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

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 (ΔH_I < 0) as well as entropically (TΔS_I > 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 (ΔH_I < 0) along with unfavorable entropy change (TΔS_I < 0) with gradually decreasing enthalpic contribution with temperature. Such differential dependences of ΔH_I and ΔH_II on temperature subsequently lead to opposing heat capacity changes underlying the formation of Complex I and II (ΔC_p^I<0andΔC_p^II>0). A negative ΔC_p underpins the pivotal role of 'hydrophobic effect' (release of ordered water molecules) for the formation of Complex I, while a positive ΔC_p 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).