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.

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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.

Summary: “Swiss‐cheese” polyelectrolyte gels, i.e., gels containing isolated voids filled with water were synthesized and studied. The gels were obtained by three‐dimensional copolymerization of neutral and charged monomers in the presence of oil/water emulsion stabilized by ionic surfactant. After removal of the surfactant and droplets of oil from the gel, the latter contains voids surrounded with charged swollen polymer network. Experiments were performed with slightly cross‐linked gels of copolymers of sodium‐2‐acrylamide‐2‐methyl‐1‐propanesulfonate with acrylamide. The gel containing voids absorbs much more anionic dyes than the control gel with the same chemical composition of the network obtained in homogeneous solution. This effect is due to strongly inhomogeneous distribution of the low molecular weight anions between the voids and the anionic matrix of the gel. The study of diffusion of the dyes in the gels with and without voids and of the kinetics of their swelling and collapse shows that the voids in the gel are isolated.

Thermo-responsive gels and cryogels with embedded microdroplets of Vaseline, olive, peanut, and linseed oils and their mixtures with hydrophobic dye Sudan 3 have been synthesized and studied. These composite gel matrices were obtained by the threedimensional copolymerization of N-isopropylacrylamide and N, N'-bis(acryloyl)cystamine in the presence of oil emulsions stabilized with sodium dodecylsulfate or Span 80. Polymerization was performed at room temperature for conventional gels and at À15 C for cryogels. It was shown that all synthesized systems exhibit heat-induced collapse at temperatures higher then 34 C. For conventional gels prepared at room temperature shrinking lasts within 20 to 80 min in accordance with gel composition. No squeezing of oil droplets was observed. In the case of cryogels, shrinking was accompanied by release of oils and response time was significantly shorter, about tens of seconds. Collapse character and release of lipophilic phase did not depend on the chemical nature of oils, dissolved compounds, and surfactant used for emulsion stabilization.

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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.

Hydroxyl-radical footprinting (HRF) is a powerful method to probe 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 it with atomistic structural models. The stages of the HYDROID protocol include extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at every nucleotide, and theoretical estimation of the DNA cleavage frequency from atomistic structural models followed by comparison of experimental and theoretical results. Example scripts for every 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 images of HRF products and optionally may 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 to other methods, HYDROID is unique in its ability to simultaneously integrate HRF data with the analysis of atomistic structural models. HYDROID is freely available at https://github.com/ncbi/HYDROID. The complete protocol takes approximately ~ 3 hours. Users should be familiar with the command line interface, the Python scripting language and PDB file formats. A graphical user interface with basic functionality (HYDROID_GUI) is also available.