A thermodynamic analysis of ethidium bromide interaction with non-complementary deoxytetranucleotides 5 '-D(CpTpGpA) and 5 '-D(GpApApG) by the H-1 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 - d ye - ethidium bromide - with non-complementary deoxytetranucleotides 5'-d(G TGA) and 5'-d(GAAG). The employed calculation procedures enabled the thermo dynamic parameters (Gibbs free energy, enthalpy, and entropy) of the reacti ons producing 1:1, 2:1, and 1:2 ethidium bromide:tetranucleotide complexes in solutions to be determined independently. The values of the thermodynami c parameters for dye interactions with deoxytetranucleotide d(GAAG) contain ing only purine bases in its chain are much lower than the appropriate para meters for reactions involving tetramer d(CTGA) whose chain contains a pyri midine-purine d(T-G) segment. This result suggests that there is a sequence -specificity in bonding of an aromatic dye with single-chain oligonucleotid e sequences. The nature of intermolecular interactions leading to formation of the complexes in solutions is analyzed.