Small molecules able to preferentially bind to specific hybrid and multistranded structures of DNA and RNA by non-covalent interactions are of great scientific interest when it comes to obtaining new and better diagnostic and therapeutic tools. Although these structures have an important biological function inside the cell, there is only a few known ligands which preferentially bind to them. The goal of this thesis is to find new structural motifs/compounds that preferentially bind to hybrid and multistranded structures compared to regular DNA and RNA structures. A small library of several groups of compounds was formed: benzothiazole derivatives and cyanine dyes obtained in collaboration with other research groups. Also, interactions of newly synthesized phenanthridine derivatives with DNA were investigated. Compounds with preferential binding to hybrid and multistranded structures of DNA and RNA were selected using competitive dialysis as a rapid screening method, as well as with melting of mixtures and RNase H assay. Further bioanalytical methods (flourescence and UV/Vis spectroscopy and circular dichroism) were used to characterize their binding interactions with selected targets in detail. The obtained results indicate that certain derivatives from the mentioned classes of compounds preferentially bind to hybrid and multistranded structures of DNA and RNA compared to regular ones, which opens the possibility of their application in antitumor therapy and for the detection of nucleic acid structures.