Feruloyl-CoA:Monolignol transferases
The invention relates to feruloyl-CoA:monolignol transferase enzymes and nucleic acids.
Ralph, John↗
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Methods of improving drought and salt resistance in a plant and genetically engineered plants with improved drought and salt resistance
The present disclosure provides methods for increasing drought resistance, salt resistance, and biomass production of a plant. The methods encompass expression of DiGeorge-Syndrome Critical Region 14 (DGCR14) gene in the plant. In comparison to a plant not manipulated in this manner, the disclosed, genetically-modified, plants display improved drought resistance and salt resistance. Also provided are plants that can be obtained by the method according to the invention, and nucleic acid vectors to be used in the described methods.
Xie, Meng↗
Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex
Nuclear Argonaute proteins, guided by their bound small RNAs to nascent target transcripts, mediate cotranscriptional silencing of transposons and repetitive genomic loci through heterochromatin formation. The molecular mechanisms involved in this process are incompletely understood. Here, we show that the SFiNX complex, a silencing mediator downstream from nuclear Piwi-piRNA complexes in Drosophila, facilitates cotranscriptional silencing as a homodimer. The dynein light chain protein Cut up/LC8 mediates SFiNX dimerization, and its function can be bypassed by a heterologous dimerization domain, arguing for a constitutive SFiNX dimer. Dimeric, but not monomeric SFiNX, is capable of forming molecular condensates in a nucleic acid-stimulated manner. Mutations that prevent SFiNX dimerization result in loss of condensate formation in vitro and the inability of Piwi to initiate heterochromatin formation and silence transposons in vivo. We propose that multivalent SFiNX-nucleic acid interactions are critical for heterochromatin establishment at piRNA target loci in a cotranscriptional manner.
59 BASIC BIOLOGICAL SCIENCES↗
Depolymerization as a Design Strategy: Depolymerization Etching of Polymerization-Induced Microphase Separations
Thermally triggered depolymerization has traditionally been viewed through the lens of sustainability and recycling, not as a constructive tool for materials design. Herein, we show that selective, thermally triggered depolymerization to gaseous monomer serves as a solvent-free strategy for generating porosity in nanostructured polymer materials, offering a means to bypass the mass transport limitations inherent in conventional solution-based etching. As a demonstration platform, we employed polymerization-induced microphase separation (PIMS) to generate disordered bicontinuous block copolymer structures with embedded depolymerizable domains. By incorporating a methacrylate block susceptible to thermal depolymerization within a cross-linked, depolymerization-resistant styrenic matrix, we developed a process we term depolymerization etching of polymerization-induced microphase separations (DEPIMS). This approach enables highly selective and efficient domain removal via reversion to monomer to produce mesoporous materials with high surface areas (>200 m 2 /g). Subsequent surface functionalization yielded mesoporous adsorbents with tunable uptake kinetics and among the highest dye adsorption capacities reported for PIMS-derived materials, demonstrating the adaptability of the DEPIMS platform for chemical separations. DEPIMS can also be extended to a gram-scale, one-pot approach to yield mesoporous materials with recoverable monomer in under 12 h. These findings reposition thermal depolymerization from a sustainability tool to a broadly enabling strategy for scalable, on-demand fabrication of functional nanostructured materials.
Depolymerization↗
How Segmental Dynamics and Mesh Confinement Determine the Selective Diffusivity of Molecules in Cross-Linked Dense Polymer Networks
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains
Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)–to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. Furthermore, these results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Formation and Nanomechanical Properties of Silver-Mediated Guanine DNA Duplexes in Aqueous Solution
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Effects of Charge Sequence Pattern and Lysine-to-Arginine Substitution on the Structural Stability of Bioinspired Polyampholytes
A comprehensive study focusing on the combined influence of the charge sequence pattern and the type of positively charged amino acids on the formation of secondary structures in sequence-specific polyampholytes is presented. The sequences of interest consisting exclusively of ionizable amino acids (lysine, K; arginine, R; and glutamic acid, E) are (EKEK) 5 , (EKKE) 5 , (ERER) 5 , (ERRE) 5 , and (EKER) 5 . The stability of the secondary structure was examined at three pH values in the presence of urea and NaCl. The results presented here underscore the combined prominent effects of the charge sequence pattern and the type of positively charged monomers on secondary structure formation. Additionally, (ERRE) 5 readily aggregated across a wide range of pH. In contrast, sequences with the same charge pattern, (EKKE) 5 , as well as the sequences with the equivalent amino acid content, (ERER) 5 , exhibited no aggregate formation under equivalent pH and concentration conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering
Abstract Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.
