A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern

We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS-CoV-2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one-round SELEX experiments using five different trimeric spike proteins from variants, followed by high-throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed K_d values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS-CoV-2 with K_d values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well-suited for molecular recognition of rapidly evolving targets such as those found in SARS-CoV-2.     

MNDO Study of reaction pathways for SN2 reactions. Menschutkin reaction potential energy surfaces

MNDO molecular orbital calculations have been employed to investigate limited reaction pathways and potential energy surfaces for a series of S_N2 reactions. Model calculations for X^? + CH₃X (X = H, F, OH, OCH₃, and CN) indicate that the MNDO method gives qualitative agreement with ab initio studies except for the hydride–CH₄ exchange. Studies involving alkylation of pyridine (Menschutkin reaction) were also carried out. For the reaction of pyridine with CH₃Cl, which involves charge separation, our MNDO studies (which do not include solvation effects) do not produce a characteristic S_N2 pathway. For the reaction of pyridine with trimethyloxonium cation [(CH₃)₃O⁺] as the alkylating agent, a well defined S_N2 reaction pathway was obtained; this reaction involves charge transfer. A potential energy surface for the pyridine–trimethyloxonium cation reaction shows the presence of a saddle point transition state that resembles starting materials, in agreement with the Hammond postulate for this exothermic reaction.     

Determination of total gaseous selenium in atmosphere by honeycomb denuder/differential pulse cathodic stripping voltammetry

A new analytical method has been developed for the determination of total gaseous selenium in the atmosphere by honeycomb denuder collection followed by differential pulse cathodic stripping voltammetry (DPCSV) measurement. Gaseous selenium was collected in a denuder coating solution containing 2% HNO(3) and 2% glycerine. The soluble product, selenious acid, was then extracted by water for DPCSV analysis. The collection efficiency for gaseous selenium was 99.1% at a flow rate of 1 l min(-1) for 3 h. Excellent linearity in DPCSV was maintained up to Se concentration of 40 ng ml(-1). This was equivalent to a working concentration of 220 ng m(-3) of selenium in the atmosphere. A precision of 1.26% RSD (n=5) for 5 ng Se was obtained, and the detection limit (3sigma) and the quantitative determination limit were estimated to be 0.96 and 3.19 ng m(-3). The average recovery of selenium in three standard samples prepared by independent digestion of NIST SRM 1648 (Urban Particulate Matter) using our analytical system was 99.0%. The total content of gaseous selenium in the atmosphere of our laboratories was 3.2-4.4 ng m(-3).     

A pyrophosphate-responsive gadolinium(III) MRI contrast agent

This study shows that the relaxivity and optical properties of functionalised lanthanide‐DTPA‐bis‐amide complexes (lanthanide=Gd³⁺ and Eu³⁺, DTPA=diethylene triamine pentaacetic acid) can be successfully modulated by addition of specific anions, without direct Ln³⁺/anion coordination. Zinc(II)‐dipicolylamine moieties, which are known to bind strongly to phosphates, were introduced in the amide “arms” of these ligands, and the interaction of the resulting Gd–Zn₂ complexes with a range of anions was screened by using indicator displacement assays (IDAs). Considerable selectivity for polyphosphorylated species (such as pyrophosphate and adenosine‐5′‐triphosphate (ATP)) over a range of other anions (including monophosphorylated anions) was apparent. In addition, we show that pyrophosphate modulates the relaxivity of the gadolinium(III) complex, this modulation being sufficiently large to be observed in imaging experiments. To establish the binding mode of the pyrophosphate and gain insight into the origin of the relaxometric modulation, a series of studies including UV/Vis and emission spectroscopy, luminescence lifetime measurements in H₂O and D₂O, ¹⁷O and ³¹P NMR spectroscopy and nuclear magnetic resonance dispersion (NMRD) studies were carried out.     

Biomimetic Bottlebrush Polymer Coatings for Fabrication of Ultralow Fouling Surfaces

Demand for long‐lasting antifouling surfaces has steered the development of accessible, novel, biocompatible and environmentally friendly materials. Inspired by lubricin (LUB), a component of mammalian synovial fluid with excellent antifouling properties, three block polymers offering stability, efficacy, and ease of use were designed. The bottlebrush‐structured polymers adsorbed strongly on silica surfaces in less than 10 minutes by a simple drop casting or online exposure method and were extremely stable in high‐salinity solutions and across a wide pH range. Antifouling properties against proteins and bacteria were evaluated with different techniques and ultralow fouling properties demonstrated. With serum albumin and lysozyme adsorption <0.2 ng cm^?2, the polymers were 50 and 25 times more effective than LUB and known ultralow fouling coatings. The antifouling properties were also tested under MPa compression pressures by direct force measurements using surface forces apparatus. The findings suggest that these polymers are among the most robust and efficient antifouling agents currently known.     

