Protoberberine Alkaloids Berberine, Palmatine, and Coralyne Binding to Poly(dT)•(Poly(dA)•Poly(dT)) Triplex: Comparative Structural Aspects and Energetics Profiles of the Interaction

The interaction of bioactive protoberberine alkaloids berberine, palmatine, and coralyne with the DNA triplex poly(dT)center dot(poly(dA)center dot poly(dT)) was studied using biophysical and calorimetric techniques. All three alkaloids bound the triplex cooperatively. Berberine and palmatine predominantly stabilized the triplex structure, while coralyne stabilized both triplex and duplex structures as inferred from optical thermal melting profiles. Fluorescence quenching, polarization, and viscometric studies hinted at an intercalative mode of binding for the alkaloids to the triplex, coralyne being more strongly intercalated compared to partial intercalation of berberine and palmatine. The overall affinity of coralyne was two order higher (2.29 x 10(7)m(-1)) than that of berberine (3.43 x 105 m(-1)) and palmatine (2.34 x 10(5) m(-1)). Isothermal titration calorimetric studies revealed that the binding to the triplex was favored by negative enthalpy change (Delta H = -3.34 kcal/mol) with favorable entropy contribution (TDS = 4.07 kcal/mol) for berberine, favored by almost equal negative enthalpy (Delta H = 3.88 kcal/mol) and entropy changes (T Delta S = 3.37 kcal/mol) for palmatine, but driven by large enthalpy contributions (DH = -25.62 kcal/mol and T Delta S = 15.21 kcal/mol) for coralyne. These results provide new insights on the binding of isoquinoline alkaloids to the DNA triplex structure.