High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes.

Each nucleosome contains four types of histone proteins, each with a histone tail. These tails are essential for the epigenetic regulation of gene expression through post-translational modifications (PTMs). However, their influence on nucleosome dynamics at the single-molecule level remains undetermined. Here, we employed high-speed atomic force microscopy to visualize nucleosome dynamics in the absence of the N-terminal tail of each histone or all of the N-terminal tails. Loss of all tails stripped 6.7 base pairs of the nucleosome from the histone core, and the DNA entry-exit angle expanded by 18° from that of wild-type nucleosomes. Tail-less nucleosomes, particularly those without H2B and H3 tails, showed a 10-fold increase in dynamics, such as nucleosome sliding and DNA unwrapping/wrapping, within 0.3 s, emphasizing their role in histone-DNA interactions. Our findings illustrate that N-terminal histone tails stabilize the nucleosome structure, suggesting that histone tail PTMs modulate nucleosome dynamics.

Exciplex Formation by Complexation of an Electron-Accepting Guest in an Electron-Donating Pillar[5]arene Host Liquid.

We present a novel system, a liquid-state pillar[5]arene decorated with tri(ethylene oxide) chains, that brings electron-donor and electron-acceptor molecules into proximity for efficient exciplex formation. The electron-accepting guests exhibit a blue-purple emission from a localized excited state upon excitation in common solvents. However, directly dissolving the guests in the electron-donating pillar[5]arene liquid (a bulk system) results in visible green emission from the formed exciplexes. In the bulk system, the guest molecules are always surrounded by excess pillar[5]arene molecules, resulting in the formation of mainly inclusion-type exciplexes. In the bulk system, energy migration occurs between the pillar[5]arene molecules. Excitation of the pillar[5]arenes results in a more intense green exciplex emission than that observed upon direct excitation of the guests. In summary, the pillar[5]arene liquid is a novel system for achieving efficient exciplex formation and energy migration that is different from typical solvent and solid systems.

Acceptor-Induced Fluorescence of Phenolic Polymers Based on Triphenylamine Derivatives.

Conductive polymers facilitate the electrical current flow through the transfer of electrons and holes. They show promise for novel photo-functional materials in photovoltaics. However, substantial electrostatic interactions between electron donors and acceptors induce polymer aggregation, limiting moldability and conductivity. In this study, robust donor polymers with high heat resistance were synthesized by bonding triphenylamine (TPA) derivatives and formaldehyde to phenolic groups. Resulting TPA-based phenolic polymers exhibited flexible structures and fluorescence due to charge transfer with acceptor molecules. Furthermore, TPA-based phenolic polymers' capacity to distinguish acceptor molecule sizes correlated with their molecular weight, reflecting upon donor-acceptor interactions. This novel optical trait in phenolic polymers holds potential for electronic components and conductive materials.

Imaging single CaMKII holoenzymes at work by high-speed atomic force microscopy.

Ca2+/calmodulin-dependent protein kinase II (CaMKII) plays a pivotal role in synaptic plasticity. It is a dodecameric serine/threonine kinase that has been highly conserved across metazoans for over a million years. Despite the extensive knowledge of the mechanisms underlying CaMKII activation, its behavior at the molecular level has remained unobserved. In this study, we used high-speed atomic force microscopy to visualize the activity-dependent structural dynamics of rat/hydra/C. elegans CaMKII with nanometer resolution. Our imaging results revealed that the dynamic behavior is dependent on CaM binding and subsequent pT286 phosphorylation. Among the species studies, only rat CaMKIIα with pT286/pT305/pT306 exhibited kinase domain oligomerization. Furthermore, we revealed that the sensitivity of CaMKII to PP2A in the three species differs, with rat, C. elegans, and hydra being less dephosphorylated in that order. The evolutionarily acquired features of mammalian CaMKIIα-specific structural arrangement and phosphatase tolerance may differentiate neuronal function between mammals and other species.

Dynamic-to-Static Planar Chirality Conversion in Pillar[5]arenes Regulated by Guest Solvents or Amplified by Crystallization.

