Institute of
bioorganic chemistry

Scientists from IBCH together with the colleagues from Federal Research Center for Physical and Chemical Medicine developed an i-motif-based pH sensor. The authors synthesized a new non- fluorescent cytosine analogue, tC O Azo , which quenches the fluorescence of the known fluorescent cytosine mimic, tC O . Incorporation of the pair into a genomic iM-forming sequence C5T resulted in a high-contrast pH sensor with a working range compatible with physiological conditions. Unlike known C5T-based sensors, which contain conventional FAM/BHQ or FAM/TAMRA labels, provide a fluorescent signal in the green/red channels and accumulate in cell nuclei, the proposed sensor localized mainly in the cytoplasm and allowed pH monitoring based on the tC O signal in the blue channel. Thus, the authors managed to overcome the common problem of preferential accumulation in the nuclei of living cells for labeled nucleic acids (antisense oligonucleotides, molecular beacons, etc.). The work was published in Sensors and Actuators: B. Chemical.

The scientists from the IBCh RAS proposed the autologous system of the hCMV-derived VMAPRTLFL (LFL) peptide stimulation without T lymphocytes and exogenous cytokines which allows to evaluate NK cell hCMV-specific responses. NK cells of individuals having high anti-hCMV-IgG levels, in contrast to NK cells of hCMV-seronegative and low-positive donors, displayed increased IFNγ production, degranulation and activation levels, and enhanced proliferation upon stimulation with the LFL peptide, presented in HLA-E. LFL-induced NK cell IFNγ production was dependent on PI3K and Ras/Raf/Mek signaling pathways. Transcriptomic profile of LFL-expanded NK cells showed increased adaptive gene expression and metabolic activation. This model may be further exploited for the identification of antigen-specific NK cells. The results are published in the Cells.

To achieve control over the formation of a biomolecular corona, it is necessary to control the surface properties of nanoparticles (NPs). Hence, approaches to study the structure and dynamics of NPs surface with high resolution are required. Researchers from IBCh RAS and IC RAS proposed to generate topography maps of NPs surface from MD simulation data, and applied them to analyze the surface structure and dynamics of ligand-containing core–shell NPs. It has been shown that topography maps of NPs surface allow one to evaluate properties important for drug delivery systems. The work was published in the Biomaterials Science journal. Preprint available at ChemRxiv.

The scientists from the Department of functioning of living systems IBCh RAS demonstrated the involvement of early (nucleolar) ribosome biogenesis factors RPF1 and ESF1 in the maturation of ribosomal subunits. shRNA-mediated knockdown of these proteins demonstrated a unique change in the pre-rRNAs profile. These proteins in human cells, unlike yeast cells, are not vital, which allows us to argue about the probable rearrangement of the process to maintain the translational activity of cells. Based on the results obtained, authors suggest that the RPF1 and ESF1 proteins perform a structural function and contribute to the correct folding of RNA-protein complexes for further stages of pre-rRNA processing. The results are published in Cells. Learn more

Researchers from the Laboratory of molecular bioengineering IBCh RAS, in collaboration with colleagues from other Russian institutions, have isolated and characterized two new virulent phages of the Obolenskvirus genus, which infect Acinetobacter baumannii, a significant nosocomial pathogen. The phages, named Brutus and Scipio, were capable of infecting A. baumannii strains corresponding to capsular types K116 and K82, respectively. The authors described the biological properties and genomic organization of the phages, and conducted comparative genomic, phylogenetic, and pangenomic analyses. Furthermore, they investigated the enzymatic activity of the tailspike depolymerase encoded in the genome of phage Scipio, marking the first registered virus to infect A. baumannii of the K82 capsular type. The exploration of new representatives within the Obolenskvirus genus enhances our understanding of the diversity of viruses in this taxonomic group and the interaction strategies between Obolenskvirus phages and their host bacteria. This work has been published in the International Journal of Molecular Sciences.