Thorough molecular configuration analysis of noncanonical AAV genomes in AAV vector preparations

The unique palindromic inverted terminal repeats (ITRs) and single-stranded nature of adeno-associated virus (AAV) DNA are major hurdles to current sequencing technologies. Due to these characteristics, sequencing noncanonical AAV genomes present in AAV vector preparations remains challenging. To address this limitation, we developed thorough molecule configuration analysis of noncanonical AAV genomes (TMCA-AAV-seq). TMCA-AAV-seq takes advantage of the documented AAV packaging mechanism in which encapsidation initiates from its 3' ITR, for AAV-seq library construction. Any AAV genome with a 3' ITR is converted to a template suitable to adapter addition by a Bst DNA polymerase-mediated extension reaction. This extension reaction helps fix ITR heterogeneity in the AAV population and allows efficient adapter addition to even noncanonical AAV genomes. The resulting library maintains the original AAV genome configurations without introducing undesired changes. Subsequently, long-read sequencing can be performed by the Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) sequencing technology platform. Finally, through comprehensive data analysis, we can recover canonical, noncanonical AAV DNA, and non-AAV vector DNA sequences, along with their molecular configurations. Our method is a robust tool for profiling thorough AAV-population genomes. TMCA-AAVseq can be further extended to all parvoviruses and their derivative vectors.

Exploring Efficient Dual-Phase Emissive Fluorophores with High Mobility by Integrating a Rigid Donor and Flexible Acceptor

Developing luminogens with a high emission efficiency in both single-molecule and aggregate states, as well as high mobility, shows promise for advancing the iteration and update of organic optoelectronic materials. However, achieving a delicate balance between the plane configuration of luminophores and the strong exciton interactions of aggregates is a formidable task from the molecular design perspective. This dilemma was overcome by integrating a rigid donor and flexible acceptor to establish donor-acceptor (D-A) type emitters. The π-conjugate-extended donor ensures the substantial planarity of these molecules, allowing strong emission in solution with photoluminescence quantum yield values of 86% and 75%. Furthermore, the restricted molecular motion of the aggregation-induced emission moiety and the formation of J-aggregates reduce the quenching effect, leading to a high emissive efficiency of 85% and 91% in the aggregate state. The mildly distorted D-A geometry builds moderate electrostatic interaction, resulting in high mobility with μM,h of 7.12 × 10-5 and 3.27 × 10-4 cm2/V s. Additionally, an improved synthesized procedure for terminal E-configured acrylonitrile with metal-free and concise reaction conditions is presented. The successful application of the synthesized compounds in organic light-emitting diode devices demonstrates the practicability of the molecular design strategy with connecting a rigid donor and flexible acceptor.

Understanding the Molecular Conformation and Viscoelasticity of Low Sol-Gel Transition Temperature Gelatin Methacryloyl Suspensions

For biomedical applications, gelatin is usually modified with methacryloyl groups to obtain gelatin methacryloyl (GelMA), which can be crosslinked by a radical reaction induced by low wavelength light to form mechanically stable hydrogels. The potential of GelMA hydrogels for tissue engineering has been well established, however, one of the main disadvantages of mammalian-origin gelatins is that their sol-gel transitions are close to room temperature, resulting in significant variations in viscosity that can be a problem for biofabrication applications. For these applications, cold-water fish-derived gelatins, such as salmon gelatin, are a good alternative due to their lower viscosity, viscoelastic and mechanical properties, as well as lower sol-gel transition temperatures, when compared with mammalian gelatins. However, information regarding GelMA (with special focus on salmon GelMA as a model for cold-water species) molecular conformation and the effect of pH prior to crosslinking, which is key for fabrication purposes since it will determine final hydrogel's structure, remains scarce. The aim of this work is to characterize salmon gelatin (SGel) and salmon methacryloyl gelatin (SGelMA) molecular configuration at two different acidic pHs (3.6 and 4.8) and to compare them to commercial porcine gelatin (PGel) and methacryloyl porcine gelatin (PGelMA), usually used for biomedical applications. Specifically, we evaluated gelatin and GelMA samples' molecular weight, isoelectric point (IEP), their molecular configuration by circular dichroism (CD), and determined their rheological and thermophysical properties. Results showed that functionalization affected gelatin molecular weight and IEP. Additionally, functionalization and pH affected gelatin molecular structure and rheological and thermal properties. Interestingly, the SGel and SGelMA molecular structure was more sensitive to pH changes, showing differences in gelation temperatures and triple helix formation than PGelMA. This work suggests that SGelMA presents high tunability as a biomaterial for biofabrication, highlighting the importance of a proper GelMA molecular configuration characterization prior to hydrogel fabrication.

