Thermodynamics of interaction of aromatic ligand with single-stranded DNA: H NMR analysis of complex formation between ethidium bromide and non-complementary isomeric deoxytetranucleotides 5′-d(CGAA) and 5′-d(AAGC)

The temperature dependences of the proton chemical shifts of the phenantridine dye ethidium bromide in the mixture with the non-complementary isomeric deoxytetranucleotides 5'-d(CGAA) and 5'-d(AAGC) have been studied in aqueous solutions by 500 MHz spectroscopy. The methods of calculation giving an opportunity to determine differentially the thermodynamic parameters of the formation of various types of the complexes in solution have been used. The free Gibbs energies, enthalpies and entropies of the reactions of 1:1, 2:1 and 1:2 complexes formation between ethidium bromide and tetranucleotides have been determined. Comparative analysis of the calculated thermodynamic parameters of the dye binding with the isomeric sequences has been made, it is concluded that there is sequence-selective interaction of ethidium bromide with single-stranded deoxytetranucleotides in solution.