[Distinctive features of the self-association of deoxyhexanucleotide 5'-D(GpCpApTpGpC) in aqueous solution: 1H NMR analysis]. / Osobennosti protsessa samoassotsiatsii molecul dezoksigeksanukleotida 5'-D(GpCpApTpGpC) v vodnom rastvore: 1H-IAMR-analiz.

The self-association of self-complementary deoxyhexanucleotide d(GCATGC) was investigated in aqueous salt solution. Homonuclear 1H NMR correlation spectroscopy (2D-TOCSY and 2D-NOESY) was used for complete assignments of nonexchangeable protons of the hexamer. The equilibrium reaction constants and thermodynamical parameters of duplex d(GCATGC)2 formation were determined from experimental concentration and temperature dependences of proton chemical shifts of the deoxyhexanucleotide. Distinctive features of the concentration dependences in the range of small concentrations at relatively low temperatures of solution enable one to assume that one single-stranded hexamer sequence forms a compact structure (similar to a hairpin) in aqueous solution. A possible spatial hairpin structure of the hexamer was proposed. Comparative analysis of the experimental and theoretical (using the "nearest neighbor" model) thermodynamical parameters of duplex formation was made.

[NMR study of complex formation of aromatic ligands with heptadeoxynucleotide 5'-d(GCGAAGC) forming stable hairpin structure in aqueous solution]. / IaMR-analiz kompleksoobrazovaniia aromaticheskikh ligandov s dezoksigeptanukleotidom 5'd(GCGAAGC), obrazuiushchim stabil'nuiu shpilechnuiu strukturu v vodnom rastvore.

Complex formation of hairpin-producing heptadeoxynucleotide 5'-d(GCGAAGC) with aromatic molecules: acridine dye proflavine and anthracycline antibiotic daunomycin was studied by one-dimensional 1H NMR and two-dimensional correlation 1H-1H (2M-TOCSY, 2M-NOESY), 1H-31P (2M-HMBC) NMR spectroscopy (500 and 600 MHz) in aqueous solution. Concentration and temperature dependences for the chemical shifts of ligand protons were measured, molecular models of equilibrium in solution were developed, and equilibrium thermodynamic parameters for the formation of intercalation complexes were calculated. Spatial structures of dye and antibiotic complexes with the heptamer hairpin were constructed on the basis of 2M-NOE data and the calculated values of limiting chemical shifts of ligand protons.

[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.

[Study of the complex formation of daunomycin with deoxytetranucleotides with bases of differing sequence in an aqueous solution by 1H-NMR spectroscopy]. / Issledovanie kompleksoobrazovaniia daunomitsina s dezoksitetranukleotidami razlichnoi posledovatel'nosti osnovanii v vodnom rastvore metodom 1H-IaMR-spektroskopii.

The complex formation of the antibiotic daunomycin with deoxytetranucleotides of different base sequence in the chain, 5'-d(GpCpGpC), 5'-d(CpGpCpG), and 5'-d(TpGpCpA) in aqueous salt solution was studied by 1D and 2D (2M-TOCSY and 2M-NOESY) 1H-NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts of molecules were measured. Based on these dependences, reaction equilibrium constants, relative content of various complexes depending on concentration and temperature, limiting values of chemical shifts of protons of daunomycin incorporated in various complexes, and the thermodynamic parameters delta H and delta S of complex formation were calculated. The analysis of the results enables the conclusion that the sites of predominant intercalation of daunomycin are triplet nucleotide sequences, the binding sites of the antibiotic with three consecutive GC pairs in the tetranucleotide duplex being more preferential. Daunomycin exhibits no sequence specificity upon binding to the single-stranded deoxynucleotide sequence. From the calculated values of induced chemical shifts of daunomycin protons and 2M-NOE data, the most probable spatial structures of complexes (1:2) of the antibiotic with deoxytetranucleotides were constructed. The binding of the second daunomycin molecule to both the single-stranded and duplex form of tetramers is of pronounced anticooperative mode, which is explained by the presence in the antibiotic of a positively charged amino sugar residue, which poses considerable steric constraints for the insertion of the second antibiotic molecule into the short tetranucleotide sequence. The results were compared with the data obtained under identical experimental conditions for typical intercalators proflavine and ethidium bromide.

[1H-NMR analysis of heteroassociation of caffeine with antibiotic actinomycin D in the aqueous solution]. / 1H-IaMR analiz geteroassotsiatsii kofeina s antibiotikom aktinomitsinom D v vodnom rastvore.

The molecular basis of the action of caffeine as a complex forming agent, an interceptor of aromatic drugs intercalating into DNA was studied by the example of the an anticancer antibiotic actinomycin D examined. The hetero-association of caffeine and actionomycin D was studied by one- and two-dimensional 1H-NMR spectroscopy (500 MHz). Concentration and temperature dependences of the proton chemical shifts of molecules in aqueous solution were measured. The equilibrium reaction constant of hetero-association of caffeine with actinomycin D (K = 246 +/- 48 M-1), the limiting chemical shifts of caffeine protons in complexes were determined. The most favourable structure of the 1:1 caffeine-actinomycin D hetero-complex in aqueous solution was constructed using the calculated values of the induced proton chemical shifts of molecules and the quantum-mechanical iso-shielding curves for caffeine and actinomycin D. The thermo-dynamical parameters of the hetero-complex formation between caffeine and actinomycin D were also determined. The structural and thermo-dynamical analysis showed that dispersive forces and hydrophobic interactions play the major role in hetero-association of caffeine and actinomycin D in aqueous-salt solution. The relative content of different complexes in mixed solutions containing caffeine and actinomycin D was calculated and distinctive features of the dynamic equilibrium of caffeine-actinomycin D hetero-associates were revealed as a function of concentration and temperature. It is concluded that hetero-association of caffeine and actinomycin D molecules a lowers the effective concentration of the drug in solution and hence the pharmacological activity of actinomycin D.

