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.

Self-Inclusion Complexation of Electron-Accepting Guest into Electron-Donating Cyclic Host by Photoexcitation.

Self-inclusion complexes consisting of host-guest conjugates are one of the unique supramolecular structures because they form in-state and out-state depending on the external stimuli. Despite many reports of the stimuli-responsive self-inclusion complex formation, study of the structural relaxation from out-state to in-state by photoexcitation has been unexplored. Herein, we report that an electron-donating host and an electron-accepting guest conjugate exhibits the structural relaxation from out-state to in-state by photoexcitation. Formation of the in-state in the excited state resulted in exciplex emission along with the locally excited emission from the out-state. Moreover, this structural relaxation by photoexcitation was suppressed not only by temperature, but also by the presence of guest molecules, resulting in changes in the ratio of the dual emission intensities.

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.

Alkoxylated Fluoranthene-Fused [3.3.3]Propellanes: Facile Film Formation against High π-Core Content.

Solid-state assembling modes are as crucial as the chemical structures of single molecules for real applications. In this work, solid-state structures and phase-transition temperatures are investigated for a series of fluoranthene-fused [3.3.3]propellanes consisting of a rigid three-dimensional (3D) π-core and varying lengths of alkoxy groups. Compounds in this series with n-butoxy or longer alkoxy groups take an amorphous state at room temperature. In these molecules, rotatable biaryl-type bonds are not incorporated and high D3h molecular symmetry is retained. Therefore, π-fused [3.3.3]propellanes present a unique platform for amorphous molecular materials with low ratios of flexible alkoxy atoms to rigid π-core ones.

Solid-State Emissive Pillar[6]arene Derivative Having Alternate Methylene and Nitrogen Bridges.

Macrocyclic arenes show conformational adaptability, which allows host-guest complexations with the size-matched guest molecules. However, their emission properties are often poor in the solid states due to the self-absorption. Herein, we newly synthesized pillar[6]arene derivatives having alternate methylene and nitrogen bridging structures. Solvatochromic study reveals that the nitrogen-embedding into the cyclic structures can strengthen the intramolecular charge transfer (CT) nature compared to that of the linear nitrogen-bridged precursor. Owing to the large Stokes shift in the solid state, one of the nitrogen-embedded pillar[6]arenes shows high absolute photoluminescence quantum yield (ΦPL=0.36). Furthermore, it displays a turn-off sensing ability toward nitrobenzene (NB) vapor; a fluorescence quenching is observed when exposed to the NB vapor. From the structural analysis before and after the exposure of NB vapor, the amorphous nitrogen-embedded pillar[6]arene efficiently co-crystallize with NB and formed non-emissive intermolecular CT complexes with NB.

Silapillar[n]arenes: Their Enhanced Electronic Conjugation and Conformational Versatility.

During recent decades, methylene-bridged macrocyclic arenes have been widely used in supramolecular chemistry. However, their π-conjugations are very weak, as the methylene bridges disrupt the electronic communication between π orbitals of the aromatic units. Herein, we successfully synthesized a series of silapillar[n]arenes (n = 4, 6, and 8) using silylene bridging. These showed enhanced electronic conjugation compared with the parent pillar[n]arenes because of σ*-π* conjugation between σ* (Si-C) orbitals and π* orbitals of the benzenes. Owing to the longer Si-C bond compared with the C-C bond, silylene-bridging provides additional structural flexibility into the pillar[n]arene scaffolds; a strained silapillar[4]arene was formed, which is unavailable in the parent pillar[n]arenes because of the steric requirements. Furthermore, silapillar[n]arenes displayed interesting size-dependent structural and optical properties.

Friedel-Crafts Acylation for Accessing Multi-Bridge-Functionalized Large Pillar[n]arenes.

Pillar[n]arenes can be constructed using a Friedel-Crafts alkylation process. However, due to the reversible nature of the alkylation, mixture of large pillar[n]arenes (n≥7) are obtained as minor products, and thus laborious purification are necessary to isolate the larger pillar[n]arenes. Moreover, inert methylene bridges are introduced during the alkylation process, and the multi-functionalization of the bridges has never been investigated. Herein, an irreversible Friedel-Crafts acylation is used to prepare pillar[n]arenes. Due to the irreversible nature of the acylation, the reaction of precursors bearing carboxylic acids and electron-rich arene rings results in a size-exclusive formation of pillar[n]arenes, in which the ring-size is determined by the precursor length. Because of this size-selective formation, laborious separation of undesired macrocycles is not necessary. Moreover, the bridges of pillar[n]arenes are selectively installed with reactive carbonyl groups using the acylation method, whose positions are determined by the precursor used. The carbonyl bridges can be easily converted into versatile functional groups, leading to various laterally modified pillar[n]arenes, which cannot be accessed by the alkylation strategy.

Combinatorial Screening of Water/Proton Permeation of Self-Assembled Pillar[5]arene Artificial Water Channel Libraries.

Artificial water channels (AWCs) that selectively transport water and reject ions through bilayer membranes have potential to act as synthetic Aquaporins (AQPs). AWCs can have a similar osmotic permeability, better stability, with simpler manufacture on a larger-scale and have higher functional density and surface permeability when inserted into the membrane. Here, we report the screening of combinatorial libraries of symmetrical and unsymmetrical rim-functionalized PAs A-D that are able to transport ca. 107 -108 water molecules/s/channel, which is within 1 order of magnitude of AQPs' and show total ion and proton rejection. Among the four channels, C and D are 3-4 times more water permeable than A and B when inserted in bilayer membranes. The binary combinations of A-D with different molar ratios could be expressed as an independent (linear ABA), a recessive (inhibition AB, AC, DB, ACA), or a dominant (amplification, DBD) behavior of the water net permeation events.

