Kinetics of the stacking of ethidium bromide by the Raman laser temperature-jump method

Thermodynamic characterization of the dimerization equilibrium of newly synthesized polymethine cyanine dyes

The monomer-dimer equilibrium and thermodynamics of three new cyanine dyes were investigated by spectrophotometric and chemometric methods. The dimerization constants of these new cyanine dyes were determined by studying the dependence of their absorption spectra on the temperature in the range 25-80?C at concentrations of 3.0?10-4, 1.9?10-4 and 1.1?10-4 M for dye 1, 2 and 3, respectively. The processing of the data, performed for the quantitative analysis of pure spectral profiles, was based on the simultaneous resolution of the overlapping bands in the whole set of absorption spectra. From the dimerization constant and its dependence on temperature, the values of the standard enthalpy change and entropy change of dimerization were calculated.

A comparison of van't Hoff and calorimetric heats of binding to DNA using an ethidium selective electrode

A liquid membrane electrode selective for ethidium ion was used to measure free ethidium in mixtures with calf thymus DNA. Electrode response was unaffected by variation in ionic strength from 1 mM to 0.5 M, and was not degraded over the temperature range studied. DNA-ethidium binding isotherms obtained with the electrode at 17.4, 25.4, 30.1, and 40.6 degrees C were fitted to a single class of excluded sites model for v ranging from 0.01 to 0.16. van't Hoff analysis of these data yielded delta H = -8300 cal/mol ethidium bound (in 0.5 M KCl, 10 mM Tris buffer, pH 10, 1 mM EDTA). Direct calorimetric measurements of the heat of complex formation led to a value of -7600 cal/mol at 25 degrees C in the same medium; the two results were not significantly different at the 95% confidence level. The agreement supports the validity of the ethidium selective electrode, and illustrates its utility in the study of ligand binding to nucleic acids and related materials.

Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid)

The Raman laser temperature-jump technique has been used to measure the kinetics of the coil to helix reaction of poly(cytidylic acid) [poly(C)] in aqueous cosolvent mixtures. The rate of helix formation has a low activation energy and is proportional to reciprocal solvent viscosity. The observations suggest helix formation is rotationally diffusion controlled. The rate of coil formation in poly(C) has an activation energy of approximately 11 kcal/mol, presumably reflecting the electronic stacking interactions which stabilize the helix. Viscous cosolvents, glycerol or sucrose, slow down the rate of coil formation; acetonitrile and formamide at 5 mol % increase the rate relative to that in water. The polar cosolvents may specifically attack a cytosine stack. The absorbance vs. temperature profiles for poly(C) are analyzed with the one-dimensional Ising model. When only optical data are used, the cooperativity parameter, sigma, and the enthalpy, delta H, cannot be uniquely determined. A method is proposed that allows determination of sigma by combining spectroscopic and calorimetric data. The values of sigma derived for poly(C) are between 0.8 and 1.0, and delta H is about -9 kcal/mol of stack. An alternative method using integration of the excess heat capacity curve and extrapolation to fully stacked and random coil species yields a delta H of -7 kcal/mol of stack.