[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.

[Self-association of deoxytetraribonucleoside triphosphates d(TpGpCpA) in an aqueous solution by 1H NMR spectroscopy]. / Issledovanie samoassotsiatsii molekul dezoksitetraribonukleozidtrifosfatov d(TpGpCpA) v vodnom rastvore metodom 1H IaMR spektroskopii.

Self-association of deoxytetraribonucleoside triphosphate 5'-d(TpGpCpA) molecules in aqueous solution has been studied by one-dimensional and two-dimensional 1H-NMR spectroscopy (500 MHz). Two-dimensional homonuclear PMR spectroscopy (2D-COSY and 2D-NOESY) was used for complete assignments of tetranucleotide proton signals. Concentration and temperature dependences of d(TpGpCpA) proton chemical shifts have been measured. Experimental results have been analyzed using dimer model of molecules association. Equilibrium association constant, values of limiting chemical shifts of tetranucleotide protons in the associate and thermodynamic parameters delta H and delta S of the association reaction have been determined. Comparative analysis of self-association characteristics for d(TpGpCpA) and its isomeric deoxytetranucleotide d(ApGpCpT) has been made.

[Study of the self-association of deoxytetraribonucleoside triphosphate molecules d(ApGpCpT) in aqueous solution by one-dimensional and two- dimensional (1)H NMR spectroscopy]. / Issledovanie samoassotsiatsii molekul dezoksitetraribonukleozidtrifosfatov d(ApGpCpT) v vodnom rastvore metodom odnomernoi i dvumernoi (1)H IaMR-spektroskopii.

Equilibrium behaviour of self-complimentary deoxytetranucleotides d(ApGpCpT) in D2O solution has been studied by the method of proton magnetic resonance spectroscopy (500 MHz). Complete assignments of the d(ApGpCpT) protons were obtained from both two-dimensional homonuclear COSY- and NOESY-experiments. Concentration and temperature dependences of tetranucleotide proton chemical shifts have been investigated. The equilibrium association constants and thermodynamical parameters of self-association of the molecules have been calculated using theoretical models and regression equations based on experimental results.

[Interaction of proflavin with deoxytetraribonucleoside triphosphate 5'-d(ApGpCpT): thermodynamic analysis from (1)H NMR data]. / Vzaimodeistvie proflavina s dezoksitetraribonukleozidtrifosfatom 5'-d(ApGpCpT): termodinamicheskii analiz po dannym (1)H IaMR.

Temperature relationships of chemical shifts of protons of proflavin mixed with deoxytetraribonucleoside triphosphate 5'-d(ApGpCpT) in water solution were investigated on impulse NMR spectrometer (500 MHz). Procedure is suggested for calculating values of mole fractions of various associates in solution as a function against temperature. Free energies of Gibbs, entalpy and entropy were determined in the reactions of complex formation 1:1, 1:2, 2:1 of proflavin with tetranucleotide. The results point to a significant role of hydrophobic interactions during the formation of dye--tetramere duplex complexes.

[Thermodynamic analysis of the interaction of the acridine dye proflavin with deoxytetranucleotides with various base sequences from (1)H-NMR data]. / Termodinamicheskii analiz vzaimodeistviia akridinovogo kasitelia provflavin s dezoksitetranukleotidami razlichnoi posledovatel'nosti osnovanii po dannym (1)H-IaMR.

Temperature dependences of proton chemical shifts of the molecules in aqueous solutions of proflavine with deoxytetraribonucleoside triphosphates of different base sequence--5'-d(CGCG), 5'-d(GCGC), 5'-d(ACGT) and 5'-d(AGCT) have been studied by 500 MHz NMR spectroscopy. Methods of calculation of thermodynamical parameters of complex formation, giving an opportunity to differentiate the contributions of the reactions leading to the formation of different types of complexes in conditions of the composite equilibrium in solution, have been suggested. Enthalpies and entropies of the reactions of 1:1, 2:1, 1:2, 2:2 complexes formation between proflavine and tetranucleotides have been determined. Comparative analysis of the calculated thermodynamical parameters has been made and assumptions about the nature of intermolecular interactions responsible for the formation of dye complexes with different tetranucleotides have been proposed.

[Study of the interaction of proflavin with deoxytetraribonucleoside triphosphate 5'-d(ApGpCpT) in aqueous solution by uni- and two-dimensional 1H-spectroscopy]. / Issledovanie vzaimodeistivia proflavina s dezoksitetraribonukleozidtrifosfatom 5'-d(ApGpCpT), v vodnom rastvore metodom odno- i dvumernoi 1H IaMR-spektroskopii.

Complex formation between acridine dye proflavine and self-complementary deoxytetraribonucleoside triphosphate 5'-d(ApGpCpT) in water-salt solution was studied by the method of one- and two-dimensional 1H-NMR spectroscopy (500 MHz). Two-dimensional homonuclear 1H-NMR spectroscopy (2D-COSY and 2D-NOESY) was used for complete assignments of proton signals of molecules in solution and for qualitative analysis of the nature of interactions between proflavine and tetranucleotide. Concentration dependences of proton chemical shifts of the molecules were measured at 293 K. Equilibrium reaction constants and limiting chemical shifts of dye protons in the complexes were determined using suggested schemes of complex formation. Based on the obtained data possible types of complexes were considered. Analysis of relative content of different types of complexes was made and special features of dynamic equilibrium were revealed as a function of correlation of dye and tetranucleotide concentrations. The most favourable structure of 1:2 complex of dye with tetranucleotide was constructed using the calculated values of induced chemical shifts of proflavine protons and 2D-NOESY spectra.

[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.