59 BASIC BIOLOGICAL SCIENCES↗
Frontal Polymerization of Dihydrofuran Comonomer Facilitates Thermoset Deconstruction
Frontal ring-opening metathesis polymerization (FROMP) is a rapid, low-energy manufacturing reaction that is useful for curing thermosetting materials. FROMP of dicyclopentadiene (DCPD) results in poly(dicyclopentadiene) (p(DCPD)), a tough thermoset with excellent mechanical performance and chemical stability. Like most thermosets, p(DCPD) cannot be reprocessed and is therefore difficult to recycle. Previous work demonstrated that the incorporation of a small quantity of cleavable units in the strand segments of p(DCPD) networks enables their deconstruction. Here, we report that a commercially available multifunctional comonomer, 2,3-dihydrofuran (DHF), both acts as a potent Grubbs catalyst inhibitor during FROMP and introduces acid cleavable units. The resulting materials retain high performance characteristics, including glass-transition temperatures ranging from 115 to 165 °C and ultimate strength ranging from 35 to 40 MPa. The addition of DHF above critical loading levels enables deconstructable thermosets. Here, we further demonstrate freeform three-dimensional (3D) printing of deconstructable thermosets via frontal polymerization.
36 MATERIALS SCIENCE↗
Dynamic Bottlebrush Polymer Networks: Self-Healing in Super-Soft Materials
Here, we introduce a design strategy to expand the range of accessible mechanical properties in covalent adaptable networks (CANs) using bottlebrush polymer building blocks. Well-defined bottlebrush polymers with rubbery poly(4-methylcaprolactone) side-chains were crosslinked in formulations that include a bislactone and strong Lewis acid (tin ethylhexanoate). The resulting materials exhibit tunable stress relaxation rates at elevated temperatures (160–180 °C) due to dynamic ester crosslinks that undergo transesterification with residual hydroxy groups. Varying the crosslinker loading or bottlebrush backbone degree of polymerization yields predictable low-frequency shear moduli ca. 10–100 kPa, well below values typical of linear polymer CANs (1 MPa). These extensible networks can be stretched to strains as large as 350% before failure and undergo efficient self-healing to recover >85% of their original toughness upon repeated fracture and melt processing. In summary, molecular architecture creates new opportunities to tailor the mechanical properties of CANs in ways that are otherwise difficult to achieve.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Integrated Strategies for Overcoming Resolution Limits in Electron Beam Lithography of Chemically Amplified Resists
Electron beam lithography (EBL) of chemically amplified resists (CARs) faces fundamental challenges, including stochastic electron scattering and acid diffusion, that limit resolution and reproducibility. Using SU-8 as a model CAR, this study systematically investigated complementary strategies to address these challenges, combining multipass exposure, proximity effect correction (PEC) with midrange correction factors, base quencher incorporation, and post-exposure bake (PEB) suppression. Monte Carlo simulations and calibrated PEC modeling revealed that extending the point spread function to include a midrange scattering component significantly improved critical dimension (CD) control across varying pattern densities, correcting deviations that conventional two-term PEC failed to capture. Multipass exposure, particularly 4-pass writing with a 25% offset, redistributed the dose to average stochastic beam and scattering fluctuations, reducing line-width roughness by more than 50% and yielding more uniform nanoscale features. Photoacid confinement was investigated by adding urea as a base quencher, which successfully reduced acid diffusion but introduced substantial sensitivity penalties without improving ultimate resolution or Z-factor performance, underscoring the trade-offs of chemical versus physical confinement. Suppressing PEB most directly minimized acid diffusion, resulting in improved Z-factors and reproducible 30 nm half-pitch dense line/space patterns. Overall, these results demonstrated that PEC with midrange correction, multipass strategies, quencher additives, and PEB-free processing addresses different aspects of the EBL process window and that their integration provides a comprehensive framework for managing stochastic scattering, diffusion, and chemical amplification effects. This framework advances dense nanoscale patterning in CARs and establishes guiding principles for optimizing resist design and process strategies in high-resolution EBL and potentially other advanced lithographies, such as extreme ultraviolet (EUV) lithography.
