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Binding of norharmane with RNA reveals two thermodynamically different binding modes with opposing heat capacity changes

Paul, Bijan K., Ghosh, Narayani, Mukherjee, Saptarshi
Journal of colloid and interface science 2019 v.538 pp. 587-596
Gibbs free energy, RNA, calorimetry, entropy, fluorescence, heat, hydrophobicity, ionic strength, photosensitizing agents, spectroscopy, temperature, titration
The binding interaction of a prospective anti-cancer photosensitizer, norharmane (NHM, 9H-pyrido[3,4-b]indole) with double stranded RNA reveals a primarily intercalative mode of binding. Steady-state and time-resolved fluorescence spectroscopic results demonstrate the occurrence of drug-RNA binding interaction as manifested through environment-sensitive prototropic equilibrium of NHM. However, the key finding of the present study lies in unraveling the complexities in the NHM-RNA binding thermodynamics. Isothermal Titration Calorimetry (ITC) results reveal the presence of two thermodynamically different binding modes for NHM. An extensive temperature-dependence investigation shows that the formation of Complex I is enthalpically (ΔHI < 0) as well as entropically (TΔSI > 0) favored with the enthalpic (entropic) contribution being increasingly predominant in the higher (lower) temperature regime. On the contrary, the formation of Complex II reveals a predominantly enthalpy-driven signature (ΔHI < 0) along with unfavorable entropy change (TΔSI < 0) with gradually decreasing enthalpic contribution with temperature. Such differential dependences of ΔHI and ΔHII on temperature subsequently lead to opposing heat capacity changes underlying the formation of Complex I and II (ΔCpI<0andΔCpII>0). A negative ΔCp underpins the pivotal role of ‘hydrophobic effect’ (release of ordered water molecules) for the formation of Complex I, while a positive ΔCp marks the thermodynamic hallmark for ‘hydrophobic hydration’ (solvation of hydrophobic (or nonpolar) molecular surfaces in aqueous medium) for formation of Complex II. A detailed investigation of the effect of ionic strength enables a component analysis of the total free energy change (ΔG).