[Thermodynamic analysis of complex formation of ethidium bromide with DNA in water solutions].

A thermodynamic analysis of two types of binding of ethidium bromide with DNA: intercalation and binding to the outer surface of a biopolymer has been performed by spectrophotometry. It has been shown that the dominant contribution to the energy of external binding of the ligand to DNA is made by hydrophobic interactions, which lead to less negative values of enthalpy and entropy and more severe negative changes in the heat capacity of complex formation as compared with the intercalation type of binding.

[1H NMR study of the complexation of the quinolone antibiotic norfloxacin with DNA].

Complexation of antibiotic norfloxacin (NOR) with DNA fragments 5'-d(TpGpCpA) and 5'-d(CpGpCpG) has been studied in aqueous solution by 1H NMR spectroscopy (500 MHz). Equilibrium parameters of the complexation with single-stranded and duplex forms of DNA oligomer--equilibrium constants, enthalpy and entropy--have been obtained for the first time. Based on the analysis of the complexation parameters as well as induced chemical shifts of the antibiotic protons within different complexes, it was found that NOR binds with the tetramer duplexes mainly by intercalation. The complexation with the single-stranded form may occur either by intercalation and external binding. The site of preferential binding of the antibiotic with DNA duplex is GC site.

[Analysis of complex formation of daunomycin with the deoxyhexanucleotide 5'-d(TpApCpGpTpA) in an aqueous solution from NMR-spectroscopy data]. / Analiz kompleksoobrazovaniia daunomitsina s dezoksigeksanukleotidom 5'-d(TpApCpGpTpA) v vodom rastvore po dannym IaMR-spektroskopii.

Self-association of hexadeoxynucleotide 5'-d(TpApCpGpTpA) and its complexation with antitumor antibiotic daunomycin were studied by one- and two-dimensional homonuclear 1H NMR spectroscopy and heteronuclear 1H-31P NMR spectroscopy in water-salt solution. The concentration and temperature dependences of proton chemical shifts of the hexadeoxynucleotide and the ligand were measured, and equilibrium constants and thermodynamic parameters of corresponding reactions were calculated on this basis using models for the formation of hexadeoxynucleotide duplex and its complex with the antibiotic. The spatial structure of daunomycin-d(TACGTA)2 complex in solution was calculated using X-PLOR software on the basis of 2D NOE spectral data and the limit values of proton chemical shifts of the ligand. Comparative analysis of different intermolecular interactions in sequence-specific binding of the antibiotic to the DNA fragment was carried out.

[1H-NMR study of complex formation between the aromatic dye ethidium bromide and the single-stranded noncomplementary deoxytetranucleotide 5'-d(CpTpGpA) in aqueous solution]. / Issledovaniie kompleksoobrazovaniia aromaticheskogo krasitelia bromistogo etidiia s odnotsepochechnym nekomplementarnym dezoksi tetranucleotidom 5'-d(CpTpGpA) v vodnom rastvore metodom 1H IaMR -spektroskopii.

Complex formation between the aromatic dye ethidium bromide (3,8-diamino-6-phenyl-5-ethylphenanthridine) and the single-stranded noncomplementary deoxytetranucleotide 5'-d(CpTpGpA) in aqueous solution was studied by one- and two-dimensional 1H NMR spectroscopy (500 and 600 MHz). Complete assignments of proton signals from the deoxytetranucleotide 5'-d(CTGA) were made using 2D-TOCSY and 2D-NOESY spectra. The concentration dependences of proton chemical shifts of the tetranucleotide were measured at T = 298 K to determine the self-association constants of tetranucleotide molecules in solution. Due to a small probability of tetranucleotide duplex formation, the complexing of dye molecules with the monomer of the tetramer plays the main role in the equilibrium of the complex in solution, which makes it possible to analyze the specificity of interactions of the aromatic ligand with the single-stranded DNA. Different schemes of complex formation were examined, and equilibrium constants for the reactions and the limiting chemical shifts of dye protons in different complexes were determined. The relative content of different types of complexes was analyzed, and specific features of the dynamic equilibrium were revealed as a function of the dye-tetranucleotide concentration ratio. The analysis indicates a sequence-specific binding of ethidium bromide to the single-stranded oligonucleotide. The structures of 1:1 complexes of the dye with the single strand of the tetranucleotide that correspond to two most probable orientations of the dye chromophore in the pyrimidine-purine T-G-site of the tetramer base sequence were constructed using the calculated values of induced chemical shifts of ethidium bromide protons.

