title: Thermodynamics of the interactions of sanguinarine with DNA: influence of ionic strength and base composition.
abstract: Using a combination of spectrophotometric and spectrofluorimetric techniques, we report the first thermodynamic characterization of sanguinarine binding to a series of natural and synthetic host DNA duplexes over a wide range of temperature and sodium concentration. The binding isotherms fit reasonably well to the neighbour exclusion model. The salt and temperature dependence of the binding constants is used to estimate the thermodynamic parameters involved in the interaction of the alkaloid with DNA. The resulting binding data are found to be sensitive to the ionic strength of the medium, base composition and sequence of base pairs. When the sodium ion concentration is increased from 0.005 M to 0.5 M, the binding free energy changes vary in a range from -8.47 to -7.1 kcal mol-1, which corresponds to a binding constant range from 1.85 x 10(6) to 1.8 x 10(5) M-1 at 20 degrees C. More distinct is the spread in the binding enthalpy changes which range from -6.35 to -2.62 kcal mol-1 corresponding to binding entropy changes from +7.22 to +15.3 cal K-1 mol-1 at 20 degrees C. On the other hand when the GC content of the host DNA duplexes is increased, the binding free energy varies in a range from -7.28 to -8.58 kcal mol-1 with the binding enthalpy changes ranging from -0.46 to -14.31 kcal mol-1, while corresponding binding entropy changes range from +23.3 to -19.56 cal K-1 mol-1 at 20 degrees C. Sanguinarine binding to natural DNAs and homo- and heteropolymers of AT is characterized by negative enthalpy changes and positive entropy changes, while binding to homo- and heteropolymers of GC is reflected by both negative enthalpy changes and entropy changes. Possible molecular contributions towards sign and magnitude of the thermodynamic parameters and their dependence on ionic strength, base composition and sequences, are discussed.
authors.affiliation: Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Calcutta, India.
authors.forename: A
authors.initials: A
authors.lastname: Sen
authors.forename: A
authors.initials: A
authors.lastname: Ray
authors.forename: M
authors.initials: M
authors.lastname: Maiti
mesh_terms: D000470:Alkaloids / Q000737:chemistry*; D053119:Benzophenanthridines; D004247:DNA / Q000737:chemistry*; D004269:DNA, Bacterial / Q000737:chemistry; D007364:Intercalating Agents / Q000737:chemistry*; D007546:Isoquinolines; D007700:Kinetics; D009994:Osmolar Concentration; D012964:Sodium / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature; D013816:Thermodynamics
chemical_list: D000470:Alkaloids; D053119:Benzophenanthridines; D004269:DNA, Bacterial; D007364:Intercalating Agents; D007546:Isoquinolines; D004247:DNA; D012964:Sodium; C005705:sanguinarine