36 MATERIALS SCIENCE↗
Tailoring Lifetimes and Properties of Carbodiimide-Fueled Covalently Cross-linked Polymer Networks
The mechanical properties of nonequilibrium polymer hydrogels obtained from the transient cross-linking of polymer chains by a chemical fuel were investigated. Aqueous polymers featuring pendant carboxylic acids were treated with a carbodiimide to give anhydride-cross-linked gels. The anhydrides spontaneously hydrolyze back to the polymer solution, and the cycle can be repeated multiple times. Oscillatory rheology was employed to study the effects of temperature, fuel concentration, chain length, and polymer composition on the storage and loss moduli of the polymeric materials as well as the time taken for the polymers to undergo decross-linking. Regardless of the temperature used, at constant carbodiimide concentration, degelation times are more sensitive to experimental temperature than are the peak storage moduli. Decross-linking times decrease with increasing temperature. As carbodiimide concentration decreases, there is a decrease in moduli and decross-linking times. Within the scope of materials studied, the polymer structure was found to have a relatively small impact on the transient properties of gel networks compared to the fuel concentration and temperature. Furthermore, these findings facilitate the design of tunable on-demand networks and gels.
36 MATERIALS SCIENCE↗
Programmable Matter: The Nanoparticle Atom and DNA Bond
Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the “atoms”) functionalized with DNA (the “bonding elements”), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the “atom” (e.g., the nanoparticle shape, size, and composition) and the “bond” (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. Here in this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.
36 MATERIALS SCIENCE↗
Structural insights into RNase H catalytic mechanism from room-temperature X-ray and neutron crystallography of apo- and RNA/DNA hybrid-bound enzyme
RNase H enzymes are sequence-nonspecific endonucleases that cleave RNA strands in RNA/DNA hybrid duplexes, an enzymatic process essential in DNA replication and repair in both prokaryotes and eukaryotes. Also, RNase H activity of the reverse transcriptase in human immunodeficiency viruses (HIV-1 and HIV-2) is indispensable for the viral replication cycle. RNase H enzymes play an central role in the development of gene therapies and are targets for novel antivirals. It is therefore of great importance to gain a detailed understanding of the RNase H catalytic mechanism to improve drug design. We utilized Bacillus halodurans RNase H1 (BhRNase H1) to shed light on its function and catalytic mechanism. Room-temperature neutron crystallography of the wild-type and inactive D132N mutant enzymes revealed that E109, belonging to the catalytic DEDD motif, can change its protonation state, allowing us to propose its role in the protonation of the leaving O3′ hydroxyl group of RNA. X-ray crystallography has demonstrated the ability of the RNA/DNA duplex to slide along the protein surface upon metal ion binding at site M A , transforming a product mimic into a Michaelis-like complex, which confirms an essential role of the M A metal ion in catalysis.
Enzyme mechanisms↗
Biochemical reconstitution and genetic characterization of the major oxidative damage base excision DNA repair pathway in Thermococcus kodakarensis
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Structural biology in the age of X-ray free-electron lasers and exascale computing
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Cyanobacterial Phycobilisome Allostery as Revealed by Quantitative Mass Spectrometry
Phycobilisomes (PBSs) are the major photosynthetic light-harvesting complexes in cyanobacteria and red algae. PBS, a multisubunit protein complex, has two major interfaces that comprise intrinsically disordered regions (IDRs): rod–core and core-membrane. IDRs do not form regular, three-dimensional structures on their own. Their presence in the photosynthetic pigment–protein complexes portends their structural and functional importance. A recent model suggests that PB-loop, an IDR located on the PBS subunit ApcE and C-terminal extension (CTE) of the PBS subunit ApcG, forms a structural protrusion on the PBS core-membrane side, facing the thylakoid membrane. Here, the structural synergy between the rod–core region and the core-membrane region was investigated using quantitative mass spectrometry (MS). The AlphaFold-predicted CpcG-CTE structure was first modeled onto the PBS rod–core region, guided and justified by the isotopically encoded structural MS data. Quantitative cross-linking MS analysis revealed that the structural proximity of the PB-loop in ApcE and ApcG-CTE is significantly disturbed in the absence of six PBS rods, which are attached to PBS via CpcG-CTE, indicative of drastic conformational changes and decreased structural integrity. Furthermore, these results suggest that CpcG-rod attachment on the PBS rod–core side is essentially required for the PBS core-membrane structural assembly. The hypothesized long-range synergy between the rod–core interface (where the orange carotenoid protein also functions) and the terminal energy emitter of PBS must have important regulatory roles in PBS core assembly, light-harvesting, and excitation energy transmission. These data also lend strategies that genetic truncation of the light-harvesting antennas aimed for improved photosynthetic productivity must rely on an in-depth understanding of their global structural integrity.
59 BASIC BIOLOGICAL SCIENCES↗