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.     

Development of capillary zone electrophoresis-electrospray ionization-mass spectrometry for the determination of lamotrigine in human plasma

A method of coupling capillary zone electrophoresis (CZE) with electrospray ionization-mass spectrometry (ESI-MS) detection has been developed for monitoring an antiepileptic drug, lamotrigine (LTG) in human plasma. The CZE-MS was developed in three stages: (i) CZE separation and ESI-MS detection of LTG and tyramine (TRM, internal standard) were simultaneously optimized by studying the influence of CZE background electrolyte (BGE) pH, BGE ionic strength, and nebulizer pressure of the MS sprayer; (ii) sheath liquid parameters, such as pH, ionic strength, organic modifier content, and flow rate of the sheath liquid, were systematically varied under optimum CZE-MS conditions developed in the first stage; (iii) MS sprayer chamber parameters (drying gas temperature and drying gas flow rate) were varied for the best MS detection of LTG. The developed assay was finally applied for the determination of LTG in plasma samples. The linear range of LTG in plasma sample assay was between 0.1-5.0 microg/mL with a limit of detection as low as 0.05 microg/mL and run time less than 6 min. Finally, the concentration-time profile of LTG in human plasma sample was found to correlate well when CZE-ESI-MS was compared to a more established method of high-performance liquid chromatography with ultraviolet detection.     

Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.     

Sequential non-linear least-square estimation for damage identification of structures with unknown inputs and unknown outputs

The detection of structural damages real-time on-line, based on vibration data measured from sensors, is an important but challenging research topic, and it has received considerable attentions recently. Due to practical limitations, it is highly desirable to install as few sensors as possible in the structural health monitoring system, leading to incomplete measurements of structural responses and excitations. The traditional time-domain analysis techniques, such as the least-square estimation (LSE) method and the extended Kalman filter (EKF) approach, require that all the external excitations (inputs) be available, which may not be the case for most structural health monitoring systems. Recently, the adaptive sequential non-linear least-square estimate (SNLSE) method has been proposed for the on-line identification of structural damages. In this paper, we extend the SNLSE method to cover the general case with unknown (unmeasured) excitations (inputs) and unknown (unmeasured) acceleration responses (outputs) in order to reduce the number of sensors required in the structural health monitoring system, referred to as the SNLSE-UI-UO. Analytic recursive solutions for the new approach are derived and presented. The accuracy and effectiveness of the proposed approach have been demonstrated using the Phase I ASCE structural health monitoring benchmark building, a 5-degree-of-freedom non-linear hysteretic building model, and a 3-story steel frame finite-element model. Simulation results indicate that the proposed approach is capable of tracking the changes of structural parameters leading to the identification of damages.     

Infrared depletion spectra of 2-aminopyridine2-pyridone, a Watson-Crick mimic of adenine.uracil

The 2-aminopyridine2-pyridone (2AP2PY) dimer is linked by N-H...O=C and N-H...N hydrogen bonds, providing a model for the Watson-Crick hydrogen bond configuration of the adenine.thymine and adenine.uracil nucleobase pairs. Mass-specific infrared spectra of 2AP2PY and its seven N-H deuterated isotopomers have been measured between 2550 and 3650 cm(-1) by IR laser depletion combined with UV two-color resonant two-photon ionization. The 2PY amide N-H stretch is a very intense band spread over the range 2700-3000 cm(-1) due to large anharmonic couplings. It is shifted to lower frequency by 710 cm(-1) or approximately 20% upon H bonding to 2AP. On the 2AP moiety, the "bound" amino N-H stretch gives rise to a sharp band at 3140 cm(-1), which is downshifted by 354 cm(-1) or approximately 10% upon H bonding to 2PY. The amino group "free" N-H stretch and the H-N-H bend overtone are sharp bands at approximately 3530 cm(-1) and 3320 cm(-1). Ab initio structures and harmonic vibrations were calculated at the Hartree-Fock level and with the PW91 and B3LYP density functionals. The PW91/6-311++G(d,p) method provides excellent predictions for the frequencies and IR intensities of all the isotopomers.     

Modulated synthesis of Zr-based metal-organic frameworks: from nano to single crystals

We present an investigation on the influence of benzoic acid, acetic acid, and water on the syntheses of the Zr-based metal-organic frameworks Zr-bdc (UiO-66), Zr-bdc-NH(2) (UiO-66-NH(2)), Zr-bpdc (UiO-67), and Zr-tpdc-NH(2) (UiO-68-NH(2)) (H(2) bdc: terephthalic acid, H(2) bpdc: biphenyl-4,4'-dicarboxylic acid, H(2) tpdc: terphenyl-4,4'-dicarboxylic acid). By varying the amount of benzoic or acetic acid, the synthesis of Zr-bdc can be modulated. With increasing concentration of the modulator, the products change from intergrown to individual crystals, the size of which can be tuned. Addition of benzoic acid also affects the size and morphology of Zr-bpdc and, additionally, makes the synthesis of Zr-bpdc highly reproducible. The control of crystal and particle size is proven by powder XRD, SEM and dynamic light scattering (DLS) measurements. Thermogravimetric analysis (TGA) and Ar sorption experiments show that the materials from modulated syntheses can be activated and that they exhibit high specific surface areas. Water proved to be essential for the formation of well-ordered Zr-bdc-NH(2) . Zr-tpdc-NH(2), a material with a structure analogous to that of Zr-bdc and Zr-bpdc, but with the longer, functionalized linker 2'-amino-1,1':4',1'-terphenyl-4,4'-dicarboxylic acid, was obtained as single crystals. This allowed the first single-crystal structural analysis of a Zr-based metal-organic framework.     

Sequential non-linear least-square estimation for damage identification of structures

An early detection of structural damage is an important goal of any structural health monitoring system. In particular, the ability to detect damages on-line, based on vibration data measured from sensors, will ensure the reliability and safety of the structures. In this connection, innovative data analysis techniques for the on-line damage detection of structures have received considerable attentions recently, although the problem is quite challenging. In this paper, we proposed a new data analysis method, referred to as the sequential non-linear least-square (SNLSE) approach, for the on-line identification of structural parameters. This new approach has significant advantages over the extended Kalman filter (EKF) approach in terms of the stability and convergence of the solution as well as the computational efforts involved. Further, an adaptive tracking technique recently proposed has been implemented in the proposed SNLSE to identify the time-varying system parameters of the structure. The accuracy and effectiveness of the proposed approach have been demonstrated using the Phase I ASCE structural health monitoring benchmark building, a non-linear elastic structure and non-linear hysteretic structures. Simulation results indicate that the proposed approach is capable of tracking on-line the changes of structural parameters leading to the identification of structural damages.