A thermodynamic analysis of ethidium bromide interaction with non-complementary deoxytetranucleotides 5′-D(CpTpGpA) and 5′-D(GpApApG) by the 1H NMR data

A pulse NMR spectrometer (500 MHz) is used to study temperature dependences of the chemical shifts of protons in solutions of a phenanthridine dye - dye - ethidium bromide - with non-complementary deoxytetranucleotides 5'-d(GTGA) and 5'-d(GAAG). The employed calculation procedures enabled the thermodynamic parameters (Gibbs free energy, enthalpy, and entropy) of the reactions producing 1:1, 2:1, and 1:2 ethidium bromide:tetranucleotide complexes in solutions to be determined independently. The values of the thermodynamic parameters for dye interactions with deoxytetranucleotide d(GAAG) containing only purine bases in its chain are much lower than the appropriate parameters for reactions involving tetramer d(CTGA) whose chain contains a pyrimidine-purine d(T-G) segment. This result suggests that there is a sequence-specificity in bonding of an aromatic dye with single-chain oligonucleotide sequences. The nature of intermolecular interactions leading to formation of the complexes in solutions is analyzed.