Structure- and interaction-based design of anti-SARS-CoV-2 aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptorbinding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variant

Magnetic Circular Dichroism Analysis of Crude Oil

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Optical and magneto-optical properties of solutions of crude oil of different origin (i.e., taken from different fields) are studied in the visible and near-UV region of optical emission. Magnetic circular dichroism (MCD) spectra of oil are obtained in the vicinity of wavelengths of ∼ 410 nm, 533 nm, and 576 nm. It is demonstrated that the intensity of the MCD signal depends on the origin of crude oil, and it is proportional to the oil concentration in the solution. The comparison of the magneto-optical spectroscopy data with the chemical composition of samples allows us to conclude that the observed magneto-optical activity is determined by the presence of VO2+ complexes in the oil samples studied. The revealed magneto-optical activity of conventional oil can form a basis of a new method for the analysis of the composition and properties of oil of different origin

Magnetic circular dichroism of CdTe nanoparticles

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Magnetic circular dichroism (MCD) of water-soluble CdTe nanoparticles was observed in the visible spectral range for the first time. Diameter of nanoparticles varied from 2.3 to 4.5nm. Absorption and photoluminescence spectra were also recorded. Absorption line at 19400cm−1and luminescent line at 18200cm−1were observed. Splitting of value 960 cm−1was revealed in the MCD spectrum. Approximately the same splitting was extracted from the absorption spectrum. The MCD was identified as the temperature independent paramagnetic mixing effect. Nature of the absorption line and of its splitting are discussed

Magnetic Circular Dichroism Analysis of Crude Oil

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Optical and magneto-optical properties of solutions of crude oil of different origin (i.e., taken from different fields) are studied in the visible and near-UV region of optical emission. Magnetic circular dichroism (MCD) spectra of oil are obtained in the vicinity of wavelengths of ∼ 410 nm, 533 nm, and 576 nm. It is demonstrated that the intensity of the MCD signal depends on the origin of crude oil, and it is proportional to the oil concentration in the solution. The comparison of the magneto-optical spectroscopy data with the chemical composition of samples allows us to conclude that the observed magneto-optical activity is determined by the presence of VO2+ complexes in the oil samples studied. The revealed magneto-optical activity of conventional oil can form a basis of a new method for the analysis of the composition and properties of oil of different origin

Optical and magneto-optical properties of FeₓGa₁₋ₓBO₃ crystals

The single crystals of FeₓGa₁₋ₓBO₃ with 0 ⁴Eg, ⁴A₁g d-d transitions and its temperature dependence were measured in the crystal containing 67 % of Fe for the first time

Aptamer-conjugated superparamagnetic ferroarabinogalactan nanoparticles for targeted magnetodynamic therapy of cancer

Nanotechnologies involving physical methods of tumor destruction using functional oligonucleotides are promising for targeted cancer therapy. Our study presents magnetodynamic therapy for selective elimination of tumor cells in vivo using DNA aptamer-functionalized magnetic nanoparticles exposed to a low frequency alternating magnetic field. We developed an enhanced targeting approach of cancer cells with aptamers and arabinogalactan. Aptamers to fibronectin (AS-14) and heat shock cognate 71 kDa protein (AS-42) facilitated the delivery of the nanoparticles to Ehrlich carcinoma cells, and arabinogalactan (AG) promoted internalization through asialoglycoprotein receptors. Specific delivery of the aptamer-modified FeAG nanoparticles to the tumor site was confirmed by magnetic resonance imaging (MRI). After the following treatment with a low frequency alternating magnetic field, AS-FeAG caused cancer cell death in vitro and tumor reduction in vivo. Histological analyses showed mechanical disruption of tumor tissues, total necrosis, cell lysis, and disruption of the extracellular matrix. The enhanced targeted magnetic theranostics with the aptamer conjugated superparamagnetic ferroarabinogalactans opens up a new venue for making biocompatible contrasting agents for MRI imaging and performing non-invasive anti-cancer therapies with a deep penetrated magnetic field