Efficient room temperature catalytic synthesis of alternating conjugated copolymers via C-S bond activation

Structural defects in conjugated copolymers are severely detrimental to the optoelectronic properties and the performance of the resulting electronic devices fabricated from them. Therefore, the much-desired precision synthesis of conjugated copolymers with highly regular repeat units is important, but presents a significant challenge to synthetic materials chemists. To this end, aryl sulfides are naturally abundant substances and offer unrealized potential in cross-coupling reactions. Here we report an efficient room temperature polycondensation protocol which implements aryl disulfide C-S activation to produce defect-minimized semiconducting conjugated copolymers with broad scope and applicability. Thus, a broad series of arylstannanes and thioethers are employed via the present protocol to afford copolymers with number-average molecular weights (Mns) of 10.0–45.0 kDa. MALDI and NMR analysis of selected copolymers reveals minimal structural defects. Moreover, the polymer trap density here is smaller and the field effect mobility higher than that in the analogous polymer synthesized through thermal-activation Stille coupling.

Synthesis of a Möbius carbon nanobelt

New technologies for the creation of topological carbon nanostructures have significantly advanced synthetic organic chemistry and materials science. While simple molecular nanocarbons with a belt topology have been constructed recently, analogous carbon nanobelts with a twist, i.e., Möbius carbon nanobelts (MCNBs), have not yet been synthesized due to their high intrinsic strain. Herein, we report the synthesis, isolation, and characterization of a MCNB. Calculations of strain energies suggested that large MCNBs are synthetically accessible. Designing a macrocyclic precursor with an odd number of repeat units led to a successful rational synthetic route via Z-selective Wittig reactions and nickel-mediated intramolecular homocoupling reactions, which yielded (25,25)MCNB over 14 steps. NMR and theoretical calculations revealed that the twist moiety of the Möbius band moves quickly around the MCNB molecule in solution. The topological chirality originating from the Möbius structure was confirmed experimentally using chiral HPLC separation and CD spectroscopy.

Cryo-EM structure provides insights into the dimer arrangement of the O-linked β-N-acetylglucosamine transferase OGT

The O-linked β-N-acetylglucosamine modification is a core signalling mechanism, with erroneous patterns leading to cancer and neurodegeneration. Although thousands of proteins are subject to this modification, only a single essential glycosyltransferase catalyses its installation, the O-GlcNAc transferase, OGT. Previous studies have provided truncated structures of OGT through X-ray crystallography, but the full-length protein has never been observed. Here, we report a 5.3 Å cryo-EM model of OGT. We show OGT is a dimer, providing a structural basis for how some X-linked intellectual disability mutations at the interface may contribute to disease. We observe that the catalytic section of OGT abuts a 13.5 tetratricopeptide repeat unit region and find the relative positioning of these sections deviate from the previously proposed, X-ray crystallography-based model. We also note that OGT exhibits considerable heterogeneity in tetratricopeptide repeat units N-terminal to the dimer interface with repercussions for how OGT binds protein ligands and partners.

Superior Gas Barrier Properties of Biodegradable PBST vs. PBAT Copolyesters: A Comparative Study

As a bio-based counterpart of poly(butylene adipate-co-terephthalate) (PBAT), the well-known commercially available biodegradable aliphatic-aromatic copolyester, poly(butylene succinate-co-terephthalate) (PBST) has comparable physical and mechanical properties, but its gas barrier properties, which are very important for packaging material and mulch film applications, have not yet been reported in literature. In this paper, the O2, CO2 and water vapor barrier properties of PBST vs. PBAT were comparatively studied and reported for the first time. Theoretical calculation of O2 and CO2 permeation coefficients via group contribution method was also conducted. The barrier properties of PBST show clear copolymer composition dependence due to different contribution of BS and BT repeat units and composition-dependent crystallinity. Comparing with PBAT, PBST with close copolymer and three-phase (crystalline, amorphous, rigid amorphous) compositions shows 3.5 times O2 and CO2 and 1.5 times water vapor barrier properties. The slower segment movement and less free volume of PBST, and therefore slower gas diffusion in PBST, accounts for its superior O2 and CO2 barrier, while the better hydrophilicity of PBST counteracts partial contribution of slower segment movement so that the improvement in water vapor barrier is not as high as in O2 and CO2 barrier.

Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions

Several strongly conserved DNA sequence patterns in and between introns and intergenic regions (IIRs) consisting of short tandem repeats (STRs) with repeat lengths <3 bp have already been described in the kingdom of Animalia. In this work, we expanded the search and analysis of conserved DNA sequence patterns to a wider range of eukaryotic genomes. Our aims were to confirm the conservation of these patterns, to support the hypothesis on their functional constraints and/or the identification of unknown patterns. We pairwise compared genomic DNA sequences of genes, exons, CDS, introns and intergenic regions of 34 Embryophyta (land plants), 30 Protista and 29 Fungi using established k-mer-based (alignment-free) comparison methods. Additionally, the results were compared with values derived for Animalia in former studies. We confirmed strong correlations between the sequence structures of IIRs spanning over the entire domain of Eukaryotes. We found that the high correlations within introns, intergenic regions and between the two are a result of conserved abundancies of STRs with repeat units ≤2 bp (e.g., (AT)n). For some sequence patterns and their inverse complementary sequences, we found a violation of equal distribution on complementary DNA strands in a subset of genomes. Looking at mismatches within the identified STR patterns, we found specific preferences for certain nucleotides stable over all four phylogenetic kingdoms. We conclude that all of these conserved patterns between IIRs indicate a shared function of these sequence structures related to STRs.

