A novel nucleic acid linker for multi-gene expression enhances plant and animal synthetic biology.

The production of compact vectors for gene stacking is hindered by a lack of effective linkers. Here, we report that a 26-nt nucleic acid linker, NAL1, from the fungus Glarea lozoyensis and its truncated derivatives could connect two genes as a bicistron, enabling independent translation in a maize protoplast transient expression system and human 293 T cells. The optimized 9-nt NAL10 linker was then used to connect four genes driven by a bidirectional promoter; this combination was successfully used to reconstruct the astaxanthin biosynthesis pathway in transgenic maize. The short and efficient nucleic acid linker NAL10 can be widely used in multi-gene expression and synthetic biology in animals and plants.

Occurrence and classification of T-shaped interactions between nucleobases in RNA structures.

Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank.

Stack-HDAC3i: A high-precision identification of HDAC3 inhibitors by exploiting a stacked ensemble-learning framework.

Epigenetics involves reversible modifications in gene expression without altering the genetic code itself. Among these modifications, histone deacetylases (HDACs) play a key role by removing acetyl groups from lysine residues on histones. Overexpression of HDACs is linked to the proliferation and survival of tumor cells. To combat this, HDAC inhibitors (HDACi) are commonly used in cancer treatments. However, pan-HDAC inhibition can lead to numerous side effects. Therefore, isoform-selective HDAC inhibitors, such as HDAC3i, could be advantageous for treating various medical conditions while minimizing off-target effects. To date, computational approaches that use only the SMILES notation without any experimental evidence have become increasingly popular and necessary for the initial discovery of novel potential therapeutic drugs. In this study, we develop an innovative and high-precision stacked-ensemble framework, called Stack-HDAC3i, which can directly identify HDAC3i using only the SMILES notation. Using an up-to-date benchmark dataset, we first employed both molecular descriptors and Mol2Vec embeddings to generate feature representations that cover multi-view information embedded in HDAC3i, such as structural and contextual information. Subsequently, these feature representations were used to train baseline models using nine popular ML algorithms. Finally, the probabilistic features derived from the selected baseline models were fused to construct the final stacked model. Both cross-validation and independent tests showed that Stack-HDAC3i is a high-accuracy prediction model with great generalization ability for identifying HDAC3i. Furthermore, in the independent test, Stack-HDAC3i achieved an accuracy of 0.926 and Matthew's correlation coefficient of 0.850, which are 0.44-6.11% and 0.83-11.90% higher than its constituent baseline models, respectively.

Tunable Multistate Ferroelectricity of Unit-Cell-Thick BaTiO3 Revived by a Ferroelectric SnS Monolayer via Interfacial Sliding.

Stabilization of multiple polarization states at the atomic scale is pivotal for realizing high-density memory devices beyond prevailing bistable ferroelectric architectures. Here, we show that two-dimensional ferroelectric SnS or GeSe is able to revive and stabilize the ferroelectric order of three-dimensional ferroelectric BaTiO3, even when the latter is thinned to one unit cell in thickness. The underlying mechanism for overcoming the conventional detrimental critical thickness effect is attributed to facile interfacial inversion symmetry breaking by robust in-plane polarization of SnS or GeSe. Furthermore, when invoking interlayer sliding, we can stabilize multiple polarization states and achieve efficient interstate switching in the heterostructures, accompanied by dynamical ferroelectric skyrmionic excitations. When invoking sliding and twisting, the moiré domains exhibit nontrivial polar vortexes, which can be laterally displaced via different sliding schemes. These findings provide an intuitive avenue for simultaneously overcoming the standing critical thickness issue in bulk ferroelectrics and weak polarization issue in sliding ferroelectricity.

Build Borophite from Borophenes: A Boron Analogue Graphite.

Unlike graphene derived from graphite, borophenes represent a distinct class of synthetic two-dimensional materials devoid of analogous bulk-layered allotropes, leading to covalent bonding within borophenes instead of van der Waals (vdW) stacking. Our investigation focuses on 665 vdW-stacking boron bilayers to uncover potential bulk-layered boron allotropes through vdW stacking. Systematic high-throughput screening and stability analysis reveal a prevailing inclination toward covalently bonded layers in the majority of boron bilayers. However, an intriguing outlier emerges in δ5 borophene, demonstrating potential as a vdW-stacking candidate. We delve into electronic and topological structural similarities between δ5 borophene and graphene, shedding light on the structural integrity and stability of vdW-stacked boron structures across bilayers, multilayers, and bulk-layered allotropes. The δ5 borophene analogues exhibit metallic properties and characteristics of phonon-mediated superconductors, boasting a critical temperature near 22 K. This study paves the way for the concept of "borophite", a long-awaited boron analogue of graphite.

Inversion Symmetry-Broken Tetralayer Graphene Probed by Second-Harmonic Generation.

