Complexation of heterocyclic ligands with DNA in aqueous solution

We have used spectrophotometry to study self-association and complexation with DNA by organic heterocyclic compounds in the acridine and phenothiazine series: proflavin, thionine, and methylene blue. Based on the experimental concentration dependences of the molar absorption coefficient of the molecules in an aqueous buffer solution (0.01 M NaCl, 0.01 M Na₂EDTA, 0.01 M Tris, pH 7.4, T = 298 K), we have determined the equilibrium dimerization constants for the dyes and the DNA complexation parameters using the Scatchard and McGhee-von Hippel models. The observed increase in the cooperativity parameters as the dimerization constants of the ligands increase allowed us to hypothesize that the same interactions occur between dye molecules adsorbed on DNA as in their self-association. The equilibrium DNA-binding constants for the ligands, obtained using the McGhee-von Hippel cooperative model, are (20.9 ± 2.7)·10³ M⁻¹ for proflavin and (33.8 ± 4.1)·10³ M⁻¹ for thionine. Using the Scatchard model, taking into account intercalation and “external” binding of ligands with DNA, we determined the DNA complexation constants for methylene blue: (26.4 ± 4.6)·10³ and (96 ± 17)·10³ M⁻¹ respectively. Based on analysis of the data obtained, we hypothesized that the predominant type of binding with DNA is intercalation binding in the case of proflavin and thionine, and “external” binding with the DNA surface in the case of methylene blue. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 75, No. 2, pp. 242–249, March–April, 2008.     

Association of riboflavin,caffeine, and sodium salicylate in aqueous solution

We have used UV and visible spectrophotometry to study self-association of aromatic riboflavin molecules (RFN, vitamin B₂, 7,8-dimethyl-10-N-(1′-D-ribityl)isoalloxazine) in aqueous solution (pH 6.86) at T = 298 K, using a dimer model. We have determined the equilibrium dimerization constant for riboflavin, K_dB = 125 ± 40 M⁻¹. We have studied heteroassociation in the system of molecules of 7,8-dimethyl-10-ribitylisoalloxazine with 1,3,7-trimethylxanthine (caffeine) and sodium salicylate (NAS) in aqueous solution (pH 6.86; T = 298 K). We have determined the heteroassociation constants for RFN-NAS and RFN-caffeine molecules in the absence and in the presence of urea in solutions using a modified Benesi-Hildebrand equation: 25 ± 4, 17 ± 3, and 74 ± 11, 53 ± 7 M⁻¹ respectively. We have determined the dimerization constants for NAS (2.7 ± 0.5 M⁻¹) and caffeine (17.0 ± 1.5 M⁻¹). We conclude that heteroassociation of the aromatic molecules leads to a lower effective riboflavin concentration in solution, and the presence of urea in mixed solutions leads to an decrease in the complexation constants for the RFN-NAS and RFN-caffeine systems. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 2, pp. 188–194, March–April, 2007.     

DNA tertiary structure and changes in DNA supercoiling upon interaction with ethidium bromide and gyrase monitored by UV resonance Raman spectroscopy

The tertiary structure of DNA is important for many of its biological functions. In this work supercoiled and relaxed forms of purified plasmid DNA pBR322 in dilute aqueous solutions are investigated by means of UVRR spectroscopy to assess changes in B‐DNA conformation. Spectral variation in the CO and exocyclic NH₂ vibration above 1600 cm⁻¹ indicate changes in hydrogen bonding. A minor shift of the CN stretching mode of adenosine and guanosine at 1487 cm⁻¹ supports these findings. Changes in ribose conformation are visible in the spectral region 1320–1360 cm⁻¹ by vibrational coupling of the ribose pucker to the vibrations of the purine and pyrimidine bases. The intercalating phenanthridinium drug ethidium bromide is known to reduce the negative supercoiling of DNA. This change in DNA topology is reflected in variations of the UVRR marker bands of DNA identified above. Principal component analysis helped to extract the features of interest from the complex spectra of the intercalation complex. Within the bacterial cells the change in DNA topology is achieved by the action of topoisomerases. In this work, the DNA‐binding subunit GyrA of the enzyme gyrase was extracted from E. coli and applied to relaxed and supercoiled pBR322. The observed changes in the vibrational signature of the relaxed DNA in the presence of GyrA indicate a change of topology towards the supercoiled form. With already supercoiled DNA no further change in DNA topology is observed. Copyright © 2007 John Wiley & Sons, Ltd.     