[Study of complex formation of ethidium bromide with the self-complementary deoxytetranucleotide 5'-d(ApGpCpT) by unidimensional and two- dimensional 1H NMR spectroscopy]. / Issledovanie kompleksoobrazovaniia bromistogo étidiia s samokomplementarnym dezoksitetranukleotidom 5'-d(ApGpCpT) metodom odnomernoi i dvumernoi 1H IaMR-spektroskopii.

Complex formation of ethidium bromide (3,8-diamino-6-phenyl-5-ethyl-phenanthridine) with the self-complementary desoxytetraribonucleosidetriphosphate d(ApGpCpT) was studied in aqueous solution by uni- and two-dimensional 1H NMR spectroscopy (500 and 600 MHz). The concentration dependence of the chemical shifts of protons of the complex at a fixed temperature (T = 308 K) were measured. The schemes of complexing of the dye with the tetranucleotide which take into account eventual molecular associates in solution are discussed. Equilibrium constants of the reactions and the limiting values for the chemical shifts of the protons of ethidium bromide incorporating into the complex were calculated. Relative contents of different complex types were analyzed. The relationship between the dynamic equilibrium and dye/tetranucleotide concentration ratio was examined. The conclusion is made that, as with the complex of proflavine with the d(AGCT) examined earlier, ethidium bromide is intercalated essentially into the G-C site of the tetranucleotide being in the duplex form. The difference in intercalation between ethidium bromide and proflavine lies in the fact that ethidium bromide incorporate on the side of the narrow groove, whereas proflavine is built in on the side of the large groove. Based on the calculated values of the induced chemical shift of ethidium bromide protons and 2-d NOE spectal data, an adequate model (1:2) of the complex of the dye with tetranucleotide in solution was constructed.

[Determination of thermodynamic parameters of proflavine interaction with ribodinucleoside monophosphates CpG and PpC in an aqueous solution from data of proton magnetic resonance]. / Opredelenie termodinamicheskikh parametrov vzaimodeistviia proflavina s ribodinukleozidmonofosfatami CpG i GpC v vodnom rastvore po dannym protonnogo magnitnogo rezonansa.

The temperature dependence of proton chemical shifts of proflavine in solution with isomeric ribodinucleoside monophosphates CpG and GpC has been studied. A scheme of calculation of thermodynamic parameters of dye aggregation and 1 : 1 and 1 : 2 complexes formation with dinucleotides has been proposed. The Gibbs' free energy, enthalpy and entropy of these reactions have been determined. It is concluded that hydrophobic interactions play an important part when 1 : 2 complex of proflavine with ribonucleosides is being formed.

[Study of the interaction of proflavine and isomeric diribonucleoside monophosphates CpG and GpC by proton magnetic resonance]. / Issledovanie vzaimodeistviia proflavina s izomernymi diribonukleozidmonofosfatami CpG i GpC metodom protonnogo magnitnogo rezonansa.

A comparative study of the interaction of proflavine with isomeric diribonucleoside monophosphates CpG and GpC has been made by the method of 1H NMR (270 MHz). A method of calculation of the parameters of complex formation from the concentration dependences of proton chemical shifts of the dye has been proposed. The equilibrium constants of 1:1 and 1:2 complexes association of these molecules and the most probable structures of the complexes have been determined.