Pakhomov V. Hairpin and duplex forms of deoxyoligonucleotides and their complexes with aromatic ligands in aqueous solution

1H-1H and 1H-31P correlation NMR spectroscopy have been used to investigate the physical mechanisms of formation of hairpin and duplexes of DNA octa-, hepta- and hexamers and their comlexes with ethidium bromide and daunomycin. The equilibrium constants and thermodymamic parameters of complexation of the oligomers with the aromatic drugs have been determined. Structures of the molecular complexes have been calculated taking into consideration the intermolecular NOE contacts in conjunction with the determined values of magnetic shielding of the ligand protons in the complexes. The conclusions about sequence-specificity of intercalative binding of aromatic ligands with the deoxyoligonucleotides and about the intermolecular forces stabilising complexes in solution have been made. The obtained results may be used in the field of biophysics, molecular and medical physics.