A mesoporous Pt/TiO2 nanoarchitecture with catalytic and photocatalytic functions

A novel metal/semiconductor nanocomposite with catalytic and photocatalytic functions has been prepared. The new material consists of highly dispersed platinum (Pt) nanoparticles embedded in a cubic mesoporous nanocrystalline anatase (meso-nc-TiO2) thin film. The porous thin film possesses a narrow pore-size distribution and a large surface area. The diameter of the Pt cluster can be controlled to below 5 nm, and the high dispersion of these clusters gives rise to catalytic activity for the oxidation of carbon monoxide, an important reaction for automobile exhaust treatment. This novel ordered mesoporous Pt/TiO2 nanoarchitecture is also a promising photochemical material, as demonstrated by the photo-driven killing of Micrococcus lylae cells on the film.     

On the Origin of the Visible‐Light Activity of Titanium Dioxide Doped with Carbonate Species

Plane‐wave‐based pseudopotential density functional theory (DFT) calculations are used to elucidate the origin of the high photocatalytic efficiency of carbonate‐doped TiO₂. Two geometrically possible doping positions are considered, including interstitial and substitutional carbon atoms on Ti sites. From the optical absorption properties calculations, we believe that the formation of carbonates after doping with interstitial carbon atoms is crucial, whereas the contribution from the cationic doping on Ti sites is negligible. The carbonate species doped TiO₂ exhibits excellent absorption in the visible‐light region of 400–800 nm, in good agreement with experimental observations. Electronic structure analysis shows that the carbonate species introduce an impurity state from Ti 3d below the conduction band. Excitations from the impurity state to the conduction band may be responsible for the high visible‐light activity of the carbon doped TiO₂ materials.     

Target‐Induced and Equipment‐Free DNA Amplification with a Simple Paper Device

We report on a paper device capable of carrying out target‐induced rolling circle amplification (RCA) to produce massive DNA amplicons that can be easily visualized. Interestingly, we observed that RCA was more proficient on paper than in solution, which we attribute to a significantly higher localized concentration of immobilized DNA. Furthermore, we have successfully engineered a fully functional paper device for sensitive DNA or microRNA detection via printing of all RCA‐enabling molecules within a polymeric sugar film formed from pullulan, which was integrated with the paper device. This encapsulation not only stabilizes the entrapped reagents at room temperature but also enables colorimetric bioassays with minimal steps.     

Molecular and vibrational structure of the extracellular bacterial signal compound N-butyryl-homoserine lactone (C4-HSL)

The molecular and vibrational structure of the title compound (C4-HSL) was studied by experimental and theoretical methods. The infrared (IR) absorption spectrum was measured in the solid state and in CCl₄ suspension. The observed absorption bands were compared with transitions obtained with B3LYP/cc-pVTZ density functional theory (DFT) calculations. Two stable molecular conformations were predicted, corresponding to an endo- and an exo-conformer with similar energies. Intermolecular amide–amide hydrogen bonding in the crystal state was approximated by a simple cluster model, leading to excellent agreement with the observed solid state IR spectrum. Due to the low solubility of C4-HSL in common solvents for IR spectroscopy, such as CS₂ and CCl₄, a liquid solution spectrum of pure, monomeric C4-HSL was not obtained. However, absorbance peaks observed in oversaturated CCl₄ solution could be assigned to distinct contributions from suspended micro-crystalline aggregates and dissolved monomeric species. The key vibrational bands of the monomeric form of C4-HSL are reported here for the first time: 3425 cm^?1 [ν(N–H)], 1784 cm^?1 [ν(CO), lactone], 1688 cm^?1 [amide I], and 1494 cm^?1 [amide II] (CCl₄).     

Acid-Catalyzed E-Ring Expansion and Isomerization of 3-Acetylbetulin: Synthesis of Cytotoxic Anhydrobetulin Saponins

22(17 → 28)abeo-Lupene derivatives 5a and 6a were obtained after the acid-catalyzed E-ring expansion of 3-acetylbetulin (1a). Glycosylation of these dehydrated triterpenoids using Schmidt's trichloroacetimidate sugar donors in the presence of trimethylsilyl trifluoromethanesulfonate (TMSOTf) provided the new anhydrobetulin saponins 7b–7e in which the terminal olefin C-20(29) isomerizes to form a C-19 tetrasubstituted alkene. The preliminary cytotoxic evaluation revealed that saponins 7b–7d exhibited a moderate cytotoxic activity against A549, DLD-1, and WS1 human cell lines with IC₅₀ ranging from 22 to 49 μM.