Molecular Dynamics Simulation of the Synergistic Effect of Alkali/Surfactant/Polymer on the Formation and Stabilization of Water-Based Foam Systems

The stable maintenance effect of a chemical oil displacement agent on a foam liquid film usually creates problems with the oilfields surface system. To achieve comprehensive insights into the influence mechanism of these chemical agent components on the foam liquid film, an "SDBS/HPAM/OH^-" water-based foam simulation system and corresponding control systems were constructed by adjusting the categories and quantities of component molecules by molecular dynamics (MD) simulation. The simulated results indicated that the foam stability follows the order of "SDBS/HPAM/OH^-" system > "SDBS/HPAM" system > "SDBS" system. The smaller the inclination angle of the SDBS molecular tail chain, the greater the tendency of the SDBS molecular configuration to be "upright" at the gas-liquid interface, which is not conducive to preventing the aggregation and penetration of gas molecules at the gas-liquid interface. Although the presence of HPAM molecules can significantly enhance the stability of the liquid film by restricting the liquid film's drainage and the diffusion of gas molecules, the addition of HPAM molecules would weaken the formation ability of the foam liquid film. Through decreasing the aggregation of cations around the co-adsorption layer, OH^- not only enhances the interfacial activity of SDBS molecules, but also reduces the electrostatic repulsion between -COO^- groups on the HPAM molecular chain, which makes the foam more stable. With an increase in the pH, SDBS concentration, and HPAM concentration, the stability of foam liquid film was strengthened. These results are helpful in facilitating new insights into the formation and stabilization mechanism of water-based foams. In particular, they provide support for the development and application of new defoaming technologies.

Diammonium Molecular Configuration-Induced Regulation of Crystal Orientation and Carrier Dynamics for Highly Efficient and Stable 2D/3D Perovskite Solar Cells

The effects from the molecular configuration of diammonium spacer cations on 2D/3D perovskite properties are still unclear. Here, we investigated systematically the mechanism of molecular configuration-induced regulation of crystallization kinetic and carrier dynamics by employing various diammonium molecules to construct Dion-Jacobson (DJ)-type 2D/3D perovskites to further facilitating the photovoltaic performance. The minimum average Pb-I-Pb angle leads to the smallest octahedral tilting of [PbX₆ ]^4- lattice in optimal diammonium molecule-incorporated DJ-type 2D/3D perovskite, which enables suitable binding energy and hydrogen-bonding between spacer cations and inorganic [PbX₆ ]^4- cages, thus contributing to the formation of high-quality perovskite film with vertical crystal orientation, mitigatory lattice distortion and efficient carrier transportation. As a consequence, a dramatically improved device efficiency of 22.68 % is achieved with excellent moisture stability.

Effect of Material Properties on the Foaming Behaviors of PP-Based Wood Polymer Composites Prepared with the Application of Spherical Cavity Mixer

For the low weight and high strength, the microcellular extrusion foaming technology was applied in the preparation of polypropylene (PP)-based wood polymer composites, and the spherical cavity mixer was used to construct an experimental platform for the uniform dispersion of wood flour (WF). The effects of PP molecular configuration on the composite properties and cell morphology of samples were also investigated. The experimental results indicated that the application of a spherical cavity mixer with a cavity radius of 5 mm could effectively improve the mixing quality and avoid the agglomeration of WF. In addition, compared with the branched molecule, the linear molecule not only increased the melting temperature by about 10 °C, but also endowed composites with a higher complex viscosity at a shear rate lower than 100 s⁻¹, which contributed to the cell morphology of more microporous samples.

