Scope of this thesis is the computational, molecular modeling study of interactions between nucleic acids and organic compounds like bis-phenanthridinium derivatives, guanidiniocarbonyl-pyrrole-aryl conjugates, phosphonium dyes and translation (benzimidazole and diaminopiperidine) inhibitors of hepatitis C virus. They bind to polynucleotide in specific way, either as intercalators orgroovebindersandin addition establishstrong electrostatic interactions with polynucleotides. The first three groups of compounds have ability of molecular recognition of nucleobases so they can be used eitheras a template for development of thenew,highly specific nucleic acids markersor antiviral drugs with the ability to selectively block transcription of specific DNA/RNA sequences. Starting points for modeling were results of spectroscopic measurements(UV-Vis and CD spectra, fluorimetric titrations) and X-ray and NMR analysis. Study wasperformed using molecular modeling methods of various degrees of complexity.In order to determinate new parameters quantum mechanics calculations were used. The study of the structure and flexibility of nucleic acids and their complexes with small organic molecules was performed using the force field methods (molecular mechanics and molecular dynamics), while influence of the nucleic acid environment, precisely polynucleotide strand and metal ions, on the ligand charge distribution was investigated by the combined quantum mechanics –molecular mechanics approach. The results obtained within the research arein accordance with the experimental findings.