Controlling dynamic chirality and memorizing the controlled chirality are important. Chirality memory has mainly been achieved using noncovalent interactions. However, in many cases, the memorized chirality arising from noncovalent interactions is erased by changing the conditions such as the solvent and temperature. In this study, the dynamic planar chirality of pillar[5]arenes was successfully converted into static planar chirality by introducing bulky groups through covalent bonds. Before introducing the bulky groups, pillar[5]arene with stereogenic carbon atoms at both rims existed as a pair of diastereomers, and thus showed planar chiral inversion that was dependent on the chain length of the guest solvent. The pS and pR forms, regulated by guest solvents, were both diastereomerically memorized by introducing bulky groups. Furthermore, the diastereomeric excess was amplified by crystallization of the pillar[5]arene. The subsequent introduction of bulky groups yielded pillar[5]arene with an excellent diastereomeric excess (95 % de).

Orientational Control of Circularly Polarized Luminescence from Pyrene Clusters by Using a DNA Scaffold.

Invited for the cover of this issue is the group of Hiromu Kashida and Hiroyuki Asanuma at Nagoya University and co-workers. The image depicts the orientation dependence of circularly polarized luminescent. Read the full text of the article at 10.1002/chem.202300182.

High-Speed Atomic Force Microscopy Reveals Spontaneous Nucleosome Sliding of H2A.Z at the Subsecond Time Scale.

Nucleosome dynamics, such as nucleosome sliding and DNA unwrapping, are important for gene regulation in eukaryotic chromatin. H2A.Z, a variant of histone H2A that is highly evolutionarily conserved, participates in gene regulation by forming unstable multipositioned nucleosomes in vivo and in vitro. However, the subsecond dynamics of this unstable nucleosome have not been directly visualized under physiological conditions. Here, we used high-speed atomic force microscopy (HS-AFM) to directly visualize the subsecond dynamics of human H2A.Z.1-nucleosomes. HS-AFM videos show nucleosome sliding along 4 nm of DNA within 0.3 s in any direction. This sliding was also visualized in an H2A.Z.1 mutant, in which the C-terminal half was replaced by the corresponding canonical H2A amino acids, indicating that the interaction between the N-terminal region of H2A.Z.1 and the DNA is responsible for nucleosome sliding. These results may reveal the relationship between nucleosome dynamics and gene regulation by histone H2A.Z.

Orientational Control of Circularly Polarized Luminescence from Pyrene Clusters by Using a DNA Scaffold.

We have investigated the chiroptical activities of pyrene clusters incorporated within a DNA duplex. Three pyrene derivatives were prepared on d-threoninol linkers to allow incorporation within a DNA strand. DNA scaffolds containing dimers, tetramers, and hexamers of the pyrene derivatives were prepared. The homodimers of 1- and of 4-pyrenecarboxylic acid, but not 2-pyrenecarboxylic acid, emitted intense circularly polarized luminescence signals. Although increasing the number of pyrene units weakened the signal, insertion of natural base pairs between two dimers enhanced its intensity. Interestingly, circularly polarized luminescence intensities varied non-monotonically depending on the number of intervening base pairs, thus indicating the importance of orientation between pyrene dimers. The results presented here could lead to the development of bright circularly polarized luminescence materials and probes.

CPL on/off control of an assembled system by water soluble macrocyclic chiral sources with planar chirality.

Herein, we report the synthesis and planar chiral properties of a pair of water-soluble cationic pillar[5]arenes with stereogenic carbons. Interestingly, although units of the molecules were rotatable, only one planar chiral diastereomer existed in water in both cases. As a new type of chiral source, these molecules transmitted chiral information from the planar chiral cavities to the assembly of a water-soluble extended π-conjugated compound, affording circularly polarized luminescence (CPL). The chirality transfer process and resulting CPL were extremely sensitive to the feed ratio of the chiral pillar[5]arenes owing to the combined action of their planar chirality, bulkiness, and strong binding properties. When a limited amount of chiral source was added, further assembly of the extended π-conjugated compound into helical fibers with CPL was triggered. Unexpectedly, larger amounts of chiral source destroyed the helical fiber assemblies, resulting in elimination of the chirality and CPL properties from the assembled structures.

Polypseudorotaxanes constructed from pillar[5]arenes and polyamides by interfacial polymerization.

