Many small organic molecules, non-covalent fluorescent sensors for the recognition of DNA, RNA or proteins, are of great importance for biomedical diagnostics and molecular biology research. In this work, we have investigated the interactions of three different groups of non-covalent fluorescent markers using UV/Vis spectroscopy, fluorescence and circular dichroism as well as temperature denaturation with DNA, RNA and BSA. The first group are analogues of the tryptophan-histidine-tryptophan (WHW) peptide, characterized by the replacement of histidine with triazolyl-alanine, and in the two new analogs one tryptophan is replaced by pyrenes. These analogues retained a high affinity of WHW peptide towards the Cu2+ cation, but also a significantly higher affinity towards DNA, RNA and BSA. Pyrene analogues cleave DNA under UV light, due to the formation of singlet oxygen. The cytotoxicity of the synthesized compounds was tested in collaboration with Dr. Majhen from the Ruđer Bošković Institute. It was found that WHW peptide analogues showed weak toxicity in vitro on malignant tumor cells and normal human fibroblasts, which was significantly increased for pyrene analogs under UV light. The second group of non-covalent fluorescent labels is based on bis-triarylboranes, which have been shown to detect and differentiate DNA, RNA, and BSA at high sensitivity in 10 nM concentrations simultaneously using fluorescence and surface-enhanced Raman spectroscopy (SERS). Investigated tetracationic bis-triarylboranes with a long bis(phenylethynyl)aryl linker exhibited strong stabilization of ds-DNA and ds-RNA in the temperature denaturation experiment, while the short anthracene analog showed weaker stabilization, highlighting the importance of the length and flexibility of the aromatic linker. Circular dichroism (CD) results showed that the compound with a 9,10-anthracene aryl linker caused unwinding of the helical structure of polynucleotides upon binding and very uniform orientation relative to the helical axis of the polynucleotide. For the third group of polycationic calixarenes and neutral analogs, it was demonstrated that they exhibit fluorescence in an aqueous medium, an unknown property of calixarenes until now. Additionally, it was shown that all compounds bind mononucleotides (NMP) with high affinity, forming a 'tweezer-like' complex. The obtained response is selective towards pyrimidine bases (uracil monophosphate and cytosine monophosphate). Only cationic analogs interact with DNA and RNA, indicating the significance of electrostatic interactions with the polyanionic backbone of DNA/RNA. The displacement experiment of DAPI from DNA grooves conducted using circular dichroism (CD) also showed better displacement with cationic calixarenes. Additional circular dichroism experiments showed that the insertion of calixarenes does not significantly affect the double helix structure.