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.     

Slow-light fourier transform interferometer

We describe a new type of Fourier transform (FT) interferometer in which the tunable optical delay between the two arms is realized by using a continuously variable slow-light medium instead of a moving arm as in a conventional setup. The spectral resolution of such a FT interferometer exceeds that of a conventional setup of comparable size by a factor equal to the maximum group index of the slow-light medium. The scheme is experimentally demonstrated by using a rubidium atomic vapor cell as the tunable slow-light medium, and the spectral resolution is enhanced by a factor of approximately 100.     

Subcentimeter depth resolution using a single-photon counting time-of-flight laser ranging system at 1550 nm wavelength

We demonstrate subcentimeter depth profiling at a stand off distance of 330 m using a time-of-flight approach based on time-correlated single-photon counting. For the first time to our knowledge, the photon-counting time-of-flight technique was demonstrated at a wavelength of 1550 nm using a superconducting nanowire single-photon detector. The performance achieved suggests that a system using superconducting detectors has the potential for low-light-level and eye-safe operation. The system's instrumental response was 70 ps full width at half-maximum, which meant that 1 cm surface-to-surface resolution could be achieved by locating the centroids of each return signal. A depth resolution of 4 mm was achieved by employing an optimized signal-processing algorithm based on a reversible jump Markov chain Monte Carlo method.     

Structurally Modelling the 2-His-1-Carboxylate Facial Triad with a Bulky N,N,O Phenolate Ligand

We present the synthesis and coordination chemistry of a bulky, tripodal N,N,O ligand, Im^Ph2NNO ^{t Bu} ( L ), designed to model the 2-His-1-carboxylate facial triad (2H1C) by means of two imidazole groups and an anionic 2,4-di-tert-butyl-subtituted phenolate. Reacting K-L with MCl₂ (M = Fe, Zn) affords the isostructural, tetrahedral non-heme complexes [Fe(L)(Cl)] ( 1 ) and [Zn(L)(Cl)] ( 2 ) in high yield. The tridentate N,N,O ligand coordination observed in their X-ray crystal structures remains intact and well-defined in MeCN and CH₂Cl₂ solution. Reacting 2 with NaSPh affords a tetrahedral zinc thiolate complex, [Zn(L)(SPh)] ( 4 ), that is relevant to isopenicillin N synthase (IPNS) biomimicry. Cyclic voltammetry studies demonstrate the ligand's redox non-innocence, where phenolate oxidation is the first electrochemical response observed in K-L , 2 and 4 . However, the first electrochemical oxidation in 1 is iron-centred, the assignment of which is supported by DFT calculations. Overall, Im^Ph2NNO ^{t Bu} provides access to well-defined mononuclear, monoligated, N,N,O-bound metal complexes, enabling more accurate structural modelling of the 2H1C to be achieved.     

Tunable Linear and Nonlinear Optical Properties from Room Temperature Phosphorescent Cyclic Triimidazole-Pyrene Bio-Probe

Organic materials with multiple emissions tunable by external stimuli represent a great challenge. TTPyr, crystallizing in different polymorphs, shows a very rich photophyisics comprising excitation-dependent fluorescence and phosphorescence at ambient conditions, and mechanochromic and thermochromic behavior. Transformation among the different species has been followed by thermal and X-ray diffraction analyses and the emissive features interpreted through structural results and DFT/TDDFT calculations. Particularly intriguing is the polymorph TTPyr(HT), serendipitously obtained at high temperature but stable also at room temperature, whose non-centrosymmetric structure guarantees an SHG efficiency 10 times higher than that of standard urea. Its crystal packing, where only the TT units are strongly rigidified by π-π stacking interactions while the Pyr moieties possess partial conformational freedom, is responsible for the observed dual fluorescence. The potentialities of TTPyr for bioimaging have been successfully established.     

Compressive Mass Analysis on Quadrupole Ion Trap Systems

Conventionally, quadrupole ion trap mass spectrometers eject ions of different mass-to-charge ratio (m/z) in a sequential fashion by performing a scan of the rf trapping voltage amplitude. Due to the inherent sparsity of most mass spectra, the detector measures no signal for much of the scan time. By exploiting this sparsity property, we propose a new compressive and multiplexed mass analysis approach—multi Resonant Frequency Excitation (mRFE) ejection. This new approach divides the mass spectrum into several mass subranges and detects all the subrange spectra in parallel for increased mass analysis speed. Mathematical estimation of standard mass spectrum is demonstrated while statistical classification on the parallel measurements remains viable because of the sparse nature of the mass spectra. This method can reduce mass analysis time by a factor of 3–6 and increase system duty cycle by 2×. The combination of reduced analysis time and accurate compound classification is demonstrated in a commercial quadrupole ion trap (QIT) system.

A Direct CH/ArH Coupling Approach to Oxindoles,Thio‐oxindoles, 3,4‐Dihydro‐1 H‐quinolin‐2‐ones,and 1,2,3,4‐Tetrahydroquinolines

A copper(II)‐catalysed approach to oxindoles, thio‐oxindoles, 3,4‐dihydro‐1H‐quinolin‐2‐ones, and 1,2,3,4‐tetrahydroquinolines via formal C?H, Ar?H coupling is described. In a new variant, copper(II) 2‐ethylhexanoate has been identified as an inexpensive and efficient catalyst for this transformation, which utilises atmospheric oxygen as the re‐oxidant.     

Cooperative,Reversible Self‐Assembly of Covalently Pre‐Linked Proteins into Giant Fibrous Structures

We demonstrate a simple bioconjugate polymer system that undergoes reversible self‐assembling into extended fibrous structures, reminiscent of those observed in living systems. It is comprised of green fluorescent protein (GFP) molecules linked into linear oligomeric strands through click step growth polymerization with dialkyne poly(ethylene oxide) (PEO). Confocal microscopy, atomic force microscopy, and dynamic light scattering revealed that such strands form high persistence length fibers, with lengths reaching tens of micrometers, and uniform, sub‐100 nm widths. We ascribe this remarkable and robust form of self‐assembly to the cooperativity arising from the known tendency of GFP molecules to dimerize through localized hydrophobic patches and from their covalent pre‐linking with flexible PEO. Dissipative particle dynamics simulations of a coarse‐grained model of the system revealed its tendency to form elongated fibrous aggregates, suggesting the general nature of this mode of self‐assembly.     

Gold‐Catalyzed Diastereoselective Cycloisomerization of Alkylidene‐Cyclopropane‐Bearing 1,6‐Diynes

An unprecedented gold‐catalyzed diastereoselective cycloisomerization of 1,6‐diynes bearing an alkylidene cyclopropane moiety has been developed. This methodology enables rapid access to a variety of 1,2‐trimethylenenorbornanes, which are important building blocks in the preparations of abiotic and sesquiterpene core structures.