Aggregation of 1,3,7-trimethylxanthine with methylene blue in aqueous solution

We have studied self-association of aromatic molecules of the thiazine dye methylene blue in aqueous solution, using a dimer model. We have determined the dimerization equilibrium constant for the dye molecules K_D = 3900 ± 800 M⁻¹ at T = 293 K. We have decomposed the experimental spectrum into dimer and monomer components. Using the ratio of the molar absorption coefficients for two absorption bands of the dimer spectrum, we obtained the “average” value of the angle between the electronic transition moments of the molecules in the dimers, α = 48°. We have studied heteroassociation of methylene blue (MB) and 1,3,7-trimethylxanthine (caffeine) molecules in aqueous solution. We have calculated the heteroassociation constant as 200 ± 34 M⁻¹. We conclude that heteroassociation of methylene blue and caffeine molecules leads to a lower effective dye concentration in solution, which hypothetically may affect its biological activity. We have determined the values of the Gibbs free energy, the enthalpy, and the entropy for dimerization of methylene blue molecules: ΔG₂₉₃ = −(20 ± 3) kJ/mol, ΔH = −(25 ± 9) kJ/mol, Δ S₂₉₃ = −(17 ± 6) J/mol·K; and for methylene blue-caffeine heteroassociation: ΔG₂₉₃ = −(13 ± 3) kJ/mol, ΔH = −(14 ± 10) kJ/mol, ΔS₂₉₃ = −(2.4 ± 0.2) J/mol·K, respectively. We have shown that the methylene blue aggregates and the heteroassociates with caffeine are predominantly stabilized by dispersion interactions between the chromophore molecules in the associates. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 73, No. 2, pp. 158–163, March–April, 2006.     

Nonlinearity of refractive index in glasses based on heavy metal oxides with different lead and tellurium contents

We have studied the nonlinearity of the refractive index at a wavelength of 1.08 μm for optical lead silicate and lead phosphate tellurite glasses of different compositions. We have shown that the nonlinear refractive index n₂ increases as the lead content increases in lead silicate glasses and as the tellurium content increases in lead phosphate tellurite glasses, where the latter are typically have higher values of n₂, as high as 24·10⁻¹³ cgs units (47·10⁻¹⁶ cm²/W), and lower Rayleigh losses. We have established a correlation between the nonlinear refractive index and the microstructure of the studied glasses. The highly nonlinear glasses are distinguished by extensive fluctuations in the heavy metal oxide concentration which are “frozen” during cooling of the glass melt. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 6, pp. 780–784, November–December, 2007.     

Complexation of niflumic acid with native and hydroxypropylated α‐ and β‐cyclodextrins in aqueous solution

Interactions between niflumic acid and native and hydroxypropylated α‐ and β‐cyclodextrins (CDs) were investigated by ¹H NMR, UV‐vis spectroscopy, densimetry, and calorimetry at pH = 7.4 (phosphate buffer) and T = 298.15 K. Thermodynamic parameters of 1:1 complex formation were calculated and discussed in terms of influence of cavity size and availability of hydroxypropyl substituents on the complex stability. The ¹H NMR data indicated the inclusion of niflumic acid into macrocyclic cavity of all CDs under study. It was found that both phenyl and pyridine rings of niflumic acid molecule can be included in the cyclodextrin cavity. The co‐existence of two different kinds of 1:1 inclusion complexes in the solution was suggested. In spite of the fact that binding of niflumic acid with α‐cyclodextrin is more enthalpically favorable, stability of the inclusion complexes is very low due to the enthalpy–entropy compensation effect. Complex formation of β‐CDs with niflumic acid is characterized by the higher enthalpy and entropy changes caused by more intense dehydration. Introduction of hydroxypropyl groups in the cyclodextrin molecule was found to promote the binding with niflumic acid. Copyright © 2008 John Wiley & Sons, Ltd.