Polypseudorotaxanes constructed from pillar[5]arene rings and polyamide chains were successfully synthesized by interfacial polymerization between diamines and dicarbonyl chlorides in the presence of pillar[5]arene. The dicarbonyl chloride length and the assocation constants of dicarbonyl chloride-pillar[5]arene complexes were important factors in producing polypseudorotaxanes with high cover ratio of pillar[5]arene rings.

Reversible "On/Off" Chiral Amplification of Pillar[5]arene Assemblies by Dual External Stimuli.

We report dual-stimuli, thermo- and photostimuli, responsive chiral assemblies, of planar-chiral pillar[5]arenes with azobenzene groups on their rims. The azobenzene-substituted planar-chiral pillar[5]arenes were synthesized by copper(I)-catalyzed alkyne-azide cycloaddition "click" reaction of azide-substituted planar-chiral pillar[5]arenes containing S or R stereogenic carbon atoms with an alkyne-substituted azobenzene. These decaazides with stereogenic carbons could act as starting points for a large library of planar-chiral pillar[5]arenes. Homeotropic alignment of azobenzenes, caused by the mesogenic property of the azobenzene groups, was induced by annealing a film of the azobenzene-substituted planar-chiral pillar[5]arenes. The alignment resulted in chiral propagation from the planar-chiral pillar[5]arene cores to the azobenzene area and caused significant chiral amplification consequently. These aligned chiral assemblies were collapsed by trans to cis photoisomerization of the azobenzene groups, resulting in chiral amplification off, and reconstructed by cis to trans thermo-isomerization, again turning on the chiral amplification.

A Pyrene-Modified Serinol Nucleic Acid Nanostructure Converts the Chirality of Threoninol Nucleic Acids into Circularly Polarized Luminescence Signals.

Herein is reported a circularly polarized luminescent (CPL) probe that can respond to the chirality of nucleic acids. An achiral nanostructure was prepared by the hybridization of symmetric serinol nucleic acid (SNA) containing pyrene-modified residues. When chiral oligomers that were complementary to the SNA were added, they induced helicity into the SNA nanowire. Efficient circular dichroism (CD) signal amplification was observed when pyrene was attached to uracil bases through a rigid alkynyl linker. Both CPL and CD signals were observed; they depended on the chirality of the added acyclic threoninol nucleic acid (aTNA) oligomer. This system can be used to convert the chirality of chiral biomolecules into chiroptical signals.

Supramolecular exfoliation of layer silicate clay by novel cationic pillar[5]arene intercalants.

Clays are multi-layered inorganic materials that can be used to prepare nanocomposite fillers. Because the multi-layered structure is thermodynamically stable, it is difficult to change a multi-layered material into single layers to improve its dispersity. Previously, clays were modified with dodecylammonium cations to promote complexation with nylon 6, nylon 66, polypropylene, polyethylene, polystyrene, and polycaprolactone to increase the mechanical strength (and/or thermal stability) of the composite material; however, complete exfoliation could not be achieved in these composites. In this study, pillar[5]arenes are synthesized and functionalized with ten cationic substituents as novel intercalants for modifying bentonite clay, which is a multi-layered metal-cation-containing silicate. The pillar[5]arenes exfoliate the clay by forming polyrotaxanes with poly(ethylene glycol) through host-guest interactions.

Thermally Responsive Poly(ethylene oxide)-Based Polyrotaxanes Bearing Hydrogen-Bonding Pillar[5]arene Rings.

Invited for the cover of this issue are Tomoki Ogoshi and co-workers at Kyoto University, Kanazawa University and Tokyo University of Agriculture and Technology. The image depicts musical notation to represent hydrogen bond networks and poly(ethylene oxide) chains. Read the full text of the article at 10.1002/chem.202005099.

Thermally Responsive Poly(ethylene oxide)-Based Polyrotaxanes Bearing Hydrogen-Bonding Pillar[5]arene Rings*.

