Aptamer's Structure Optimization for Better Diagnosis and Treatment of Glial Tumors.

Oncological diseases are a major focus in medicine, with millions diagnosed each year, leading researchers to seek new diagnostic and treatment methods. One promising avenue is the development of targeted therapies and rapid diagnostic tests using recognition molecules. The pharmaceutical industry is increasingly exploring nucleic acid-based therapeutics.

Using Computer Modeling and Experimental Methods to Screen for Aptamers That Bind to the VV-GMCSF-LACT Virus.

Oncolytic virotherapy is a promising approach for cancer treatment. However, when introduced into the body, the virus provokes the production of virus-neutralizing antibodies, which can reduce its antitumor effect. To shield viruses from the immune system, aptamers that can cover the membrane of the viral particle are used.

Visualization of Brain Tumors with Infrared-Labeled Aptamers for Fluorescence-Guided Surgery.

Gliomas remain challenging brain tumors to treat due to their infiltrative nature. Accurately identifying tumor boundaries during surgery is crucial for successful resection. This study introduces an innovative intraoperative visualization method utilizing surgical fluorescence microscopy to precisely locate tumor cell dissemination.

Characterizing Aptamer Interaction with the Oncolytic Virus VV-GMCSF-Lact.

Aptamers are currently being investigated for their potential to improve virotherapy. They offer several advantages, including the ability to prevent the aggregation of viral particles, enhance target specificity, and protect against the neutralizing effects of antibodies. The purpose of this study was to comprehensively investigate an aptamer capable of enhancing virotherapy.

Effects of Endohedral Gd-Containing Fullerenols with a Different Number of Oxygen Substituents on Bacterial Bioluminescence.

Gadolinium (Gd)-containing fullerenols are perspective agents for magnetic resonance imaging and cancer research. They combine the unique paramagnetic properties of Gd with solubility in water, low toxicity and antiradical activity of fullerenols. We compared the bioeffects of two Gd-containing fullerenols with a different number of oxygen groups-20 and 42: Gd@COH and Gd@COH.

Synthesis, Photo- and Electroluminescence of New Polyfluorene Copolymers Containing Dicyanostilbene and 9,10-Dicyanophenanthrene in the Main Chain.

Using palladium-catalyzed Suzuki polycondensation, we synthesized new light-emitting fluorene copolymers containing the dicyano derivatives of stilbene and phenanthrene and characterized them by gel permeation chromatography, UV-vis absorption spectroscopy, spectrofluorimetry, and cyclic voltammetry. The photoluminescence spectra of the synthesized polymers show significant energy transfer from the fluorene segments to the dicyanostilbene and 9,10-dicyanophenanthrene units, which is in agreement with the data of theoretical calculations. OLEDs based on these polymers were fabricated with an ITO/PEDOT-PSS (35 nm)/p-TPD (30 nm)/PVK (5 nm)/light emitting layer (70-75 nm)/PF-PO (20 nm)/LiF (1 nm)/Al (80 nm) configuration.

Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples.

Breast cancer (BC) diagnostics lack noninvasive methods and procedures for screening and monitoring disease dynamics. Admitted CellSearch is used for fluid biopsy and capture of circulating tumor cells of only epithelial origin. Here we describe an RNA aptamer (MDA231) for detecting BC cells in clinical samples, including blood.

Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells.

Here, we present DNA aptamers capable of specific binding to glial tumor cells , , and for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies.

Structure and Vibrational Spectroscopy of C Fullerenol Valent Isomers: An Experimental and Theoretical Joint Study.

Gd@COH endohedral complexes for advanced biomedical applications (computer tomography, cancer treatment, etc.) were synthesized using high-frequency arc plasma discharge through a mixture of graphite and GdO oxide. The Gd@C endohedral complex was isolated by high-efficiency liquid chromatography and consequently oxidized with the formation of a family of Gd endohedral fullerenols with gross formula Gd@CO(OH).

Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics.

The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein.

Ca-Triggered Coelenterazine-Binding Protein Renilla: Expected and Unexpected Features.

Ca-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay.

Nucleic Acid Aptamers Increase the Anticancer Efficiency and Reduce the Toxicity of Cisplatin-Arabinogalactan Conjugates .

Cisplatin is an effective drug for treating various cancer types. However, it is highly toxic for both healthy and tumor cells. Therefore, there is a need to reduce its therapeutic dose and increase targeted bioavailability.

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.

C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography- computed tomography.

Identification of primary tumors and metastasis sites is an essential step in cancer diagnostics and the following treatment. Positron emission tomography-computed tomography (PET/CT) is one of the most reliable methods for scanning the whole organism for malignancies. In this work, we synthesized an C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer.

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer.

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity.

Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time-dependent density functional theory.

Active hydromedusan and ctenophore Ca-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460-470 nm, ctenophore photoproteins absorb at 437 nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein-substrate complex was optimized using a linear scaling quantum-mechanical method.

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.

Charge-transfer plasmons with narrow conductive molecular bridges: A quantum-classical theory.

We analyze a new type of plasmon system arising from small metal nanoparticles linked by narrow conductive molecular bridges. In contrast to the well-known charge-transfer plasmons, the bridge in these systems consists only of a narrow conductive molecule or polymer in which the electrons move in a ballistic mode, showing quantum effects. The plasmonic system is studied by an original hybrid quantum-classical model accounting for the quantum effects, with the main parameters obtained from first-principles density functional theory simulations.

Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C-Met by Proteolytic Affinity-Mass Spectrometry.

C-Met protein is a glycosylated receptor tyrosine kinase of the hepatocyte growth factor (HGF), composed of an α and a β chain. Upon ligand binding, C-Met transmits intracellular signals by a unique multi-substrate docking site. C-Met can be aberrantly activated leading to tumorigenesis and other diseases, and has been recognized as a biomarker in cancer diagnosis.

Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation.

Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR).

Estimation of the thermal and photochemical stabilities of pheromones.

The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value L corresponding to the breaking of the bond under temperature excitation. The kinetic stability calculation only requires the eigenfrequencies and vibrational mode vectors in the molecule ground state to be calculated, without determining the transition states.

Two-dimensional hexagonal CrN with promising magnetic and optical properties: A theoretical prediction.

Half-metallic ferromagnetic materials with planar forms are promising for spintronics applications. A wide range of 2D lattices like graphene, h-BN, transition metal dichalcogenides, etc. are non-magnetic or weakly magnetic.

Ultraviolet fluorescence of coelenteramide and coelenteramide-containing fluorescent proteins. Experimental and theoretical study.

Coelenteramide-containing fluorescent proteins are products of bioluminescent reactions of marine coelenterates. They are called 'discharged photoproteins'. Their light-induced fluorescence spectra are variable, depending considerably on external conditions.

[Stability of lepidopterous pheromone molecules of forest insects to environmental factors].

The interactions of the pheromones of some representatives of the Lepidoptera order with each other and with materials contained in the forest air, as well as the effect of electromagnetic radiation on pheromone have been studied. It was found that the reactions of pheromones with substances contained in the forest air are irreversible and proceed with the liberation of heat. Electromagnetic radiation affects very strongly the structure of pheromones.

[The mechanism of formation of emitter by fluorescence of calcium-discharged obelin].

It is known that bioluminescence of obelin is triggered by Ca2+ the binding of which to the protein induces the decarboxylation of 2-hydroperoxycoelenterazine. The molecular mechanism of fluorescence of obelin, which determines the fluorescence of see hydroid Obelia Longissima, has been investigated with the use of quantum chemical calculations. According to quantum chemical calculations, the emitter of the reaction is the ion-pair state of phenolate-anion of coelenteramide.