Bandgap Engineering of an Aryl-Fused Tetrathianaphthalene for Visible-Blind Organic Field-Effect Transistors

Stability problem of organic semiconductors (OSCs) because of photoabsorption has become a major barrier to large scale applications in organic field-effect transistors (OFETs). It is imperative to design OSCs which are insensitive to visible and near-infrared (VNIR) light to obtain both environmental and operational stability. Herein, taking a 2,3,8,9-tetramethoxy [1,4]benzodithiino[2,3-b][1,4]benzodithiine (TTN2) as an example, we show that controlling molecular configuration is an effective strategy to tune the bandgaps of OSCs for visible-blind OFETs. TTN2 adopts an armchair-like configuration, which is different from the prevailing planar structure of common OSCs. Because of the large bandgap, TTN2 exhibits no photoabsorption in the VNIR region and OFETs based on TTN2 show high environmental stability. The devices worked well after being stored in ambient air, (i.e. in the presence of oxygen and water) and light for over two years. Moreover, the OFETs show no observable response to light irradiation from 405–1,020 nm, which is also favorable for high operational stability.

Vinylene-Bridged Cyclic Dipyrrin and BODIPY Trimers

Vinylene-bridged cyclic boron–difluoride complex of dipyrrin (BODIPY) trimers were successfully prepared from expanded dimethyl-vinylene bridged hexaphyrin(2.1.2.1.2.1) Me-Hex that has the structure of alternate dipyrrins and vinylene bridges. The hexaphyrin(2.1.2.1.2.1) Me-Hex can coordinate with boron ions to afford five kinds of cyclic BODIPYs given by step-by-step boron complexations. Crystal structures of all cyclic BODIPYs except for 3BF₂-Me-Hex(b) formed non-planar structures. The theoretical calculation predicted that mono-/bis-boron cyclic BODIPYs show the intramolecular charge transfer (ICT) characteristics, whereas tri-boron cyclic BODIPYs have no ICT characteristics. Reflecting these electronic properties, tri-boron cyclic BODIPYs exhibit weak fluorescence in the red region, but mono-/bis-boron cyclic BODIPYs exhibit no emission. Vinylene bridged cyclic dipyrrin trimer Me-Hex is the novel porphyrinoid ligand allowed to control the boron coordination under different reaction conditions to form various boron complexes.

Significantly Enhanced Thermoelectric Properties of Organic-Inorganic Hybrids with a Periodically Ordered Structure

The deficient order in amorphous components severely affects the thermoelectric (TE) properties in polymers. Encouragingly, two-dimensional layered double hydroxides (LDHs) have been regarded as an efficient host material to tune the conformation of guest molecules and construct ordered hybrids. Herein, we report a facile construction of periodically ordered organic-inorganic TE hybrids by alternative stacking of inorganic LDH nanosheets and organic poly(3,4-ethylenedioxythiophene)-poly(styrene sulfonate) (PEDOT:PSS) molecules. The ordered structure of PEDOT:PSS-LDH gave rise to the extended molecular configuration of PEDOT:PSS, resulting in the improved carrier mobility in the hybrids. Moreover, the energy filtering was induced by such a periodically ordered structure, which blocked the low-energy carriers preferentially and improved the Seebeck coefficient in the hybrids. Therefore, the power factor of the PEDOT:PSS-LDH hybrid was 120-fold higher than that of pristine PEDOT:PSS. These results not only establish an effective method for the construction of periodically ordered TE materials but also address the significance of an ordered structure of molecules in TE materials.

Glycerol Phosphate Cytidylyltransferase Stereospecificity Is Key to Understanding the Distinct Stereochemical Compositions of Glycerophosphoinositol in Bacteria and Archaea