Stacking orders provide a unique way to tune the properties of two-dimensional materials. Recently, ABCB-stacked tetralayer graphene has been predicted to possess atypical elemental ferroelectricity arising from its symmetry breaking but has been experimentally explored very little. Here, we observe pronounced nonlinear optical second-harmonic generation (SHG) in ABCB-stacked tetralayer graphene while absent in both ABAB- and ABCA-stacked allotropes. Our results provide direct evidence of symmetry breaking in ABCB-stacked tetralayer graphene. The remarkable contrast in the SHG spectra of tetralayer graphene allows straightforward identification of ABCB domains from the other two kinds of stacking order and facilitates the characterization of their crystalline orientation. The employed SHG technique serves as a convenient tool for exploring the intriguing physics and novel nonlinear optics in ABCB-stacked graphene, where spontaneous polarization and intrinsically gapped flat bands coexist. Our results establish ABCB-stacked graphene as a unique platform for studying the rare ferroelectricity in noncentrosymmetric elemental structures.

Atomically Unraveling Highly Crystalline Self-Intercalated Tantalum Sulfide with Correlated Stacking Registry-Dependent Magnetism.

In self-intercalated two-dimensional (ic-2D) materials, understanding the local chemical environment and the topology of the filling site remains elusive, and the subsequent correlation with the macroscopically manifested physical properties has rarely been investigated. Herein, highly crystalline gram-scale ic-2D Ta1.33S2 crystals were successfully grown by the high-pressure high-temperature method. Employing combined atomic-resolution scanning transmission electron microscopy annular dark field imaging and density functional theory calculations, we systematically unveiled the atomic structures of an atlas of stacking registries in a well-defined √3(a) × âˆš3(a) Ta1.33S2 superlattice. Ferromagnetic order was observed in the AC' stacking registry, and it evolves into an antiferromagnetic state in AA/AB/AB' stacking registries; the AA' stacking registry shows ferrimagnetic ordering. Therefore, we present a novel approach for fabricating large-scale highly crystalline ic-2D crystals and shed light on a powerful means of modulating the magnetic order of ic-2D systems via stacking engineering, i.e., stackingtronics.

Picosecond Ultrasonics in Magnetic Topological Insulator MnBi2Te4.

MnBi2Te4 is a magnetic topological insulator with layered A-type antiferromagnetic order. It exhibits a rich layer- and magnetic-state dependent topological phase diagram; however, much about the coupling between spin, charge, and lattice remains to be explored. In this work, we report that MnBi2Te4 is an excellent acoustic phonon cavity by realizing phonon frequency combs using picosecond ultrasonics. With the generated acoustic phonon wavepackets, we demonstrate that the timing and phase of acoustic echoes can be used to detect the presence of stacking faults between van der Waals layers buried deep within the crystal. Furthermore, by implementing this nondestructive ultrafast optical measurement in conjunction with time-resolved magneto-optical Kerr effect experiments, we uncover that out-of-plane vibrations in MnBi2Te4 do not couple to the magnetic order, i.e. there is no appreciable magnetostriction. Our work points out how a well-developed technique can probe the structural defects and phonon pulse engineering in layered topological insulators.

Phase Transition of Cubic Ice to Hexagonal Ice during Growth and Decomposition.

Ice, one of the most enigmatic materials on Earth, exhibits diverse polymorphism, with research mainly focusing on the most commonly observed phases: hexagonal ice (Ih), cubic ice (Ic), and stacking-disordered ice (Isd). While their formation or structural changes are crucial for advancements in cloud science, climate modeling, and cryogenic technology, the molecular mechanisms driving these phenomena remain unexplored. Herein, utilizing cryogenic transmission electron microscopy, we investigate the formation of ice at two different temperatures, demonstrating a size-dependent phase shift from Ic to Isd. Furthermore, a relatively metastable cubic phase in Isd transitions to a hexagonal phase under electron beam radiation. This transition, facilitated by crystal defects, contrasts with perfect crystalline Ic, which maintains its original phase, emphasizing the importance of defects in polymorphic phase transitions. Our findings provide novel insights on phase control during the ice growth processes and polymorphic phase transitions from the cubic-to-hexagonal phases.

In Situ Monitoring and Tuning Multilayer Stacking of Polymer Lamellar Crystals in Solution with Aggregation-Induced Emission.

Many types of self-assembled 2D materials with fascinating morphologies and novel properties have been prepared and used in solution. However, it is still a challenge to monitor their in situ growth in solution and to control the number of layers in these materials. Here, we demonstrate that the aggregation-induced emission (AIE) effect can be applied for the in situ decoupled tracing of the lateral growth and multilayer stacking of polymer lamellar crystals in solution. Multilayer stacking considerably enhances the photoluminescence intensity of the AIE molecules sandwiched between two layers of lamellar crystals, which is 2.4 times that on the surface of monolayer crystals. Both variation of the self-seeding temperature of crystal seeds and addition of a trace amount of long polymer chains during growth can control multilayer lamellar stacking, which are applied to produce tunable fluorescent patterns for functional applications.