Diastereoselective Rotaxane Synthesis with Pillar[5]arenes via Co-crystallization and Solid-State Mechanochemical Processes.

Chiral rotaxanes have attracted much attention in recent decades for their unique chirality based on their interlocked structures. Thus, selective synthesis methods of chiral rotaxanes have been developed. The introduction of substituents with chiral centers to produce diastereomers is a powerful strategy for the construction of chiral rotaxanes. However, in case of a small energy difference between the diastereomers, diastereoselective synthesis is extremely difficult. Herein, we report a new diastereoselective rotaxane synthesis method using solid-phase diastereoselective [3]pseudorotaxane formation and mechanochemical solid-phase end-capping reactions of the [3]pseudorotaxanes. By co-crystallization of stereodynamic planar chiral pillar[5]arene with stereogenic carbons at both rims and axles with suitable end groups and lengths, the [3]pseudorotaxane with a high diastereomeric excess (ca. 92% de) was generated in the solid state because of higher effective molarity with aid by packing effects and significant energy differences between [3]pseudorotaxane diastereomers. In contrast, the de of the pillar[5]arene was low in solution (ca. 10% de) because of a small energy difference between diastereomers. Subsequent end-capping reactions of the polycrystalline [3]pseudorotaxane with high de in solvent-free conditions successfully yielded rotaxanes while maintaining the high de generated by the co-crystallization.

Alignment and Dynamic Inversion of Planar Chirality in Pillar[n]arenes.

Pillar[n]arenes are symmetrical macrocyclic compounds composed of benzene panels with para-methylene linkages. Each panel usually exhibits planar chirality and prefers chirality-aligned states. Because of this feature, pillar[n]arenes are attractive scaffolds for chiroptical materials that are easy to prepare and optically resolve and show intense circular dichroism (CD) signals. In addition, rotation of the panels endows the chirality of pillar[n]arenes with a dynamic nature. The chirality in tubular oligomers and supramolecular assemblies sometimes show time- and procedure-dependent alignment phenomena. Furthermore, the CD signals of some pillar[n]arenes respond to the addition of chiral guests when their dynamic chirality is coupled with host-guest properties. By using diastereomeric pillar[n]arenes with additional chiral structures, the response can also be caused by achiral guests and changes of the environment, providing molecular sensors.

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.

Efficient synthesis and unit-selective π-extension of π-fused [4.3.3]propellane as a chiral building block.

A three-dimensional skeleton, π-fused [4.3.3]propellane, was constructed and derivatized by selective π-extension at the two naphthalene units. The obtained propellanes existed as stereoisomers different in spatial arrangement, one of which displayed a chiroptical response originating from through-space interactions between 5-azachrysenes in a skew position.

Adaptive Planar Chirality of Pillar[5]arenes Invertible by n-Alkane Lengths.

Chirality of host molecules can be induced and/or inverted by the guest molecules. However, the adapting chirality of hosts to the length of n-alkanes remains a great challenge because n-alkanes are neutral, achiral, and linear molecules, resulting in a weak interaction with most compounds. Herein, we report a system with chirality adapted to n-alkane lengths, using a pillar[5]arene-based macrocyclic host, S-Br, which contains five stereogenic carbons and five terminal bromine atoms on each rim. The electron-rich cavity of S-Br could include n-alkanes and the planar-chiral isomers sensitively inverted in response to the lengths of the complexed n-alkanes. The inclusion of a short n-alkane such as n-pentane made S-Br more inclined to be in the pS-form, whereas the inclusion of long n-alkanes such as n-heptane made the pR-form more favorable. The difference in the stability of the isomers was supported by the crystal structures and the theoretical calculations. Furthermore, temperature drives the adaptive chirality of S-Br with n-alkanes. An n-alkane with middle length, n-hexane, showed the dominance of the pR-form of S-Br at a higher temperature, whereas the pS-form was shown at a lower temperature.

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.

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).

Per-Arylation of Pillar[n]arenes: An Effective Tool to Modify the Properties of Macrocycles.

Installation of various substituents is a reliable and versatile way to alter the properties of macrocyclic molecules, but high-yield and controlled methods are not always available especially for multifold reactions. Herein, we report 10- and 12-fold introduction of aryl substituents onto both rims of cylinder-shaped pillar[n]arenes, which usually have alkoxy substituents slanting to the cylinder axes. Although alkoxy pillar[5]arenes exist as D5-symmetric enantiomeric pairs, arylated pillar[5]arenes provide crushed single-crystal structures and stereoisomerism including C2-symmetric conformations depending on the aryl groups. Pillar[n]arenes with 2-benzofuranyl groups display bright fluorescence with quantum yields of 88-90% and no host-guest complexation with electron-deficient molecules in solution due to large deviation from alkoxy compounds. A benzofuran-appended pillar[6]arene instead captures small gaseous molecules in the solid state, probably owing to outside spaces surrounded by aromatic rings.

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.

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.

A Twisted Chiral Cavitand with 5-Fold Symmetry and Its Length-Selective Binding Properties.

Controlling bottom-up syntheses from chiral seeds to construct architectures with specific chiralities is currently challenging. Herein, a twisted chiral cavitand with 5-fold symmetry was constructed by bottom-up synthesis using corannulene as the chiral seed and pillar[5]arene as the chiral wall. After docking between the seed and the wall, their dynamic chiralities (M and P) are fixed. Moreover, the formed hedges also exhibit M and P chirality. Through dynamic covalent bonding, the thermodynamically stable product is obtained selectively as a pair of enantiomers (MMM and PPP), where all three subcomponents, i.e., the corannulene, hedges, and pillar[5]arene, are tilted in the same direction. Furthermore, the twisted cavitand exhibits length-selective binding to alkylene dibromides, with three maximum binding constants being unexpectedly observed.