1H NMR Structural Analysis of the Interactions of Proflavine with Self-Complementary Deoxytetranucleosides of Different Base Sequence

Abstract

The molecular associations and structures of the complexes between the acridine dye, proflavine, and self-complementary deoxytetraribonucleoside triphosphates 5′-d(GpCpGpC), 5′-d(CpGpCpG), 5′-d(ApCpGpT), 5′-d(ApGpCpT) in aqueous solution have been investigated using one-dimensional and two-dimensional 500 MHz ¹H NMR spectroscopy.     

Hetero-association of caffeine and aromatic drugs and their competitive binding with a DNA oligomer

NMR spectroscopy has been used to elucidate the molecular basis of the action of caffeine (CAF) on the complexation with DNA of mutagens such as ethidium bromide, propidium iodide, proflavine and acridine orange, and anticancer drugs such as actinomycin D and daunomycin. The hetero-association of CAF and each of the aromatic ligands in 0.1 mol L(-1) phosphate buffer (pD=7.1) has been investigated as a function of concentration and temperature by 500 MHz 1H NMR spectroscopy and analysed in terms of a statistical-thermodynamic model, in which molecules form indefinite aggregates for both self-association and hetero-association. The analysis leads to determination of the equilibrium constants of hetero-association and to the values of the limiting chemical shifts of the heteroassociation of CAF with each of the aromatic molecules. The hetero-association constants between CAF and each of the aromatic drugs/dyes are found to be intermediate in magnitude between those for self-association of CAF and the corresponding drug/dye. The most probable structures of the 1:1 CAF + ligand hetero-association complexes have been determined from the calculated values of the induced limiting chemical shifts of the drug protons. Knowledge of the equilibrium constants for self-association of CAF and the aromatic ligands, for their hetero-association and their complexation with a DNA fragment, the deoxytetranucleotide 5'-d(TpGpCpA), enabled the relative content of each of the CAF-ligand and CAF-ligand-d(TGCA) complexes to be calculated as a function of CAF concentration in mixed solutions. It is concluded that, on addition of CAF to the solution, the decrease in binding of drug or mutagen with DNA is due both to competition for the binding sites by CAF and the aromatic molecules, and to formation of CAF-ligand hetero-association complexes in the mixed solution; the relative importance of each process depends on the drug or mutagen being considered.     

1H NMR Thermodynamical Analysis of the Interactions of Proflavine with Self-Complementary Deoxytetranucleotides of Different Base Sequence

Abstract

Enthalpies and entropies of complex formation (1:1, 2:1, 1:2, and 2:2 complexes) between proflavine and tetranucleotides of different base sequence have been determined by 500 MHz proton NMR chemical shifts, enabling the contributions to be differentiated for the formation of different types of complexes in solution. Comparison of the calculated thermodynamical parameters has lead to an understanding of the nature of the intermolecular interactions responsible for the formation of dye complexes with the different tetranucleotides.     

NMR Study of Daunomycin Complexation with Hexadeoxynucleotide 5"-d(TpApCpGpTpA) in Aqueous Solution

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)₂complex 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.     

Structural analysis of the complex of phenoxazone antibiotic actinocyl-bis-(2-deoxytetranucleotide 5'-d(TpGpCpA) by the methods of two dimensional 1H-NMR-spectroscopy and molecular mechanics

The spatial structures of intercalated complexes of synthetic phenoxazone antibiotic actinocyl-bis-(2-dimethylaminoethyl) amide with self-complementary deoxytetranucleotide 5'-d(TpGpCpA) have been investigated. Analysis has been made using two-dimensional NMR (2D-NOESY) data in aqueous solution and molecular mechanics simulation. Distinctive features of the conformation of drug-DNA complexes have been determined at two possible orientations of the chromophore of phenoxazone antibiotic at the intercalation site.     

Structural analysis of the complex of phenoxazone antibiotic actinocyl-bis(2-dimethylaminoethyl)amide with deoxytetranucleotide 5′-d(TpGpCpA) by two-dimensional <Superscript>1</Superscript>H-NMR spectroscopy and molecular mechanics

The spatial structure of an intercalated complex of the synthetic phenoxazone antibiotic actinocyl-bis-(2-dimethylaminoethyl)amide (ActII) and the self-complementary deoxytetranucleotide 5-d(TpGpCpA) was studied using two-dimensional NMR (2D-NOESY) spectroscopy of the complex in an aqueous solution and molecular mechanics simulation. Distinctive features of the conformation of ActII-DNA complexes were determined for two possible orientations of the ActII chromophore at the intercalation site.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 2, 2005, pp. 336–344.Original Russian Text Copyright © 2005 by A. Veselkov, Djimant, K. Veselkov, Davies.Deceased.     

NMR Study of Complexation of Aromatic Ligands with Heptadeoxynucleotide 5"-d(GCGAAGC) Forming Stable Hairpin Structure in Aqueous Solution

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 (2D-TOCSY, 2D-NOESY), ¹H–³¹P (2D-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 2D-NOE data and the calculated values of limiting chemical shifts of ligand protons.