Poly(ethylene oxide)s (PEOs) are useful polymers with good water solubility, biological compatibility, and commercial availability. PEOs with various end groups were threaded into pillar[5]arene rings in a mixture of water and methanol to afford pseudopolyrotaxanes. Corresponding polyrotaxanes were also constructed by capping COOH-terminated pseudopolyrotaxanes with bulky amines, in which multiple hydrogen bonds involving the pillar[5]arene OH groups were critically important to prevent dethreading. The number of threaded ring components could be rationally controlled in these materials, providing a simple and versatile method to tune the mechanical and thermal properties. Specifically, a polyrotaxane with a high-molecular-weight axle became elastic upon heating above the melting point of PEOs and exhibited temperature-dependent shape memory property because of the topological confinement and crosslinked hydrogen bonds.

The carbonization of aromatic molecules with three-dimensional structures affords carbon materials with controlled pore sizes at the Ångstrom-level.

Carbon materials with controlled pore sizes at the nanometer level have been obtained by template methods, chemical vapor desorption, and extraction of metals from carbides. However, to produce porous carbons with controlled pore sizes at the Ångstrom-level, syntheses that are simple, versatile, and reproducible are desired. Here, we report a synthetic method to prepare porous carbon materials with pore sizes that can be precisely controlled at the Ångstrom-level. Heating first induces thermal polymerization of selected three-dimensional aromatic molecules as the carbon sources, further heating results in extremely high carbonization yields (>86%). The porous carbon obtained from a tetrabiphenylmethane structure has a larger pore size (4.40 Å) than those from a spirobifluorene (4.07 Å) or a tetraphenylmethane precursor (4.05 Å). The porous carbon obtained from tetraphenylmethane is applied as an anode material for sodium-ion battery.

A light-operated pillar[6]arene-based molecular shuttle.

A molecular shuttle comprising a pillar[6]arene macrocyclic ring and an axle with two equal-energy-level stations connected by an azobenzene unit was synthesised. The E isomer of the azobenzene functioned as "open gate", allowing the pillar[6]arene ring to rapidly shuttle back-and-forth between the two stations. Ultraviolet irradiation induced photo-isomerisation of the azobenzene from E to Z form. The Z isomer of the azobenzene functioned as a "closed gate", inhibiting shuttling of the pillar[6]arene ring.

High Refractive-Index Hybrids Consisting of Water-Soluble Matrices with Bipyridine-Modified Polyhedral Oligomeric Silsesquioxane and Lanthanoid Cations.

We report high refractive-index (RI) films composed of polyhedral oligomeric silsesquioxane (SSQ) matrices and various lanthanoid cations. The SSQ matrices were constructed from octaammonium SSQ by connecting with bipyridine dicarboxylic acid, which is expected to capture cations. By modulating the feed ratio between SSQ and dicarboxylic acid, the series of the SSQ matrices were obtained with variable cross-linking ratios among the SSQ units. Thin transparent films were able to be prepared through the drop-casting method with the aqueous mixtures containing SSQ matrices and various kinds of lanthanoid salts up to 40 wt %. From RI measurements, it was revealed that the increase of the amount of the metal ion can significantly lift up the RI values. In particular, critical losses of Abbe numbers, which theoretically have the trade-off relationship toward increases in RI values, were hardly detected. This effect could be obtained by cation assembly in local spots that are assisted by SSQ.

Holding of planar chirality of pillar[5]arene by kinetic trapping using host-guest interactions with achiral guest solvents.

We report a solvent-dependent switching and holding of planar chirality of pillar[5]arene with stereogenic carbons at both rims by host-guest complexation with achiral guest solvents. The planar chirality could be held for a given length of time at 25 °C in long linear guest solvents by kinetic trapping through host-guest complexation. The kinetic trapping worked at 25 °C, but not at 60 °C, thus a planar-chiral inversion using kinetic trapping based on host-guest complexation in the long linear solvents was demonstrated.

Obvious vapochromic color changes of a pillar[6]arene containing one benzoquinone unit with a mechanochromic change before vapor exposure.

We developed a color changeable aromatic vapor detection system by combining the mechanochromism and vapochromism of pillar[6]arene containing one benzoquinone unit. The color of pillar[6]arene solid was changed by mechanochromism before vapor exposure. Different aromatic vapors then induced an obvious vapochromic color change from dark red to light orange or vice versa.