of tetradecane stabilized with sodium dodecylsulfate. Polymerization was performed at room temperature and below the water crystallization temperature. Both composite gels and cryogels were capable of heat-induced collapse. The extent of the collapse of the composite gel prepared at room temperature was much smaller and without squeezing of the lipophilic phase out of the shrunk composite gel. In contrast, shrinking of the composite cryogel was accompanied by release of tetradecane emulsion.