This bachelor’s thesis addresses the issue of non-canonical local structures in nucleic acids, specifically G-quadruplexes, in the genomes of selected pathogens transmitted by the castor bean tick (Ixodes ricinus). The aim of the thesis was to detect and characterize sequences with the potential to form G-quadruplexes (PQS) in tick-borne encephalitis virus (TBEV) and bacteria of the genus Borrelia. In the first part, an extensive in silico analysis was performed using seven different bioinformatics tools (G4Hunter, Pqsfinder, G-QINDER, DeepG4, QUFIND, Quadron, and G4Catchall) to evaluate the frequency and spatial distribution of these motifs. The results showed that despite its smaller size, the TBEV genome exhibits an order of magnitude higher relative density of PQS than the Borrelia genome, which directly correlates with a higher guanine and cytosine content. Furthermore, the analysis revealed a non-random distribution of these structures. In Borrelia, PQS significantly accumulate in promoter regions of non-coding RNAs. In TBEV, PQS were detected at the boundaries of non-structural protein‑coding regions (e.g., NS2a/NS2b, NS4b/RdRp). In the second part of the study, a selected TBEV viral sequence was experimentally tested in vitro based on the results of in silico analysis. Using fluorescence binding assays with Thioflavin T (ThT) and N‑methylmesoporphyrin IX (NMM) probes and circular dichroism (CD) spectroscopy, the ability of this sequence to form a thermodynamically stable G-quadruplex, which preferentially adopts an antiparallel topology in the presence of potassium cations, was confirmed. The findings suggest that G-quadruplexes could represent significant regulatory elements in these pathogens and potential targets for future antimicrobial and antiviral therapies.