Glycerophosphoinositol (GPI) is a compatible solute present in a few hyperthermophiles. Interestingly, different GPI stereoisomers accumulate in Bacteria and Archaea, and the basis for this domain-dependent specificity was investigated herein. The archaeon Archaeoglobus fulgidus and the bacterium Aquifex aeolicus were used as model organisms. The synthesis of GPI involves glycerol phosphate cytidylyltransferase (GCT), which catalyzes the production of CDP-glycerol from CTP and glycerol phosphate, and di-myo-inositol phosphate-phosphate synthase (DIPPS), catalyzing the formation of phosphorylated GPI from CDP-glycerol and l-myo-inositol 1-phosphate. DIPPS of A. fulgidus recognized the two CDP-glycerol stereoisomers similarly. This feature and the ability of ³¹P nuclear magnetic resonance (NMR) to distinguish the GPI diastereomers provided a means to study the stereospecificity of GCTs. The AF1418 gene and genes aq_185 and aq_1368 are annotated as putative GCT genes in the genomes of A. fulgidus and Aq. aeolicus, respectively. The functions of these genes were determined by assaying the activity of the respective recombinant proteins: AQ1368 and AQ185 are GCTs, while AF1418 has flavin adenine dinucleotide (FAD) synthetase activity. AQ185 is absolutely specific for sn-glycerol 3-phosphate, while AQ1368 recognizes the two enantiomers but has a 2:1 preference for sn-glycerol 3-phosphate. In contrast, the partially purified A. fulgidus GCT uses sn-glycerol 1-phosphate preferentially (4:1). Significantly, the predominant GPI stereoforms found in the bacterium and the archaeon reflect the distinct stereospecificities of the respective GCTs: i.e., A. fulgidus accumulates predominantly sn-glycero-1-phospho-3-l-myo-inositol, while Aq. aeolicus accumulates sn-glycero-3-phospho-3-l-myo-inositol.

IMPORTANCE

Compatible solutes of hyperthermophiles show high efficacy in thermal protection of proteins in comparison with solutes typical of mesophiles; therefore, they are potentially useful in several biotechnological applications. Glycerophosphoinositol (GPI) is synthesized from CDP-glycerol and l-myo-inositol 1-phosphate in a few hyperthermophiles. In this study, the molecular configuration of the GPI stereoisomers accumulated by members of the Bacteria and Archaea was established. The stereospecificity of glycerol phosphate cytidylyltransferase (GCT), the enzyme catalyzing the synthesis of CDP-glycerol, is crucial to the stereochemistry of GPI. However, the stereospecific properties of GCTs have not been investigated thus far. We devised a method to characterize GCT stereospecificity which does not require sn-glycerol 1-phosphate, a commercially unavailable substrate. This led us to understand the biochemical basis for the distinct GPI stereoisomer composition observed in archaea and bacteria.

Chirality and numbering of substituted tropane alkaloids

The strict application of IUPAC rules for the numbering of tropane alkaloids is not always applied by authors and there is hence a lot of confusion in the literature. In most cases, the notation of 3, 6/7-disubstituted derivatives has been chosen arbitrarily, based on NMR and MS data, without taking into account the absolute configuration of these two carbons. This paper discusses the problem and the relevance of CD and NMR to determine molecular configurations. We report on the use of (1)H-NMR anisochrony (Δδ) induced by the Mosher's chiral auxiliary reagents (R)-(-)- and (S)-(+)-α-methoxy-α-trifluoromethyl-phenylacetyl chlorides (MTPA-Cl), to determine the absolute configuration of (3R,6R)-3α-hydroxy-6β-senecioyloxytropane, a disubstituted tropane alkaloid isolated from the aerial parts of Schizanthus grahamii (Solanaceae). These analytical tools should help future works in correctly assigning the configuration of additional 3, 6/7 disubstituted tropane derivatives.

Tandem inverted repeats in mitochondrial DNA of petite mutants of Saccharomyces cerevisiae

Denatured mitochondrial DNA (mtDNA) from a grande (wild-type) yeast strain and a series of derived genetically characterized cytoplasmic petite mutants was examined in the electron microscope as DNA-protein monolayers prepared under conditions that permitted little bimolecular renaturation. In the grande and some petite strains, the mtDNA remained predominantly single-stranded. However, in several petite strains, a large proportion of molecules contained double-stranded segments indicative of unimolecular renaturation due to the presence of inverted repeat sequences. The length of the double-stranded segments of strain E41 was compared to the periodicity seen on denaturation maps. A repeat spacing twice the length of the inverted repeats was observed in the denaturation map. Inverted repeat length was similar to contour length of circular mtDNA molecules in this strain. On the basis of these observations most of the mtDNA from petite strain E41 appeared to consist of polymers of tandem inverted repeats interspersed with a small single-stranded "spacer" sequence between the repeat segments. In contrast, petite strain F13 mtDNA had few or no inverted repeats and showed a regular periodicity of 0.14 mum in the denaturation map, similar in length to the 0.13-mum circles present in the isolated mtDNA.