Precise Characterization of Bombyx mori Fibroin Heavy Chain Gene Using Cpf1-Based Enrichment and Oxford Nanopore Technologies

To study the evolution of gene function and a species, it is essential to characterize the tandem repetitive sequences distributed across the genome. Cas9-based enrichment combined with nanopore sequencing is an important technique for targeting repetitive sequences. Cpf1 has low molecular weight, low off-target efficiency, and the same editing efficiency as Cas9. There are numerous studies on enrichment sequencing using Cas9 combined with nanopore, while there are only a few studies on the enrichment sequencing of long and highly repetitive genes using Cpf1. We developed Cpf1-based enrichment combined with ONT sequencing (CEO) to characterize the B. mori FibH gene, which is composed of many repeat units with a long and GC-rich sequence up to 17 kb and is not easily amplified by means of a polymerase chain reaction (PCR). CEO has four steps: the dephosphorylation of genomic DNA, the Cpf1 targeted cleavage of FibH, adapter ligation, and ONT sequencing. Using CEO, we determined the fine structure of B. moriFibH, which is 16,845 bp long and includes 12 repetitive domains separated by amorphous regions. Except for the difference of three bases in the intron from the reference gene, the other sequences are identical. Surprisingly, many methylated CG sites were found and distributed unevenly on the FibH repeat unit. The CEO we established is an available means to depict highly repetitive genes, but also a supplement to the enrichment method based on Cas9.

Identification of a region in Shigella flexneri WzyB disrupting the interaction with Wzz pHS2

Shigella flexneri can synthesise polysaccharide chains having complex sugars and a regulated number of repeating units. S. flexneri lipopolysaccharide O antigen (Oag) is synthesised by the Wzy-dependent pathway which is the most common pathway used in bacteria for polysaccharide synthesis. The inner membrane protein WzyB polymerizes the Oag repeat units into chains, while the polysaccharide co-polymerases WzzB and Wzz pHS2 determine the average number of repeat units or “the modal length”, termed short-type and very long-type. Our data show for the first time a direct interaction between WzyB and Wzz pHS2 , with and without the use of the chemical cross-linker dithiobis (succinimidyl propionate) (DSP). Additionally mutations, generated via random and site directed mutagenesis, identify a region of WzyB that caused diminished function and significantly decreased very-long Oag chain polymerisation, and that affected the aforementioned interaction. These results provide insight into the mechanisms underlying the regulation of Oag biosynthesis. Importance Complex polysaccharide chains are synthesised by bacteria, usually at a regulated number of repeating units, which has broad implications for bacterial pathogenesis. One example is the O antigen (Oag) component of lipopolysaccharide that is predominantly synthesised by the Wzy-dependent pathway. Our findings show for the first time a direct physical interaction between WzyB and Wzz pHS2 . Additionally, a set of Wzy mutant constructs were generated revealing a proposed active site/switch region involved in the activity of WzyB and the physical interaction with Wzz pHS2 . Combined, these findings further the understanding of the Wzy-dependent pathway. The identification of a novel interaction with the polysacchraride co-polymerase Wzz pHS2, and the region of WzyB that is involved in this aforementioned interaction and its impact on WzyB Oag synthesis activity, have significant implication for the prevention/treatment of bacterial diseases, and discovery of novel biotechnologies.

Zeolite-like performance for xylene isomer purification using polymer-derived carbon membranes

Polymers of intrinsic microporosity (PIMs) have been used as precursors for the fabrication of porous carbon molecular sieve (CMS) membranes. PIM-1, a prototypical PIM material, uses a fused-ring structure to increase chain rigidity between spirobisindane repeat units. These two factors inhibit effective chain packing, thus resulting in high free volume within the membrane. However, a decrease of pore size and porosity was observed after pyrolytic conversion of PIM-1 to CMS membranes, attributed to the destruction of the spirocenter, which results in the “flattening” of the polymer backbone and graphite-like stacking of carbonaceous strands. Here, a spirobifluorene-based polymer of intrinsic microporosity (PIM-SBF) was synthesized and used to fabricate CMS membranes that showed significant increases in p-xylene permeability (approximately four times), with little loss in p-xylene/o-xylene selectivity (13.4 versus 14.7) for equimolar xylene vapor separations when compared to PIM-1–derived CMS membranes. This work suggests that it is feasible to fabricate such highly microporous CMS membranes with performances that exceed current state-of-the-art zeolites at high xylene loadings.

Application of PCR-HRM method for microsatellite polymorphism genotyping in the LDHA gene of pigeons (Columba livia)

High-resolution melting (HRM) is a post-PCR method that allows to discriminate genotypes based on fluorescence changes during the melting phase. HRM is used to detect mutations or polymorphisms (e.g. microsatellites, SNPs, indels). Here, the (TTTAT)3-5 microsatellite polymorphism within intron 6 of the LDHA gene in pigeons was analysed using the HRM method. Individuals (123 homing pigeons) were genotyped using conventional PCR. Birds were classified into groups based on genotype type and the results were tested by qPCR-HRM and verified using sequencing. Based on the evaluated protocol, five genotypes were identified that vary in the number of TTTAT repeat units (3/3, 4/4, 3/4, 4/5, and 5/5). Sequencing have confirmed the results obtained with qPCR-HRM and verified that HRM is a suitable method for identification of three-allele microsatellite polymorphisms. It can be concluded that the high-resolution melting (HRM) method can be effectively used for rapid (one-step) discrimination of the (TTTAT)3-5 microsatellite polymorphism in the pigeon’s LDHA gene.